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Evaluation of Fecal Microbiota Transfer as Treatment for Postweaning Diarrhea in Research-Colony Puppies
Abstract
Frequently just prior to or at weaning (approximate age, 6 to 8 wk), puppies in research settings often develop diarrheal disease, which may be due, in part, to an immature and unstable intestinal microbiota that is permissive to opportunistic pathogens. The overall objective of this study was to assess whether fecal microbiota transfer (FMT) increased the transmission of a stable maternal microbiota to pups and decreased the incidence of postweaning diarrhea. Puppies were designated by litter as treated (FMT) or sham-treated. The FMT group received fecal inoculum orally for 5 consecutive days during weaning (at 6 to 8 wk of age). Diarrhea was evaluated according to a published scoring system for 11 d during the weaning period. Fresh feces were collected from dams and puppies at 3 d before weaning and 3, 10, and 24 d after weaning for analysis of the fecal microbiota by using 16S rRNA amplicon sequencing. The composition of fecal inoculum refrigerated at 3 to 5 °C was stable for at least 5 d. No diarrhea was reported in either group during the study period, making comparison of treated and control groups problematic. However, 16S rRNA gene analysis revealed microbial variability across time in both groups. Therefore, although the fecal microbiota of neither group of puppies mirrored the dam at any of the designated time points, the data provided fundamental and novel information regarding the dynamic maturation process of the fecal microbiota of puppies after weaning. Copyright 2016 by the American Association for Laboratory Animal Science.
... Dogs treated with FMT recovered faster from acute diarrhea, presented lower abundances of E. coli and Streptococcus spp., a more diverse gut microbiota and a decreased DI value, than dogs treated with metronidazole (111). Only a few studies addressed usage of the FMT in puppies (125,126). Pereira et al. did find that treatment with FMT allowed a faster resolution of diarrhea induced by CPV2 compared to puppies treated with antimicrobials (126). Though, the gut microbiota composition was not analyzed in this study. ...
... Though, the gut microbiota composition was not analyzed in this study. One study evaluated the microbiota profile of puppies (approximate age, 6-8 weeks) transplanted with the fecal microbiota of their mothers (125). It was found the gut microbiota of the puppies did unexpectedly not resemble the maternal one after transfer. ...
... For example, two studies observing puppies around the age of 7 weeks, reported a relative abundance of Firmicutes of respectively 22% (39) and 78% (75) of the sequences read. Such differences of composition and abundance among studies tend to indicate that interindividual variability also plays an important role in the intestinal microbiome development during the first months following weaning (125). This individual variability can be an expression of many factors, such as genetic, breed, diet or type of birth, which mixed together, form each puppy own specific gut microbiome. ...
... Dogs treated with FMT recovered faster from acute diarrhea, presented lower abundances of E. coli and Streptococcus spp., a more diverse gut microbiota and a decreased DI value, than dogs treated with metronidazole (111). Only a few studies addressed usage of the FMT in puppies (125,126). Pereira et al. did find that treatment with FMT allowed a faster resolution of diarrhea induced by CPV2 compared to puppies treated with antimicrobials (126). Though, the gut microbiota composition was not analyzed in this study. ...
... Though, the gut microbiota composition was not analyzed in this study. One study evaluated the microbiota profile of puppies (approximate age, 6-8 weeks) transplanted with the fecal microbiota of their mothers (125). It was found the gut microbiota of the puppies did unexpectedly not resemble the maternal one after transfer. ...
... For example, two studies observing puppies around the age of 7 weeks, reported a relative abundance of Firmicutes of respectively 22% (39) and 78% (75) of the sequences read. Such differences of composition and abundance among studies tend to indicate that interindividual variability also plays an important role in the intestinal microbiome development during the first months following weaning (125). This individual variability can be an expression of many factors, such as genetic, breed, diet or type of birth, which mixed together, form each puppy own specific gut microbiome. ...
Microorganisms of the gastrointestinal tract play a crucial role in the health, metabolism and development of their host by modulating vital functions such as digestion, production of key metabolites or stimulation of the immune system. This review aims to provide an overview on the current knowledge of factors shaping the gut microbiota of young dogs. The composition of the gut microbiota is modulated by many intrinsic (i.e., age, physiology, pathology) and extrinsic factors (i.e., nutrition, environment, medication) which can cause both beneficial and harmful effects depending on the nature of the changes. The composition of the gut microbiota is quickly evolving during the early development of the dog, and some crucial bacteria, mostly anaerobic, progressively colonize the gut before the puppy reaches adulthood. Those bacterial communities are of paramount importance for the host health, with disturbance in their composition potentially leading to altered metabolic states such as acute diarrhea or inflammatory bowel disease. While many studies focused on the microbiota of young children, there is still a lack of knowledge concerning the development of gut microbiota in puppies. Understanding this early evolution is becoming a key aspect to improve dogs' short and long-term health and wellbeing.
... If we look at veterinary literature (dogs and cats), only a few clinical studies (including case reports and case series) have been published, compared to human ones. More precisely, to the best of our knowledge, six case reports (1 as abstract proceedings) (7-12) and 12 clinical studies/case series (6 of which as abstracts) (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24) are reported in the literature, plus one commentary (25), one review (6), and one observational study (5), in addition to other articles not only focused on canine and feline FMT but also referring to it at different levels [for example, (26,27)]. Considering variables such as study design, donor and recipient selection, number of patients included, species (dog vs. cat), disease treated, route of administration, dosage (how much, for how many days, etc.,), and follow-up, although providing invaluable information, such literature needs to be enriched. ...
... In a recent survey aiming at collecting information on the usage of FMT in dogs, it was found that it is mainly used for chronic enteropathies (64%) and then in acute diarrheic forms (36%), including parvovirosis (5). Similarly, previous literature reports its usage in dogs and cats in around 53% of cases in chronic enteropathies (including refractory Clostridium perfringensassociated diarrhea) and in 47% of acute diarrheas (7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24). In this case report, we describe the use of FMT in one dog presenting with chronic relapsing diarrhea, needing a continuous low prednisolone dose to maintain the condition under acceptable control, however not preventing it from periodic relapses. ...
... Finally, with regard to FMT's safety and efficacy in veterinary medicine, both aspects are generally considered positively (7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24). Similarly, in the case described herein, neither short-nor midterm (1.5 year) adverse effects were noted and a reduction of the CIBDAI score, as well as of bloating and episodes of painful defecation, was observed. ...
The present case report describes the effects of orally administered fecal microbiota transplantation (FMT) (frozen capsules) in a dog suffering from relapsing chronic diarrhea, needing a continuous low prednisolone dose to maintain the condition under acceptable control. Through FMT, we aimed at evaluating the possibility of improving the clinical score and/or reducing/suspending steroid administration. During a first period of strict monitoring (21 days), the canine inflammatory bowel disease activity index (CIBDAI) score passed from mild to clinically insignificant disease. Furthermore, two additional gastrointestinal signs that had been reported, bloating and episodes of painful defecation, rapidly improved (bloating) or even resolved (painful defecation). The patient was then followed for 18 months (to the authors' knowledge, the longest follow-up time ever reported in a dog), during which no serious relapses occurred and no increase in prednisolone dose was necessary. No adverse clinical effects were ever reported during monitoring. The present description provides a further experience increasing those already present in the veterinary literature, in which an agreement on how to use FMT has not yet been achieved although strongly needed and recommended.
... In veterinary medicine, the practice of microbiota transplantation has been used for many years, especially in horses [13][14][15] and ruminants [16]. In dogs, however, this practice is still limite-and despite the growth in interest, few studies have reported its application and effectiveness in animals with chronic enteropathies [17][18][19][20][21][22][23][24][25][26][27]. This is probably related to the fact that transplantation has been generally performed by endoscopy or enema, with the obvious limitations related to the availability of the technique and its invasiveness [16]. ...
... This is probably related to the fact that transplantation has been generally performed by endoscopy or enema, with the obvious limitations related to the availability of the technique and its invasiveness [16]. On the other hand, the oral route is still underutilized, due to the lack of a standardised and available method of FMT administration [17,20,23,27]. To date, no moderate or severe side effects of FMT in dogs have been reported, probably due to the limited data availability [16]. ...
... Conversely, in studies performed in dogs, rectal enema is the most used route of administration of faecal microbiota [18,21,22,24,25,27]. Other studies reported the use of descending endoscopy [20], the oral route [19,20,23,27], colonoscopy [26] and the orogastric probe [17]. However, the effectiveness of different administration techniques for FMT in dogs has not yet been adequately studied. ...
Chronic enteropathies (CE) are gastrointestinal diseases that afflict about one in five dogs in Europe. Conventional therapeutic approaches include dietary intervention, pharmacological treatment and probiotic supplements. The patient response can be highly variable and the interventions are often not resolutive. Moreover, the therapeutic strategy is usually planned (and gradually corrected) based on the patient’s response to empirical treatment, with few indirect gut health indicators useful to drive clinicians’ decisions. The ever-diminishing cost of high-throughput sequencing (HTS) allows clinicians to directly follow and characterise the evolution of the whole gut microbial community in order to highlight possible weaknesses. In this framework, faecal microbiome transplantation (FMT) is emerging as a feasible solution to CE, based on the implant of a balanced, eubiotic microbial community from a healthy donor to a dysbiotic patient. In this study, we report the promising results of FMT carried out in a 9-year-old dog suffering from CE for the last 3 years. The patient underwent a two-cycle oral treatment of FMT and the microbiota evolution was monitored by 16S rRNA gene sequencing both prior to FMT and after the two administrations. We evaluated the variation of microbial composition by calculating three different alpha diversity indices and compared the patient and donor data to a healthy control population of 94 dogs. After FMT, the patient’s microbiome and clinical parameters gradually shifted to values similar to those observed in healthy dogs. Symptoms disappeared during a follow-up period of six months after the second FMT. We believe that this study opens the door for potential applications of FMT in clinical veterinary practice and highlights the need to improve our knowledge on this relevant topic.
... [9][10][11][12] Fecal microbiota transplantation has received limited study in dogs. 13,14 Encouraging results were reported for the treatment of chronic diarrhea in dogs in a pilot study, and the clinical response was consistent with significant changes in fecal microbiota after treatment. 15 Our objectives were to evaluate the effectiveness and safety of FMT in puppies with acute hemorrhagic diarrhea syndrome. ...
... The procedure proved to be safe with no adverse effects on the animals studied, which is in agreement with other studies. 14,15 No discomfort was identified during the procedure with the volume used, and there was no need for physical restraint, sedation, or analgesia. In addition to decreasing cost and euthanasia for economic reasons, shorter hospital stays also decrease the risk of hospital-associated infections and other complications. ...
... 18 Although scientific evidence about FMT is scarce, response to the procedure is likely related to reconstitution of the intestinal microbiota and its corresponding metabolites. 6,7 Evaluation of the microbiota has been performed in a small number of FMT studies in humans and in 1 study in puppies, 14 but was not done in our study. Further evaluation of the mechanism of FMT response in CPV or other conditions would improve the understanding of the pathophysiology of these diseases and perhaps lead to refinements in FMT to provide a more specific, standardized approach. ...
Background:
Diarrhea associated with parvovirus infection is common in dogs. Supportive care is the mainstay of treatment, but recovery may be prolonged and mortality rate can be high. Modification of the intestinal bacterial microbiota has been promising in human and veterinary medicine as an adjunctive treatment of various enteric diseases.
Objectives:
To investigate the safety and efficacy of fecal microbiota transplantation (FMT) on the clinical recovery of puppies with acute hemorrhagic diarrhea syndrome.
Animals:
Sixty-six puppies with parvovirus infection were evaluated at 2 veterinary hospitals.
Methods:
Randomized clinical trial. Puppies were randomly distributed into 2 groups: standard treatment (STD) and standard treatment + FMT (STD + FMT). The STD puppies (n = 33) received only treatment with IV fluids and antimicrobials and the STD + FMT puppies (n = 33) received FMT in addition to standard treatment. For FMT, 10 g of feces from a healthy dog diluted in 10 mL of saline were administered rectally 6-12 hours post-admission.
Results:
Among survivors, treatment with FMT was associated with faster resolution of diarrhea (P < .001) and shorter hospitalization time (P = .001; median, 3 days in STD + FMT; median, 6 days in STD) compared to standard treatment. Mortality in STD was 36.4% (12/33) as compared to 21.2% (7/33) in puppies treated with FMT, but there was no statistical difference between groups (P = .174). Polymerase chain reaction indicated that all animals carried canine parvovirus, strain CPV-2b.
Conclusions:
Fecal microbiota transplantation in parvovirus-infected puppies was associated with faster resolution of diarrhea.
... Given changes regarding gut microbiota linked to several diorders, manoeuvre for restoration or optimization of the microbiota might involve fecal microbiota transplantation (FMT), briefly denoted fecal material obtained from a healthy donor (age matched, preferably) to those of administered to diseased case. The latter FMT procedure paid attention in selected study in dogs (5,7). Satisfactory results were deemed available for gastrointestinal diseases among dogs after FMT treatment (21,32). ...
... CADESI-04 and VAS pruritus scores: Both CADESI-04 and VAS pruritus scores were declined in all 8 dogs enrolled. The day 0 scores (50-128) belonging to 7 severe and 1 moderate CAD cases, were significantly higher than scores on day 28 (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21) switching the severity of the disease to mild status. Day 0 VAS pruritus scores were ranging between 5 to 10, whereas owner VAS pruritus score had decreased, which corresponds to a reduction from "severe itching" to "absent (0) or normal (2)" on day 28 (after completion of treatment) ( Figure 1). ...
... 1,2 While there are numerous studies pertaining to the microbiome in adult dogs, few describe the postnatal development of the GI microbiome. [3][4][5] The microbiome increases in species richness beginning on day 2 after birth, and a major shift occurs from predominantly Firmicutes on day 2 to a codominance of Bacteroidetes, Fusobacteria, and Firmicutes by day 21 of age in dogs. 3 Further characterization is merited, as development of the microbiome is important for the health of the developing puppy. ...
... These results are consistent with previous studies that show puppies under 6 weeks of age to have different fecal and GI microbial communities from adult dogs. [3][4][5] The increased DI in young dogs appeared to be driven by an increased abundance of E. coli and a decreased abundance of anaerobic bacterial groups (ie, Faecalibacterium, Turicibacter, and C. hiranonis). As the abundance of E. coli decreased and that of C. hiranonis, Faecalibacterium, Blautia, and Turicibacter increased, the microbiome of puppies started to become similar to that of adult dogs and the DI was negative in older puppies. ...
Background
The fecal microbiota, fecal bile acid concentrations, and abundance of Clostridium perfringens and Clostridium difficile are altered in acute and chronic gastrointestinal disease in adult dogs. However, less is known in young puppies.
Hypothesis/Objectives
To determine composition of the fecal microbiota, assess development of fecal bile acid profiles, and determine the abundance of Clostridial species in puppies, young adult dogs, and adult dogs.
Animals
Healthy puppies from a whelping kennel (n = 53) and healthy client‐owned dogs <1 year old (n = 20) were separated into 6 age groups, then compared to client‐owned dogs over 1 year of age (n = 13).
Methods
Prospective observational study. Naturally voided fecal samples were analyzed by quantitative polymerase chain reaction to measure bacterial abundances. Fecal bile acids were quantified using gas chromatography‐mass spectrometry.
Results
Puppies up to 5 to 6 weeks of age had increased Dysbiosis Index (median [min‐max]: 5.39 [1.32‐8.6], P < .001), increased abundance of C. difficile (4.1 [0.01‐4.85] log DNA, P < .001), decreased secondary bile acid concentrations (0.61 [0.28‐5.06] μg/mg, P = .006), and decreased abundance of C. hiranonis (0.84 [0.01‐6.71], P = .005) compared to adult dogs (−4.62 [−8.36 to −0.61], 0.01 [0.01‐0.01], 4.12 [0.32‐8.94], and 6.02 [5.06‐7.00], respectively). Secondary bile acid concentration positively correlated with C. hiranonis abundance (ρ = 0.77; P < .001).
Conclusions and Clinical Importance
The increase in secondary bile acids and simultaneous decrease of C. difficile and C. perfringens after 5 to 6 weeks of age warrants further investigation into regulatory impacts that secondary bile acids could have on clostridial species in dogs.
... In nursing pigs, individuals given fecal material from healthy, high-parity sows experienced reduced mortality, increased weight gain, and sustained production of antibodies when infected with porcine circoviruses compared to individuals that did not undergo FMT treatment [26]. Similarly, dogs given maternal fecal inoculum during the weaning period demonstrated decreased incidence of diarrhea compared to dogs who did not receive FMTs [27]. These lines of evidence suggest that microbes can be introduced from a donor into the microbiome of a recipient, where they can be maintained for a period of time, potentially leading to improved health outcomes. ...
There is growing interest in the application of fecal microbiota transplants (FMTs) in small animal medicine, but there are few published studies that have tested their effectiveness in the domestic cat (Felis catus). Here we use 16S rRNA gene sequencing to examine fecal microbiome changes in 68 domestic cats with chronic digestive issues that underwent FMT treatment using lyophilized stool that was delivered in oral capsules. Fecal samples were collected from FMT recipients before and two weeks after treatment, as well as from their stool donors, and healthy animals. We found that according to their owners, 77% of cats were reported to show improvement in their clinical signs (termed ‘Responders’), and 23% were reported to exhibit no change or a worsening of their clinical signs (termed ‘Non-Responders’). Variation in the fecal microbiomes of FMT recipients most strongly correlated with host clinical signs, diet, and IBD diagnosis. The relative abundances of Collinsella, Negativibacillus, Parabacteroides, and Peptoclostridium changed differentially in FMT recipients. Overall, on average 13% of the bacterial amplicon sequence variants (ASVs) were shared between stool donors and FMT recipients (excluding ASVs already present in FMT recipients prior to treatment). The most commonly shared ASVs were classified as Prevotella 9, Peptoclostridium, Bacteroides, Collinsella and unclassified Lachnospiraceae. Lastly, FMT recipients that had recently taken antibiotics exhibited increases in microbiome similarity to an age-matched healthy reference set compared to other cats. Cats that had diarrhea or diarrhea with vomiting became more similar to healthy cats than did cats exhibiting other clinical signs. Overall, our results suggest that oral capsule FMT treatment was effective in this group of cats and microbiome responses may be modulated by the FMT recipient’s initial presenting clinical signs, prior IBD diagnosis, recent antibiotic use, and their diet.
... To date, however, there is limited evidence of efficacy and safety regarding the administration of FMT in dogs, mainly in the form of case reports or case series [11][12][13][14][15][16][17][18][19][20][21]. The routes of administration most used by the various authors are rectal enema [14,15,18,19] and endoscopy [11,12,16,17]. ...
Fecal microbiota transplantation (FMT) represents a very promising approach to decreasing disease activity in canine chronic enteropathies (CE). However, the relationship between remission mechanisms and microbiome changes has not been elucidated yet. The main objective of this study was to report the clinical effects of oral freeze-dried FMT in CE dogs, comparing the fecal microbiomes of three groups: pre-FMT CE-affected dogs, post-FMT dogs, and healthy dogs. Diversity analysis, differential abundance analysis, and machine learning algorithms were applied to investigate the differences in microbiome composition between healthy and pre-FMT samples, while Canine Chronic Enteropathy Clinical Activity Index (CCECAI) changes and microbial diversity metrics were used to evaluate FMT effects. In the healthy/pre-FMT comparison, significant differences were noted in alpha and beta diversity and a list of differentially abundant taxa was identified, while machine learning algorithms predicted sample categories with 0.97 (random forest) and 0.87 (sPLS-DA) accuracy. Clinical signs of improvement were observed in 74% (20/27) of CE-affected dogs, together with a statistically significant decrease in CCECAI (median value from 5 to 2 median). Alpha and beta diversity variations between pre- and post-FMT were observed for each receiver, with a high heterogeneity in the response. This highlighted the necessity for further research on a larger dataset that could identify different healing patterns of microbiome changes.
... Exposure to microbes during delivery, early diet, and antibiotic exposure have all been shown to impact gut microbial development (22,51,52). Early influences have clinical impactcolonization with C. difficile during the first months of life is associated with increased risk of atopic disorders such as asthma and eczema in children (53). Microbiome compositions in pre-weened puppies display instability of prominent taxa. ...
The microbiome has clearly been established as a cutting-edge field in tumor immunology and immunotherapy. Growing evidence supports the role of the microbiome in immune surveillance, self-tolerance, and response to immune checkpoint inhibitors such as anti PD-L1 and CTLA-4 blockade ( 1 – 6 ). Moreover, recent studies including those using fecal microbial transplantation (FMT) have demonstrated that response to checkpoint immunotherapies may be conferred or eliminated through gut microbiome modulation ( 7 , 8 ). Consequently, studies evaluating microbiota-host immune and metabolic interactions remain an area of high impact research. While observations in murine models have highlighted the importance of the microbiome in response to therapy, we lack sufficient understanding of the exact mechanisms underlying these interactions. Furthermore, mouse and human gut microbiome composition may be too dissimilar for discovery of all relevant gut microbial biomarkers. Multiple cancers in dogs, including lymphoma, high grade gliomas, melanomas and osteosarcoma (OSA) closely resemble their human analogues, particularly in regard to metastasis, disease recurrence and response to treatment. Importantly, dogs with these spontaneous cancers also have intact immune systems, suggesting that microbiome analyses in these subjects may provide high yield information, especially in the setting of novel immunotherapy regimens which are currently expanding rapidly in canine comparative oncology ( 9 , 10 ). Additionally, as onco-microbiotic therapies are developed to modify gut microbiomes for maximal responsiveness, large animal models with intact immune systems will be useful for trialing interventions and monitoring adverse events. Together, pre-clinical mechanistic studies and large animal trials can help fully unlock the potential of the microbiome as a diagnostic and therapeutic target in cancer.
... Burton et al. tried to prevent postweaning diarrhoea in puppies by oral administration of the faecal inoculum. In this case, no clinical improvement was noticed [166]. In another study, the researchers tried to increase the survival of puppies with parvovirus infection by a combination of standard treatment with FMT. ...
Alterations in the composition of the intestinal microbiome, also known as dysbiosis, are the result of many factors such as diet, antibiotics, stress, diseases, etc. There are currently several ways to modulate intestinal microbiome such as dietary modulation, the use of antimicrobials, prebiotics, probiotics, postbiotics, and synbiotics. Faecal microbiota transplantation (FMT) represents one new method of gut microbiota modulation in humans with the aim of reconstructing the intestinal microbiome of the recipient. In human medicine, this form of bacteriotherapy is successfully used in cases of recurrent Clostridium difficile infection (CDI). FMT has been known in large animal medicine for several years. In small animal medicine, the use of FMT is not part of normal practice.
... Fecal microbiota transplantation is based on the observation that transfer of intestinal contents from a healthy donor to a diseased one can improve gut health. This therapy has been recently tested in dogs for the treatment of post-weaning diarrhea, acute diarrhea, IBD, chronic enteropathies, or parvovirus infections and seems to be promising (Burton et al., 2016;Pereira et al., 2018;Niina et al., 2019;Chaitman and Gaschen, 2020;. ...
Dogs occupy a full place in the family and their well-being is of paramount importance to their owners. Digestion, a complex process involving physicochemical, mechanical, and microbial parameters, plays a central in maintaining animals healthy. As in vivo studies in dogs are more and more restricted by ethical, regulatory, societal, and cost reasons, an alternative option resides in the use of in vitro models simulating the different parts of the canine gastrointestinal tract. This review paper first introduces digestion and gut microbiota as key factors in dog nutrition and health, under both healthy and diseased conditions (obesity and inflammatory bowel disease), by highlighting when relevant similarities or differences between human and canine digestion process. Then, we provide for the first time an in-depth description of currently available models of the canine digestive tract, discuss technical and scientific challenges that need to be addressed and introduce potential applications of in vitro gut models in food and veterinary fields. Even if the development of some in vitro models remains limited by a lack of in vivo data in dogs necessary for a relevant configuration and validation, translation of long-term expertise on human in vitro gut models to dog's ecosystem opens avenues for canine in vitro gut model development and their adaptation to specific digestive conditions associated to various ages, sizes, breeds and/or diets, under both physiological and diseased states.
... A pesar del tratamiento convencional instaurado en la paciente, se recurrió al trasplante de microbiota fecal como terapia adicional. No se identificaron molestias en el paciente durante el procedimiento ni hubo necesidad de sujeción física o sedación, lo que coincide con los resultados reportados por Burton et al. (2016). En el presente caso se apreció una resolución de la gastroenteritis hemorrágica (diarrea) en menos de 24 horas del trasplante fecal. ...
RESUMEN El presente estudio muestra el caso de una cachorra de cuatro meses de edad que ingresó a la consulta de la clínica veterinaria «Vet Center», Bucaramanga, Colombia, por un cuadro gastroentérico severo. La paciente mostraba signos de depresión, vómito, deshidratación y fiebre. La valoración hematológica reveló una ligera anemia, y la prueba de parvovirus canino resultó positiva. Para la estabilización y tratamiento de la paciente se colocó un catéter intravenoso para el suministro de soluciones endovenosas de Ringer lactato, antibióticos, antieméticos y vitaminas. Además, se realizó como terapia adicional un trasplante de microbiota fecal al cabo de 12 horas de hospitalización, repitiéndose a las 12 horas, dando resultados satisfactorios que se discuten en este reporte clínico. ABSTRACT It is reported the case of a four-month-old puppy that was admitted to the consultation at the veterinary clinic «Vet Center», Bucaramanga, Colombia, due to a severe gastroenteric disturbance. The patient showed signs of depression, vomiting,
... 144 Treatment of clinical intestinal infection diseases encompasses the administration of antibiotics, metronidazole (nitroimidazole antibiotic), or even fecal transplantation. Indeed, a study by Burton et al. 145 investigated oral-fecal microbiota transfer from dams to puppies, for 5 consecutive days during weaning, observing a decreased incidence of postweaning diarrhea, without finding substantial differences in the microbiota of puppies. Chaitman et al. 140 compared metronidazole and fecal transplantation for treatment of acute diarrhea and observed that both improved fecal consistencies, despite fecal microbiota and metabolome profiles were differently affected by the two treatments. ...
Microbiota and microbiome, which refers, respectively, to the microorganisms and conjoint of microorganisms and genes are known to live in symbiosis with hosts, being implicated in health and disease. The advancements and cost reduction associated with high-throughput sequencing techniques have allowed expanding the knowledge of microbial communities in several species, including dogs. Throughout their body, dogs harbor distinct microbial communities according to the location (e.g., skin, ear canal, conjunctiva, respiratory tract, genitourinary tract, gut), which have been a target of study mostly in the last couple of years. Although there might be a core microbiota for different body sites, shared by dogs, it is likely influenced by intrinsic factors such as age, breed, and sex, but also by extrinsic factors such as the environment (e.g., lifestyle, urban vs rural), and diet. It starts to become clear that some medical conditions are mediated by alterations in microbiota namely dysbiosis. Moreover, understanding microbial colonization and function can be used to prevent medical conditions, for instance, modulation of gut microbiota of puppies is more effective to ensure a healthy gut than interventions in adults. This paper gathers current knowledge of dogs’ microbial communities, exploring their function, implications in the development of diseases, and potential interactions among communities while providing hints for further research.
... The mechanisms underlying the effects of FMT are not fully understood, but may be associated with enhanced numbers of beneficial microbes, increased microbial diversity, and restoration of normal flora [13]. Published papers, but not conference abstracts, have demonstrated that FMT is effective for the treatment of several GI diseases in dogs, including canine parvovirus infection [22], postweaning diarrhea [4], acute diarrhea [6], and Clostridium difficile-associated diarrhea [26]. A previous pilot study reported that repeated oral or endoscopic FMT into the duodenum, ileum, or colon improved GI signs in most but not all of 16 dogs with IBD [3]. ...
A 7-year 6-month-old, castrated male Shiba dog presented with a 1-month history of lethargy, anorexia, vomiting, and frequent watery diarrhea. Weight loss, hypoalbuminemia, anemia, and leukocytosis were detected at the first visit. The dog was diagnosed with non-responsive enteropathy (NRE) based on clinical and histopathological examinations. Since the dog did not respond to the immunosuppressive drugs, fecal microbiota transplantation (FMT) was performed during the treatment with chlorambucil. A single endoscopic FMT into the cecum and colon drastically recovered clinical signs and clinicopathological abnormalities and corrected dysbiosis in the dog. No recurrence or adverse events were observed. The present case report suggests that FMT, possibly together with chlorambucil, might be a treatment option for NRE in Shiba dogs that have poorer prognosis compared with other dog breeds.
... Fecal microbiota transplantation has been used anecdotally for the management of canine CIE, but results are variable and evidence-based data are lacking. [74][75][76] Mesenchymal stem cells have been used in small cohort studies, and their intravenous application led to clinical remission in 9/11 dogs, but histologic remission was not achieved [77]. Larger sized RCTs are needed to confirm efficacy and best application of alternative and novel treatments in CIE. ...
... By the time the puppies had reached 56 days of age, their faecal microbiota included a higher greater diversity of phylum level bacteria, dominated by Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria (Guard et al., 2017). This is similar to humans, where the relative abundance of Lactobacillus and Bifidobacterium decreased with age, while Bacteriodes and bacterial genes associated with the ability to metabolize complex carbon sources increased with age (Burton et al., 2016). ...
The long-standing hypothesis that the neonatal microbiome is acquired during and after birth has been challenged by recent studies in humans using advanced molecular technologies, which identified bacteria and bacterial DNA and RNA in amniotic fluid, placenta, and meconium. Similar studies have recently been conducted on canine neonates, giving a description of the gut microbiota of newborn puppies and a comparison of different types of parturition on theirdevelopment. In this review, we summarize the current knowledge of microbiome and microbial alterations in the canine gut, vagina and oral cavity throughout pregnancy, and their effects on the microbiome of the placenta and the meconium in neonatal puppies. We further compare the microbiome knowledge gained in the last decade on human neonates and draw parallels with canine pregnancy and the neonatal microbiome.
... Unfortunately, large scale studies on the clinical effect (short-and long-term effects) or the efficacy of restoring eubiosis by administration of faecal microbiota transplantation are currently lacking. The optimal donor screening and indication, as well as the best modality and frequency of administration of faecal microbiota transplantation in dogs, is currently unknown, because only a few studies are available (Chaitman et al. 2016, Burton et al. 2016, Pereira et al. 2018. We are still a far way away from suggesting its use as a routine treatment in dogs with acute and/or chronic diarrhoea, because scientific evidence from appropriately designed prospective studies is lacking. ...
Chronic diarrhoea is a frequent complaint in canine practice and the diagnostic path is often characterised by numerous diagnostic tests and stepwise empirical treatments, often applied before gastrointestinal (GI) endoscopy/mucosal biopsies. These include dietary interventions (novel protein, hydrolysed protein diet), parasiticides and still, in many cases, antibacterials. Indiscriminate use of antibacterial drugs risks detrimental consequences for both the individual patient (antimicrobial resistance, long‐term disruption of intestinal bacterial populations, potential worsening of GI signs) and general public. For that reason, in this Perspective essay we advocate use of antibacterials only after histopathologic evaluation of GI biopsies or, for those cases in which endoscopy is not possible, after other therapeutic trials, such as diet/pre‐probiotics or anti‐inflammatory drugs have proven unsuccessful. They should be reserved, after appropriate dietary trials, for those canine chronic diarrhoeic patients with signs of true primary infection (i.e. signs of systemic inflammatory response syndrome or evidence of adherent‐invasive bacteria) that justify antibacterial use.
... In one of the few case-control studies in dogs so far, puppies infected with parvovirus treated with FMT had significant reduction in hospitalization time and recovered faster than puppies receiving standard treatment (115). However, when oral FMT was used on puppies during weaning in a research setting, no improvement was seen in fecal scores, and FMT did not prevent weaning-associated diarrhea (116). A study (117) reported good results, albeit transient, in a case series of 16 dogs with IBD, with prolonged remission observed when dogs were maintained on a daily oral dosing of frozen donor stool following FMT. ...
The gut microbiome contributes to host metabolism, protects against pathogens, educates the immune system, and, through these basic functions, affects directly or indirectly most physiologic functions of its host. Molecular techniques have allowed us to expand our knowledge by unveiling a wide range of unculturable bacteria that were previously unknown. Most bacterial sequences identified in the canine gastrointestinal (GI) tract fall into five phyla: Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria. While there are variations in the microbiome composition along the GI tract, most clinical studies concentrate on fecal microbiota. Age, diet, and many other environmental factors may play a significant role in the maintenance of a healthy microbiome, however, the alterations they cause pale in comparison with the alterations found in diseased animals. GI dysfunctions are the most obvious association with gut dysbiosis. In dogs, intestinal inflammation, whether chronic or acute, is associated with significant differences in the composition of the intestinal microbiota. Gut dysbiosis happens when such alterations result in functional changes in the microbial transcriptome, proteome, or metabolome. Commonly affected metabolites include short-chain fatty acids, and amino acids, including tryptophan and its catabolites. A recently developed PCR-based algorithm termed “Dysbiosis Index” is a tool that allows veterinarians to quantify gut dysbiosis and can be used to monitor disease progression and response to treatment. Alterations or imbalances in the microbiota affect immune function, and strategies to manipulate the gut microbiome may be useful for GI related diseases. Antibiotic usage induces a rapid and significant drop in taxonomic richness, diversity, and evenness. For that reason, a renewed interest has been put on probiotics, prebiotics, and fecal microbiota transplantation (FMT). Although probiotics are typically unable to colonize the gut, the metabolites they produce during their transit through the GI tract can ameliorate clinical signs and modify microbiome composition. Another interesting development is FMT, which may be a promising tool to aid recovery from dysbiosis, but further studies are needed to evaluate its potential and limitations.
... Dogs that responded to the dietary trial without relapse were defined as having FRE and were enrolled in the study. A positive response to the treatment was defined as clinical improvement of GI signs (Canine Inflammatory Bowel Disease Activity Index [CIBDAI] 28 score, 0-3 point; clinically not relevant) with a normal Fecal Score (FS; 7-point Nestlè Purina Fecal Scoring System; FS < 6) 29 after the dietary trial. ...
Background
Dietary interventions are thought to modify gut microbial communities in healthy individuals. In dogs with chronic enteropathies, resolution of dysbiosis, along with remission of clinical signs, is expected with treatment.
Hypothesis/Objective
To evaluate changes in the fecal microbiota in dogs with food‐responsive chronic enteropathy (FRE) and in healthy control (HC) dogs before and after an elimination dietary trial with an animal protein‐free diet (APFD).
Animals
Dogs with FRE (n = 10) and HC (n = 14).
Methods
Dogs were fed the APFD for 60 days. Fecal microbiota was analyzed by Illumina 16S rRNA sequencing and quantitative polymerase chain reaction (PCR).
Results
A significantly lower bacterial alpha‐diversity was observed in dogs with FRE compared with HC dogs at baseline, and compared with FRE dogs after the trial. Distinct microbial communities were observed in dogs with FRE at baseline compared with HC dogs at baseline and compared with dogs with FRE after the trial. Microbial communities still were different in FRE dogs after the trial compared with HC dogs at baseline. In HC dogs, the fecal microbiota did not show a significant modification after administration of the APFD.
Conclusion and Clinical Importance
Our results suggest that, in FRE dogs, treatment with the APFD led to a partial recovery of the fecal microbiota by significantly increasing microbiota richness, which was significantly closer to a healthy microbiota after the treatment. In contrast, no changes were detected in the fecal microbiota of HC dogs fed the same APFD.
... Only 1 study has employed DNA sequencing methods to investigate the gut microbiome in puppies, revealing that temporal instability and substantial interindividual variability are also features of the puppy fecal microbiome. 44 Other studies designed to assess the impact of diet have revealed valuable information about the intestinal microbiome in young cats. In 1 such study, the fecal microbiomes of kittens fed high-or moderate-protein diets after weaning were more similar between littermates at 8 weeks of age, but at 12 weeks of age, the effect of kinship was diminished and diet emerged as the primary factor driving interindividual similarities between the cats. ...
The gastrointestinal microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit the gut of all mammals. Studies in humans and other mammals have implicated the microbiome in a range of physiologic processes that are vital to host health including energy homeostasis, metabolism, gut epithelial health, immunologic activity, and neurobehavioral development. The microbial genome confers metabolic capabilities exceeding those of the host organism alone, making the gut microbiome an active participant in host physiology. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of microbiomics, permitting mechanistic evaluation of the relationships between an animal and its microbial symbionts. Changes in the gastrointestinal microbiome are associated with diseases in humans and animals including inflammatory bowel disease, asthma, obesity, metabolic syndrome, cardiovascular disease, immune-mediated conditions, and neurodevelopmental conditions such as autism spectrum disorder. While there remains a paucity of data regarding the intestinal microbiome in small animals, recent studies have helped to characterize its role in host animal health and associated disease states. This review is intended to familiarize small animal veterinarians with recent advances in the field of microbiomics and to prime them for a future in which diagnostic tests and therapies will incorporate these developments into clinical practice.
Currently, the most progressively occurring incident cancer is melanoma. The mouse is the most popular model in human melanoma research given its various benefits as a laboratory animal. Nevertheless, unlike humans, mice do not develop melanoma spontaneously, so they need to be genetically manipulated. In opposition, there are several reports of other animals, ranging from wild to domesticated animals, that spontaneously develop melanoma and that have cancer pathways that are similar to those of humans. The influence of the gut microbiome on health and disease is being the aim of many recent studies. It has been proven that the microbiome is a determinant of the host's immune status and disease prevention. In human medicine, there is increasing evidence that changes in the microbiome influences malignant melanoma progression and response to therapy. There are several similarities between some animals and human melanoma, especially between canine and human oral malignant melanoma as well as between the gut microbiome of both species. However, microbiome studies are scarce in veterinary medicine, especially in the oncology field. Future studies need to address the relevance of gut and tissue microbiome for canine malignant melanoma development, which results will certainly benefit both species in the context of translational medicine.
Fecal microbiota transplantation (FMT) is an emerging therapeutic option for a variety of diseases, and is characterized as the transfer of fecal microorganisms from a healthy donor into the intestinal tract of a diseased recipient. In human clinics, FMT has been used for treating diseases for decades, with promising results. In recent years, veterinary specialists adapted FMT in canine patients; however, compared to humans, canine FMT is more inclined towards research purposes than practical applications in most cases, due to safety concerns. Therefore, in order to facilitate the application of fecal transplant therapy in dogs, in this paper, we review recent applications of FMT in canine clinical treatments, as well as possible mechanisms that are involved in the process of the therapeutic effect of FMT. More research is needed to explore more effective and safer approaches for conducting FMT in dogs.
In people, fecal microbiota transplantation is recognized as the best treatment modality for recurrent Clostridioides difficile infection in people, and its value is currently investigated in the treatment of other diseases associated with an abnormal gut microbiome. In dogs, intestinal dysbiosis has been documented in many acute and chronic digestive diseases as well as in diseases of other organ systems. There are only few published studies evaluating the benefits of fecal microbiota transplantation (FMT) in canine gastrointestinal disorders. They provide evidence that FMT may be beneficial in the treatment of acute intestinal diseases and hope that the technique might also be useful for the management of chronic enteropathies.
Practical relevance:
Feline triaditis describes concurrent pancreatitis, cholangitis and inflammatory bowel disease (IBD). The reported prevalence is 17-39% in ill referral patients. While the aetiology is poorly understood, it is known to include infectious, autoimmune and physical components. What is not known is whether different organs are affected by different diseases, or the same process; indeed, triaditis may be part of a multiorgan inflammatory disease. Feline gastrointestinal tract anatomy plays its role too. Specifically, the short small intestine, high bacterial load and anatomic feature whereby the pancreatic duct joins the common bile duct before entering the duodenal papilla all increase the risk of bacterial reflux and parenchymal inflammation. Inflammation may also be a sequela of bowel bacterial translocation and systemic bacteraemia.
Diagnostic challenges:
Cholangitis, pancreatitis and IBD manifest with overlapping, vague and non-specific clinical signs. Cholangitis may be accompanied by increased serum liver enzymes, total bilirubin and bile acid concentrations, and variable ultrasonographic changes. A presumptive diagnosis of pancreatitis is based on increased serum pancreatic lipase immunoreactivity or feline pancreas-specific lipase, and/or abnormal pancreatic changes on ultrasonography, though these tests have low sensitivity. Diagnosis of IBD is challenging without histopathology; ultrasound findings vary from normal to mucosal thickening or loss of layering. Triaditis may cause decreased serum folate or cobalamin (B12) concentrations due to intestinal disease and/or pancreatitis. Triaditis can only be confirmed with histopathology; hence, it remains a presumptive diagnosis in most cases.
Evidence base:
The literature on feline triaditis, pancreatitis, cholangitis and IBD is reviewed, focusing on histopathology, clinical significance and diagnostic challenges. Current management recommendations are provided. Further studies are needed to understand the complex pathophysiology, and in turn improve diagnosis and treatment.
Fecal microbiota transplantation (FMT) is the process by which fecal microbiota are donated from a healthy individual and subsequently transplanted into a diseased or young individual. The mechanism by which FMT is effective is believed to be due to enhanced beneficial microbes, increased microbiome diversity, and restored normal flora. Beneficial gut microorganisms not only play a role in maintaining an intestinal barrier and metabolizing nutrients, but importantly, these microbes help regulate local and systemic immune function. Although FMT has been described for several centuries, only recently has it been utilized as a mainstream therapy in humans and significantly considered for applications in other species. In humans and animals, gastrointestinal diseases are by far the most widely accepted FMT-treatable conditions; however, recent research has shown exceptional promise for FMT being used to treat or prevent other conditions, including those outside of the gastrointestinal tract. Overall, FMT is likely an underutilized, widely-available, and inexpensive tool for improving the health and response to disease in animals. In this review, the effects of FMT on veterinary diseases and potential applications for FMT in animals are discussed.
The commensal gut microbiota has been implicated as a determinant in several human diseases and conditions. There is mounting evidence that the gut microbiota of laboratory mice (Mus musculus) similarly modulates the phenotype of mouse models used to study human disease and development. While differing model phenotypes have been reported using mice purchased from different vendors, the composition and uniformity of the fecal microbiota in mice of various genetic backgrounds from different vendors is unclear. Using culture-independent methods and robust statistical analysis, we demonstrate significant differences in the richness and diversity of fecal microbial populations in mice purchased from two large commercial vendors. Moreover, the abundance of many operational taxonomic units, often identified to the species level, as well as several higher taxa, differed in vendor- and strain-dependent manners. Such differences were evident in the fecal microbiota of weanling mice and persisted throughout the study, to twenty-four weeks of age. These data provide the first in-depth analysis of the developmental trajectory of the fecal microbiota in mice from different vendors, and a starting point from which researchers may be able to refine animal models affected by differences in the gut microbiota and thus possibly reduce the number of animals required to perform studies with sufficient statistical power.
Human microbial colonization begins at birth and continues to develop and modulate in species abundance for about 3 years, until the microbiota becomes adult-like. During the same time period, children experience significant developmental changes that influence their health status as well as their immune system. An ever-expanding number of articles associate several diseases with early-life imbalances of the gut microbiota, also referred to as gut microbial dysbiosis. Whether early-life dysbiosis precedes and plays a role in disease pathogenesis, or simply originates from the disease process itself is a question that is beginning to be answered in a few diseases, including IBD, obesity, and asthma. This review describes the gut microbiome structure and function during the formative first years of life, as well as the environmental factors that determine its composition. It also aims to discuss the recent advances in understanding the role of the early-life gut microbiota in the development of immune-mediated, metabolic, and neurological diseases. A greater understanding of how the early-life gut microbiota impacts our immune development could potentially lead to novel microbial-derived therapies that target disease prevention at an early age.
Diarrhea represents one of the most frequent disorders in dogs. In puppies, degradation of feces quality is associated with a reduced daily weight gain and an increased risk of death. Prevention of diarrhea in puppies requires a global approach encompassing enteropathogens, environment and management practices especially when housed in groups. The purpose of this study was to determine prevalence of enteropathogens in puppies in breeding kennels and to identify risk factors of diarrhea. Two hundred and sixty six puppies (between 5 and 14 weeks of age) from 29 French breeding kennels were included. For each kennel, data about environment, management of the kennel and puppies’ characteristics (age, sex and breed) were collected. For each puppy, fecal consistency and fecal excretion of enteropathogens (viruses and parasites) was evaluated. At least one enteropathogen was identified in 77.1% of puppies and 24.8% of puppies presented abnormal feces. The main risk factor of weaning diarrhea was fecal excretion of canine parvovirus type 2 (Odd ratio = 5; Confidence Interval 95%: 1.7-14.7). A targeted sanitary and medical prophylaxis against canine parvovirus type 2 should be implemented to decrease risk of weaning diarrhea.
A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification
using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at
the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates.
Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
Recent molecular studies have revealed a highly complex bacterial assembly in the canine intestinal tract. There is mounting evidence that microbes play an important role in the pathogenesis of acute and chronic enteropathies of dogs, including idiopathic inflammatory bowel disease (IBD). The aim of this study was to characterize the bacterial microbiota in dogs with various gastrointestinal disorders.
Fecal samples from healthy dogs (n = 32), dogs with acute non-hemorrhagic diarrhea (NHD; n = 12), dogs with acute hemorrhagic diarrhea (AHD; n = 13), and dogs with active (n = 9) and therapeutically controlled idiopathic IBD (n = 10) were analyzed by 454-pyrosequencing of the 16S rRNA gene and qPCR assays. Dogs with acute diarrhea, especially those with AHD, had the most profound alterations in their microbiome, as significant separations were observed on PCoA plots of unweighted Unifrac distances. Dogs with AHD had significant decreases in Blautia, Ruminococcaceae including Faecalibacterium, and Turicibacter spp., and significant increases in genus Sutterella and Clostridium perfringens when compared to healthy dogs. No significant separation on PCoA plots was observed for the dogs with IBD. Faecalibacterium spp. and Fusobacteria were, however, decreased in the dogs with clinically active IBD, but increased during time periods of clinically insignificant IBD, as defined by a clinical IBD activity index (CIBDAI).
Results of this study revealed a bacterial dysbiosis in fecal samples of dogs with various GI disorders. The observed changes in the microbiome differed between acute and chronic disease states. The bacterial groups that were commonly decreased during diarrhea are considered to be important short-chain fatty acid producers and may be important for canine intestinal health. Future studies should correlate these observed phylogenetic differences with functional changes in the intestinal microbiome of dogs with defined disease phenotypes.
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic, and statistical refinements permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is described for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position Specific Iterated BLAST (PSLBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities.
In puppies weaning is a high risk period. Fecal changes are frequent and can be signs of infection by digestive pathogens (bacteria, viruses, parasites) and indicators of nutritional and environmental stress. The aim of this study was to define a pathological fecal score for weaning puppies, and to study the impact on that score of two intestinal viruses (canine parvovirus type 2 and canine coronavirus). For this, the quality of stools was evaluated on 154 puppies between 4 and 8 weeks of age (100 from small breeds and 54 from large breeds). The scoring was performed immediately after a spontaneous defecation based on a 13-point scale (from 1; liquid to 13; dry and hard feces). Fecal samples were frozen for further viral analysis. Each puppy was weighed once a week during the study period. The fecal score regarded as pathological was the highest score associated with a significant reduction in average daily gain (ADG). Fecal samples were checked by semi-quantitative PCR or RT-PCR for canine parvovirus type 2 and canine coronavirus identification, respectively. The quality of feces was affected by both age and breed size. In small breeds, the ADG was significantly reduced under a fecal score of 6 and 7 for puppies at 4-5 and 6-8 weeks of age, respectively. In large breeds, the ADG was significantly reduced under a fecal score of 5 whatever the age of the puppy. Whereas a high viral load of canine parvovirus type 2 significantly impacted feces quality, no effect was recorded for canine coronavirus. This study provides an objective threshold for evaluation of fecal quality in weaning puppies. It also emphasizes the importance to be given to age and breed size in that evaluation.
QIIME (canonically pronounced “chime”) is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities. Curr. Protoc. Microbiol. 27:1E.5.1-1E.5.20. © 2012 by John Wiley & Sons, Inc.
Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome.
We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash.
t.magoc@gmail.com.
An association between luminal commensal bacteria and inflammatory bowel disease (IBD) has been suggested in humans, but studies investigating the intestinal microbial communities of dogs with IBD have not been published. The aim of this study was to characterize differences of the small intestinal microbial communities between dogs with IBD and healthy control dogs. Duodenal brush cytology samples were endoscopically collected from 10 dogs with IBD and nine healthy control dogs. DNA was extracted and 16S rRNA gene was amplified using universal bacterial primers. Constructed 16S rRNA gene clone libraries were compared between groups. From a total of 1240 selected clones, 156 unique 16S rRNA gene sequences were identified, belonging to six phyla: Firmicutes (53.4%), Proteobacteria (28.4%), Bacteroidetes (7.0%), Spirochaetes (5.2%), Fusobacteria (3.4%), Actinobacteria (1.1%), and Incertae sedis (1.5%). Species richness was significantly lower in the IBD group (P=0.038). Principal component analysis indicated that the small intestinal microbial communities of IBD and control dogs are composed of distinct microbial communities. The most profound difference involved enrichment of the IBD dogs with members of the Enterobacteriaceae family. However, differences involving members of other families, such as Clostridiaceae, Bacteroidetes and Spirochaetes, were also identified. In conclusion, canine IBD is associated with altered duodenal microbial communities compared with healthy controls.
This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503,280 (K9C) and 505,061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised ∼35% of all sequences, followed by Proteobacteria (13-15%) and Fusobacteria (7-8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented ∼1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease.
To determine age, breed, sex, body condition score, and diet of dogs and cats examined at private veterinary practices in the United States during 1995, and estimate prevalences of the most common disorders for these animals.
Cross-sectional study.
31,484 dogs and 15,226 cats examined by veterinary practitioners at 52 private veterinary practices.
Information on age, breed, sex, body condition score, diet, and assigned diagnostic codes were collected electronically from participating practices and transferred to a relational database. Prevalence estimates and frequencies for population description were generated using statistical software.
Dental calculus and gingivitis were the most commonly reported disorders. About 7% of dogs and 10% of cats examined by practitioners during the study were considered healthy. Many conditions were common to both species (e.g., flea infestation, conjunctivitis, diarrhea, vomiting). Dogs were likely to be examined because of lameness, disk disease, lipoma, and allergic dermatitis. Cats were likely to be examined because of renal disease, cystitis, feline urologic syndrome, and inappetence.
Results can be used by veterinary practitioners to better understand and anticipate health problems of importance in cats and dogs they examine and to better communicate with clients regarding the most prevalent disorders in cats and dogs.
Several DNA extraction methods have been reported for use with digesta or fecal samples, but problems are often encountered in terms of relatively low DNA yields and/or recovering DNA free of inhibitory substances. Here we report a modified method to extract PCR-quality microbial community DNA from these types of samples, which employs bead beating in the presence of high concentrations of sodium dodecyl sulfate (SDS), salt, and EDTA, and with subsequent DNA purification by QIAamp columns [referred to as repeated bead beating plus column (RBB + C) method]. The RBB + C method resulted in a 1.5- to 6-fold increase in DNA yield when compared to three other widely used methods. The community DNA prepared with the RBB + C method was also free of inhibitory substances and resulted in improved denaturing gradient gel electrophoresis (DGGE) profiles, which is indicative of a more complete lysis and representation of microbial diversity present in such samples.
The study aim was to describe the diversity of the intraluminal intestinal microbial community in dogs by direct sequence analysis of the 16S rRNA gene. Intestinal content was collected from the duodenum, jejunum, ileum, and colon from six healthy dogs. Bacterial 16S rRNA gene was amplified with universal bacterial primers. Amplicons were ligated into cloning vectors and near-full-length 16S rRNA gene inserts were analyzed. From a total of 864 clones analyzed, 106 nonredundant 16S rRNA gene sequences were identified. Forty-two (40%) sequences showed<98% sequence similarity to 16S rRNA gene sequences reported previously. Operation taxonomic units were classified into four phyla: Firmicutes, Fusobacteria, Bacteroidetes, and Proteobacteria. Clostridiales predominated in the duodenum (40% of clones) and jejunum (39%), and were highly abundant in the ileum (25%) and colon (26%). Sequences affiliated with Clostridium cluster XI and Clostridium cluster XIVa dominated in the proximal small intestine and colon, respectively. Fusobacteriales and Bacteroidales were the most abundant bacterial order in the ileum (33%) and colon (30%). Enterobacteriales were more commonly observed in the small intestine than in the colon. Lactobacillales occurred commonly in all parts of the intestine.
Importance
Fecal microbiota transplantation (FMT) has been shown to be effective in treating relapsing or refractory Clostridium difficile infection, but practical barriers and safety concerns have prevented its widespread use.Objective
To evaluate the safety and rate of resolution of diarrhea following administration of frozen FMT capsules from prescreened unrelated donors to patients with recurrent C difficile infection.Design, Setting, and Participants
Open-label, single-group, preliminary feasibility study conducted from August 2013 through June 2014 at Massachusetts General Hospital, Boston. Twenty patients (median age, 64.5 years; range, 11-89 years) with at least 3 episodes of mild to moderate C difficile infection and failure of a 6- to 8-week taper with vancomycin or at least 2 episodes of severe C difficile infection requiring hospitalization were enrolled.Interventions
Healthy volunteers were screened as potential donors and FMT capsules were generated and stored at −80°C (−112°F). Patients received 15 capsules on 2 consecutive days and were followed up for symptom resolution and adverse events for up to 6 months.Main Outcomes and Measures
The primary end points were safety, assessed by adverse events of grade 2 or above, and clinical resolution of diarrhea with no relapse at 8 weeks. Secondary end points included improvement in subjective well-being per standardized questionnaires and daily number of bowel movements.Results
No serious adverse events attributed to FMT were observed. Resolution of diarrhea was achieved in 14 patients (70%; 95% CI, 47%-85%) after a single capsule-based FMT. All 6 nonresponders were re-treated; 4 had resolution of diarrhea, resulting in an overall 90% (95% CI, 68%-98%) rate of clinical resolution of diarrhea (18/20). Daily number of bowel movements decreased from a median of 5 (interquartile range [IQR], 3-6) the day prior to administration to 2 (IQR, 1-3) at day 3 (P = .001) and 1 (IQR, 1-2) at 8 weeks (P < .001). Self-ranked health scores improved significantly on a scale of 1 to 10 from a median of 5 (IQR, 5-7) for overall health and 4.5 (IQR, 3-7) for gastrointestinal-specific health on the day prior to FMT to 8 (IQR, 7-9) after FMT administration for both overall and gastrointestinal health (P = .001). Patients needing a second treatment to obtain resolution of diarrhea had lower pretreatment health scores (median, 6.5 [IQR, 5-7.3] vs 5 [IQR, 2.8-5]; P = .02).Conclusions and Relevance
This preliminary study among patients with relapsing C difficile infection provides data on adverse events and rates of resolution of diarrhea following administration of FMT using frozen encapsulated inoculum from unrelated donors. Larger studies are needed to confirm these results and to evaluate long-term safety and effectiveness.Trial Registration
clinicaltrials.gov Identifier: NCT01914731
There has been growing interest in the use of fecal microbiota for treatment of chronic gastrointestinal infections and inflammatory bowel diseases. Lately, there has also been interest in its therapeutic potential for cardiometabolic, autoimmune, and other extra-intestinal conditions that were not previously considered to be associated with the intestinal microbiota. Although it is not clear if changes in the microbiota cause these conditions, we review the most current and best methods for performing fecal microbiota transplantation and summarize clinical observations that have implicated the intestinal microbiota in various diseases. We also discuss case reports of fecal microbiota transplantations for different disorders, including Clostridium difficile infection, irritable bowel syndrome, inflammatory bowel diseases, insulin resistance, multiple sclerosis, and idiopathic thrombocytopenic purpura. There has been increasing focus on the interaction between the intestinal microbiome, obesity, and cardio-metabolic diseases-we explore these relationships and the potential roles of different microbial strains. We might someday be able to mine for intestinal bacterial strains that can be used in diagnosis or treatment of these diseases.
Background:
Clostridium difficile infection (CDI) continues to increase in incidence and severity, and was the most common nosocomial infection in the USA in 2010. Most cases of CDI respond to a standard course of antibiotics, but recurrent C. difficile infection (RCDI) has become increasingly frequent, and alternative treatments are needed. We examined the efficacy of fecal microbiota transplantation (FMT) instilled into the upper gastrointestinal tract for RCDI.
Materials and methods:
The medical records for all patients treated with FMT during a 9-year period at a single institution in northern Minnesota were reviewed retrospectively. Eighty-nine FMT courses were provided by nasogastric tube to 87 patients, and demographic and clinical data were abstracted, including details of treatments prior to FMT, rate of FMT treatment success and clinical course during a 60-day post FMT follow up period. Fourteen FMT courses failed to meet criteria for inclusion.
Results:
Each patient served as his or her own control, having failed standard treatment. After exclusions, the case series included 75 FMT courses administered to 74 patients. Fifty-nine FMT courses resulted in clinical resolution of diarrhea for a primary cure rate of 79%. Diarrhea relapsed following 16 FMT courses; in 9 of these cases diarrhea subsequently resolved after a single course of vancomycin. No adverse events were noted.
Conclusions:
Our findings parallel findings from other studies when FMT has been provided via the upper GI tract, and suggest that patients with recurrent CDI may resolve diarrhea by introducing stool from healthy donors into the upper GI tract via nasogastric tube.
Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.
Clostridium difficile infection (CDI) has emerged as a major complication associated with the use of systemic antimicrobial agents. Broad-spectrum antimicrobial agents disrupt the ecological bacterial balance in the colon and create an opportunity for C. difficile overgrowth with attendant production of toxins and clinical symptoms of colitis. Recommended therapies for CDI include oral administration of metronidazole or vancomycin for 10-14 days. However, 5% to 35% of patients experience infection relapse after completion of treatment. Recently, patients who failed to resolve their infection with conventional therapies and went on to develop chronic relapsing CDI were successfully treated with fecal bacteriotherapy. Stool obtained from a healthy individual was instilled from either end of the GI tract. Although the published experience with fecal bacteriotherapy is still limited, the published treatment results for 100 patients have demonstrated an average success-rate close to 90%. Fecal bacteriotherapy is a low tech procedure which is easy to perform, and breaks the cycles of repeated antibiotic use, which in turn reduces the risk of antibiotic associated resistance and adds potential cost savings when compared to repeated antibiotic administration and hospitalizations.
To evaluate the prevalence of enteric pathogens in dogs of north-central Colorado, fecal samples were obtained from client-owned dogs presented to the Veterinary Teaching Hospital at Colorado State University for evaluation of acute small-bowel, large-bowel, or mixed-bowel diarrhea (n=71) and from age-matched, client-owned, healthy dogs (n=59). Infectious agents potentially associated with gastrointestinal disease were detected in 34 of 130 (26.1%) fecal samples. Agents with zoonotic potential were detected in feces from 21 (16.2%) of 130 dogs and included Giardia spp. (5.4%), Cryptosporidium parvum (3.8%), Toxocara canis (3.1%), Salmonella spp. (2.3%), Ancylostoma caninum (0.8%), and Campylobacter jejuni (0.8%). Positive test results occurred in dogs with or without gastrointestinal signs of disease. Dogs, particularly those in homes of immunocompromised humans, should be evaluated for enteric zoonotic agents.
Fourteen dogs had shown chronic or intermittent diarrhea for more than 1 year. Diarrhea had been successfully treated with tylosin for at least 6 months but recurred when treatment was withdrawn on at least 2 occasions. Tylosin-responsive diarrhea (TRD) affects typically middle-aged, large-breed dogs and clinical signs indicate that TRD affects both the small and large intestine. Treatment with tylosin eliminated diarrhea in all dogs within 3 days and in most dogs within 24 hours. Tylosin administration controlled diarrhea in all dogs, but after it was discontinued, diarrhea reappeared in 12 (85.7%) of 14 dogs within 30 days. Prednisone given for 3 days did not completely resolve diarrhea. Probiotic Lactobacillus rhamnosus GG did not prevent the relapse of diarrhea in any of 9 dogs so treated. The etiology of TRD, a likely form of antibiotic-responsive diarrhea (ARD) is unclear. The following reasons for chronic diarrhea were excluded or found to be unlikely: parasites, exocrine pancreatic insufficiency, inflammatory bowel disease, small intestinal bacterial overgrowth, enteropathogenic bacteria (Salmonella spp., Campylobacter spp., Yersinia spp., or Lawsoni intracellularis), and Clostridium perfringens enterotoxin and Clostridium difficile A toxin. A possible etiologic factor is a specific enteropathogenic organism that is a common resident in the canine gastrointestinal tract and is sensitive to tylosin but difficult to eradicate. Additional studies are required to identify the specific cause of TRD.
Isospora spp. are the causative agents of canine isosporosis. Of the 3590 diagnostic samples from Austrian dogs (< or = 2 years old), 8.7% contained Isospora oocysts, 78% of which from dogs up to 4 months of age. Non-haemorrhagic and haemorrhagic diarrhoea were significantly more prevalent in Isospora-infected animals than in coccidia-negative ones. Twelve of 15 litters from a large commercial dog breeding unit (examined from the third to the 10th week of life) also excreted Isospora (average prevalence: 36.4%) in intensities from 333 to 35,000 oocysts per gram of faeces (opg). In experimental trials 26 3-week-old Beagle puppies were infected with low (600-6000), medium (10,000) or high (20,000) dose of Isospora ohioensis-group or Isospora canis field isolates. Additionally 21 puppies were infected as above and treated with a symmetrical triazintrione. Parasitological and clinical parameters were examined. The two Isospora species differed significantly concerning intensity and duration of excretion. The pre-patent period was 6-7 days for I. ohioensis and 10-12 days for I. canis. The latter species showed significantly longer excretion and higher opg. This was not influenced by simultaneous infections with both species. Individual patterns of faecal consistency were very variable, irrespective of the infection dose. Treatment significantly reduced both the intensity and the duration of oocysts excretion as well as diarrhoea in comparison with the infected, untreated group and thus proved to be effective against coccidiosis in experimental infections.
Diversity, stability and resilience of the human gut microbiota
- Ca Lozupone
- Ji Stombaugh
- Ji Gordon
- Jk Jansson
- R Knight
Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R.
2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220-230.