Ricardo Araujo

• University of Porto

Introduction Although the oral cavity and the gut are anatomically continuous regions of the gastrointestinal tract, research on the relationship between oral and gut microbiota remains sparse. Oral-gut bacterial translocation is mostly studied in pathological contexts, thus evidence of translocation in healthy conditions is still scarce. Studying...

Background and Aims Recent evidence observed changes in saliva composition and an oral dysbiosis in end-stage renal disease (ESRD) patients. Despite of that, the relationship between oral microbiome and oral peptidome in kidney transplant recipients (KTR) is still unexplored. Therefore, the aim of this study is to investigate the interplay between...

Introduction and objectives: Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specific...

The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationship...

Background and Objective Recent reports describe the existence of a blood microbiome profile not associated with an infection state. Given the high impact that the dysbiotic human microbiome appears to have in chronic kidney disease and, in particular, in the outcome of kidney transplant recipients (KTRs), we aimed to explore the variations and cor...

The classical dermatophytes diagnosis is based on mycological culture and microscopy observation both human and animal hair, skin and nail samples. The aim of this work was to develop the new in-house real-time PCR with pan-dematophyte reaction for detection and identification of the main dermatophytes directly from hair samples, providing a simple...

Objectives: In early life, children are exposed to microorganisms from maternal and environmental sources, which influence the development of their microbiome throughout life. Several studies have demonstrated the influence of the delivery mode and breastfeeding on the oral microbiome of children, mostly regarding bacterial colonization. However,...

Trichophyton verrucosum is the most commonly dermatophyte involved in cattle ringworm. This work reported a case of bovine dermatophytosis due to Trichophyton verrucosum detected from the clinical sample by SYBR-Green real-time PCR. The strategy was based on the DNA extraction directly from the infected hair followed by real‐time PCR and melting‐po...

Heart failure (HF) is a debilitating disease with a significant clinical and economic impact worldwide. Multiple factors seem to increase the risk of developing HF, such as hypertension, obesity and diabetes. Since chronic inflammation plays a significant role in HF pathophysiology and gut dysbiosis is associated with low-grade chronic inflammation...

Yeast acquisition begins at birth; however, the contribution of the mother on yeast transmission to the offspring and associated resistance is yet to be clarified. The aim of this study was to explore the vertical transmission of yeasts and their antifungal susceptibility profile in early life. Oral, fecal, and breastmilk samples were collected fro...

Metabolic syndrome (MS) comprises a vast range of metabolic dysfunctions, which can be associated to cardiovascular disease risk factors. MS is reaching pandemic levels worldwide and it currently affects around 25% in the adult population of developed countries. The definition states for the diagnosis of MS may be clear, but it is also relevant to...

Purpose It has been proved that the gut microbiome is altered in patients with chronic kidney disease. This contributes to chronic inflammation and increases cardiovascular risk and mortality, especially in those undergoing hemodialysis. Phosphate binders may potentially induce changes in their microbiome. This trial aimed to compare the changes in...

Human-Gut Microbiome Establishment and Interactions Developments in Microbiology 2022, Pages 233-263 Chapter 13 - The gut microbiome in chronic kidney disease Author links open overlay panelAnaMerino-RibasabcBeneditaSampaio-Maiaah https://doi.org/10.1016/B978-0-323-91313-3.00012-X Get rights and content Abstract Chronic kidney disease (CKD) is a co...

Vascular calcification (VC) is a frequent condition in chronic kidney disease (CKD) and a well-established risk factor for the development of cardiovascular disease (CVD). Gut dysbiosis may contribute to CVD and inflammation in CKD patients. Nonetheless, the role of gut and blood microbiomes in CKD-associated VC remains unknown. Therefore, this pil...

The preservation of natural ecosystems, as well as the correct management of human societies, largely depends on the maintenance of critical microbial functions associated with soils. Soils are biodiversity rich pools, and rhizosphere soils can be associated with increased plant functions in addition to the regulation of nutrient cycling, litter de...

BACKGROUND AND AIMS Cardiovascular disease (CVD) is the leading cause of death among patients with chronic kidney disease (CKD). In addition to diabetes, hypertension, dyslipidaemia and inflammation, vascular calcification and its severity have long been recognized as a major factor in the development of CVD in patients with CKD. CKD favours gut dy...

Fibrosis is a pathological process associated with most chronic inflammatory diseases. It is defined by an excessive deposition of extracellular matrix proteins and can affect nearly every tissue and organ system in the body. Fibroproliferative diseases, such as intestinal fibrosis, liver cirrhosis, progressive kidney disease and cardiovascular dis...

The editors of Microbiology Spectrum sincerely thank all the reviewers who contributed to the peer review process from the relaunch of the journal through 2 December 2021. We recognize and greatly appreciate their time, effort, and expertise.

Alginate, a natural polysaccharide derived from brown seaweed, is finding multiple applications in biomedicine via its transformation through chemical, physical, and, increasingly, en-zymatic processes. In this study a novel alginate lyase, AlyDS44, was purified and characterized from a marine actinobacterium, Streptomyces luridiscabiei, which was...

A new and easy polymerase chain reaction (PCR) multiplex strategy, for the identification of the most common fungal species involved in invasive fungal infections (IFI) was developed in this work. Two panels with species-specific markers were designed, the Candida Panel for the identification of Candida species, and the Filamentous Fungi Panel for...

Sporotrichosis is a disease caused by thermally dimorphic fungi belonging to the Sporothrix schenckii complex. We report the occurrence of multiple cases of sporotrichosis in cats in Porto Alegre (RS), Brazil, from 2015 to 2019. A set of 21 fungal isolates were collected and the partial sequence of calmodulin (CAL) gene compared. All isolates were...

A ten year-old Holstein cow had an intermittent bloody diarrhea, evolving to anorexia and recumbency, followed by death. Mycotic segmental enteritis was diagnosed based on the pathological and immunohistochemical findings. Rhizopus microsporus was identified as the causal agent through fungal culture and PCR analysis. Intestinal mucormycosis is poo...

Actinobacteria play key roles in terrestrial ecosystem functioning. They contribute to global carbon cycling through the decomposition of soil organic matter, they increase plant productivity and are widely known as prolific producers of bioactive compounds essential for human and animal health. The almost century-old search for new members of the...

Two Pythium‐infested soils were used to compare the wheat root and rhizosphere soil microbial communities from plants grown in the field or in greenhouse trials and their stability in the presence of biocontrol agents. Bacteria showed the highest diversity at early stages of wheat growth in both field and greenhouse trials, while fungal diversity i...

Postnatal acquisition of microorganisms from maternal and environmental sources contributes to the child microbiome development. Several studies showed that the mode of delivery and breastfeeding may have impact on the oral bacterial colonization, however, the influence on oral fungal colonization is still unknown. We performed a systematic literat...

Factors influencing the occurrence of peritoneal dialysis (PD)-related infections are still far from fully understood. Recent studies described the existence of specific microbiomes in body sites previously considered microbiome-free, unravelling new microbial pathways in the human body. In the present study, we analyzed the peritoneum of end-stage...

Mucormycosis infections are infrequent yet aggressive and serious fungal infections. Early diagnosis of mucormycosis and its discrimination from other fungal infections is required for targeted treatment and more favorable patient outcomes. The majority of the molecular assays use 18 S rDNA. In the current study, we aimed to explore the potential o...

The endosphere and the rhizosphere are pertinent milieus with microbial communities that perturb the agronomic traits of crop plants through beneficial or detrimental interactions. In this study, we challenged these communities by adding Streptomyces biocontrol strains to wheat seeds in soils with severe Rhizoctonia solani infestation. Wheat plants...

The endosphere and the rhizosphere are pertinent milieus with microbial communities that perturb the agronomic traits of crop plants through beneficial or detrimental interactions. In this study we challenged these communities by adding Streptomyces biocontrol strains to wheat seeds in soils with severe Rhizoctonia solani infestation. Wheat plants...

Deep fungal infections of the orbit and nasal passages causing rhinitis and ulcerative keratomycosis are uncommonly reported in cats. Hyalohyphomycetes and phaeohyphomycetes have rarely been associated with this disorder. Sino-orbital fungal diseases are emerging and more invasive than sino-nasal fungal diseases with poor response to therapy and a...

Objectives: Chronic kidney disease (CKD) is a public health problem worldwide. Currently, the link between oral health status, dialysis modality, and dialysis vintage is still not clear. The aim of this study was to evaluate periodontal disease, dental caries, and Candida colonization among patients under hemodialysis (HD) therapy, peritoneal dial...

Background Aspergillus fumigatus is the species section Fumigati most frequently isolated from the respiratory tract of cystic fibrosis (CF) patients. Recent studies suggest that mutations in the Cyp51 gene, particularly TR34/L98H, are responsible for azole resistance. Objectives and Methods The focus of this study was on section Fumigati isolates...

Chronic kidney disease (CKD) is associated with an imbalanced human microbiome due not only to CKD-associated factors such as uremia, increased inflammation and immunosuppression, but also to pharmacological therapies and dietary restrictions. End-stage renal disease patients require renal replacement therapies commonly in the form of hemodialysis...

Peritonitis and exit-site infections are important complications in peritoneal dialysis (PD) patients that are occasionally caused by opportunistic fungi inhabiting distant body sites. In this study, the oral yeast colonization of PD patients and the antifungal susceptibility profile of the isolated yeasts were accessed and correlated with fungal i...

Endophytic actinobacteria have been proven to be effective partners that have beneficial functions with a number of crop plants. A large number of studies have been carried out, showing these positive effects in laboratories and glasshouses, but with fewer reports of their effectiveness in the field. This chapter highlights the results of field tri...

The complete genome sequences of two endophytic Streptomyces sp. strains, LUP30 and LUP47B, were analyzed. These strains were isolated from surface-sterilized roots of lucerne plants from South Australia and were found to promote the growth of the rhizobial partner in vitro and significantly increased nodulation and nitrogen fixation in lucerne pla...

The availability of complete fungal genomes is expanding rapidly and is offering an extensive and accurate view of this “kingdom.” The scientific milestone of free access to more than 1000 fungal genomes of different species was reached, and new and stimulating projects have meanwhile been released. The “1000 Fungal Genomes Project” represents one...

The complete genome sequences of three endophytic Streptomyces species were compared. Strains EN16, EN23, and EN27 were isolated from surface-sterilized roots of wheat plants from South Australia. In field trials, these strains are effective in suppressing fungal root diseases of wheat when added as spore coatings to wheat seed.

Aspergillosis is one of the main causes of mortality in birds. The pulmonary system is most frequently affected, with lesions observed in the air sacs and lungs of a wide variety of bird species. The aim of this study was to confirm by molecular methods the identification and the genetic diversity of Aspergillus fumigatus isolates of lung's samples...

We propose an optimized protocol for extensive population analysis of Burkholderia cepacia and Burkholderia contaminans . Seven new polymorphisms were added to the recently proposed SNaPBcen assay, and a total of 18 markers assured the clear identification and distinction of B. cepacia and B. contaminans isolates and high genotypic discrimination (...

Chronic kidney disease (CKD) is estimated to affect nearly 500 million people worldwide and cardiovascular (CV) disease is a major cause of death in this population. However, therapeutic interventions targeting traditional CV risks are not effective at lowering the incidence of CV events or at delaying the progression of the disease in CKD patients...

The oral microbiome can alter the balance between health and disease, locally and systemically. Within the oral cavity, bacteria, archaea, fungi, protozoa, and viruses may all be found, each having a particular role, but strongly interacting with each other and with the host, in sickness or in health. A description on how colonization occurs and ho...

Aspergillus fumigatus conidia have been linked to severe aspergillosis in immunocompromised patients. Recently, the cytotoxic effect of secondary metabolites from A.fumigatus conidia was reported. In the present work, a methodology used to detect cell death markers in fungal hyphae was adapted to study conidia cell death. Additionally, the mechanis...

Aim: Triazole resistance in Aspergillus fumigatus is associated with mutations in cyp51 genes, therefore, a single-tube multiplex PCR was proposed for rapid detection of such mutations. Methods: Relevant markers (n = 21) located in cyp51A and cyp51B were amplified in a multiplex reaction and subsequently analyzed by mini-sequencing. Results: A...

The first evidence of sexual reproduction in Aspergillus fumigatus was reported in 2009. Nevertheless, it remains difficult to understand how A. fumigatus is able to reproduce through this mode in its natural environment and how frequently this occurs. The aim of this study was to analyse single nucleotide polymorphisms (SNP) in a set of environmen...

Amphotericin B and posaconazole susceptibility patterns were determined for the most prevalent Mucorales following EUCAST (European Committee on Antimicrobical Suscepibility Testing) broth microdilution guidelines. In parallel, Etest® was performed and evaluated against EUCAST. Overall agreement of MICs gained with Etest® and EUCAST was 75.1%; ther...

Tri-azoles represent the front-line drugs for the treatment of mould diseases; nevertheless, some emerging moulds, such as Fusarium spp., Scedosporium spp., Mucorales and others, may be less susceptible or resistant to these antifungals. A review of the literature was conducted on the susceptibility of rare moulds to the tri-azoles itraconazole, po...

There is no standard methodology for the molecular identification and genotyping of Pseudomonas aeruginosa which are frequently isolated in bronchiectasis patients. Hence, the main goal of this work was to propose a methodology capable to simultaneously identify and genotype, in less than 6 h, clinical P. aeruginosa collected from cystic fibrosis (...

Practical schemes based on single nucleotide polymorphisms (SNP) have been proposed as alternatives to simplify and replace the molecular methodologies based on the extensive sequencing analysis of genes. SNaPshot mini-sequencing has been progressively experienced during the last decade and represents a fast and robust strategy to analyze critical...

Several fungi have recently been described as capable to recombine and drive large genetic diversity in clinical samples and in the environment. Among the genotyping methods, microsatellite analysis is frequently reported as preferred for studying local epidemiology, but single nucleotide polymorphisms represent the best markers for evaluation of r...

Oral microbiota is one of the most complex and diverse microbial communities in the human body. In the present study, we aimed to characterize oral fungi biodiversity and stability over time in a group of healthy participants with good oral health. Oral health and oral fungal microbiota were evaluated in 40 healthy individuals. A follow-up of 10 pa...

Microbial multilocus sequence typing is a course‐grained approach for classifying micro‐organisms that involves intense gene sequencing, limiting its application in clinical and research laboratories. Multiplexes targeting single‐nucleotide polymorphisms might replace this impractical method by providing the SN aP profile. We here describe mlst@sna...

Early diagnosis of invasive aspergillosis is essential for positive patient outcome. Likewise genotyping of fungal isolates is desirable for outbreak control in clinical setting. We designed a molecular assay that combines detection, identification, and genotyping of Aspergillus fumigatus in a single reaction. To this aim we combined 20 markers in...

Burkholderia cenocepacia is the most prevalent and feared member of the Burkholderia cepacia complex in lung infections of cystic fibrosis (CF). Genotyping and monitoring of long-term colonization are critical at clinical units; however, the differentiation of specific lineages performed by multilocus sequence typing (MLST) is still limited to a sm...

Multilocus sequence typing (MLST) represents the gold standard genotyping method in studies concerning microbial population structure, being particularly helpful in the detection of clonal relatedness. However, its applicability on large-scale genotyping is limited due to the high cost and time spent on the task. The selection of the most informati...

This study aimed to assess the effect of smoking on the biodiversity of the oral fungal microbiota of healthy young subjects, using an improved culture method that assesses both total and pathogenic viable fungi. Forty individuals (20 smokers and 20 non-smokers) were selected. All individuals presented fungal growth (100% for molds and 92.5% for ye...

Detection and typing of bovine mastitis pathogens are currently limited by time-consuming and culture-based techniques. In this work, a novel genus-specific DNA marker for Streptococcus and species-specific DNA markers for the prevalent mastitis pathogens Streptococcus agalactiae and Streptococcus uberis were designed and assessed. In order to enab...

The term "complex" emerged in the literature at the beginning of the genomic era associated to taxonomy and grouping organisms that belong to different species but exhibited similar patterns according to their morphological, physiological and/or other phenotypic features. DNA-DNA hybridization values ⩾70% and high identity on 16S rRNA gene sequence...

The epidemiology of fungal diseases changed, and molds have been increasingly associated with high mortality in severe immunocompromised patients. Invasive mold diseases may originate from the airborne conidia through inhalation or inoculation in skin fissures associated with indwelling catheters, wounds, burns, or onychomycosis. The diagnosis and...

Microsatellites (or short tandem repeats, STRs) are the genetic markers of choice for studying Aspergillus fumigatus molecular epidemiology due to its reproducibility and high discrimination power. However, the specificity of these markers must be investigated in a group of isolates from closely related species. The aim of this work was to test a m...

Invasive aspergillosis is associated with high morbidity and mortality rates; nevertheless, blood cultures almost invariably yield a negative result. The recovery and detection time of Aspergillus fumigatus, Aspergillus flavus and Aspergillus terreus were studied in BACTEC Plus Aerobic/F, Mycosis-IC/F and Myco/F Lytic vials, incubated in the BACTEC...

New fungal species that are morphologically similar to Aspergillus fumigatus were recently described and included in section Fumigati. Misidentification of such fungal species, particularly of the human pathogens, Aspergillus lentulus, Neosartorya fischeri, Neosartorya hiratsukae, Neosartorya pseudofischeri and Neosartorya udagawae, has been increa...

The incidence of life-threatening fungal infections, a critical public health threat, has dramatically increased, and infections due to resistant strains represent a therapeutic drug selection challenge. Although MICs are not the best predictors of patient response to therapy and clinical breakpoints are still not available for all licensed agent/s...

The increase in critical care and immunosuppressed patients all over the world during recent decades is due to a general medical concern with regard to fungal infections, particularly regarding patients admitted at intensive care, haematological, stem cell and solid organ transplant and burn units. The wide use of intense suppressive therapies whic...

It is probably true to say that moulds cannot be completely eliminated from indoor environments. Normal buildings contain a diversity of materials and substrates that allow growth and sporulation of many species of fungi. Some strategies can be used to reduce indoor fungal load in wards receiving high-risk patients, namely by adding air filters and...

The characterization, analysis and validation of evidence that concludes the description of an intentional act of biocrime or bioterrorism represent the main target of microbial forensics. But, even nowadays with the most recent tech-nical advances, it remains extremely difficult, labour-demanding and time consuming to investigate and confirm the o...

Environmental isolates of Aspergillus fumigatus are less studied than those recovered from clinical sources. In the present study, the genetic diversity among such environmental isolates was assessed, as well as their dispersion ability and the acquisition of new strains in 19 medical units of the same hospital. A. fumigatus isolates were genotyped...

Exposure of Aspergillus fumigatus to stressful antifungal therapies may result in decreased susceptibility. The aim of the present work was to evaluate the susceptibility to azole and non-azole antifungals of 159 isolates of A. fumigatus collected from cystic fibrosis (CF) patients receiving azole antifungal therapy. The genetic diversity of the fu...

Microbial community profiling is an important issue for microbial forensics. Some works support a large-scale dispersion of microbes and weak or absent biogeography, while others report the existence of endemic strains. Fungi have recently been used for soil discriminatory and definition of specific ecosystems. The advent of large-scale genotyping...

E-test methodology was compared with Clinical and Laboratory Standards Institute (CLSI) broth microdilution, particularly concerning the detection of resistance to posaconazole among clinical fungal isolates. The susceptibility of a large set of fungal strains (n = 300) was evaluated following 24 and 48 h in two different culture media (RPMI 1640 a...

The answers to important questions concerning Aspergillus fumigatus pathogenicity, transmissions routes and efficacy of treatments require highly discriminating and reproducible genotyping methods. The present study was aimed at improving microsatellite methodology for A. fumigatus typing by reducing the task of strain identification to a single mu...

Posaconazole MICs for 50 Aspergillus fumigatus isolates with distinct genotypes were determined by three methods. MICs were ≥0.5 μg/ml for 5, 11, and 15 strains by the CLSI reference M38-A2, Etest (48-h), and oxygen consumption methods, respectively. The levels of categorical agreement between the results obtained by the CLSI method and those obtai...

Antifungal stress conditions affect fungal germination and growth. The assessment of oxygen consumption resulting from the challenge of Aspergillus fumigatus conidia with antifungal agents might be predictive of the susceptibility of this species to the agents evaluated. The antifungal susceptibilities of A. fumigatus to amphotericin B, itraconazol...

The Haemato-Oncology Unit, Hospital S. Joao, suffered extensive refurbishing intervention in order to adapt for autotransplant patients. Eight new individual rooms with central HEPA filtration system were built. All patients admitted in the department during 14 months prior to and 14 months after renovation works were enrolled. A total of 403 admis...

High-efficiency particulate air (HEPA) filters do not completely prevent nosocomial fungal infections. The first aim of this study was to evaluate the impact of different filters and access conditions upon airborne fungi in hospital facilities. Additionally, this study identified fungal indicators of indoor air concentrations. Eighteen rooms and wa...

The administration of non-antifungal drugs during patient hospitalization might be responsible for discrepancies between in vitro and in vivo susceptibility to antifungals. Propofol is often administered to intensive care units as a sedative. The purpose of this study was to evaluate the effect of propofol lipidic infusion upon the growth and susce...

The objective of this study was to compare the “honey jar” (HJ) sedimentation method with the reference Andersen collection method and validate this new proposed technique for performing environmental monitoring of Aspergillus in health care and other working facilities. Sterile plastic jars were left open in an operating room and adjacent rooms an...

The objective of this study was to compare the antifungal susceptibility profiles of 307 environmental strains and 139 clinical isolates of Aspergillus belonging to six different species. Clinical and environmental strains with minimal inhibitory concentrations (MICs) or minimal effective concentrations >or=4microg/mL to amphotericin B (AMB), itrac...

Physical treatments, like heating or irradiation, may reduce the viability or eradicate Aspergillus conidia, which in turn might help to prevent infections by members of this genus. Chemical treatments can also prevent infection resulting from contaminated hospital fabrics or surfaces. Our objectives were to study the kinetics of survival of the co...

Aspergillus spp. are responsible for an increasing number of fungal infections in immunocompromised and transplant patients. Local anaesthetics (LAs) are growth inhibitors of bacteria and yeasts. Subinhibitory concentrations of the LAs lidocaine and bupivacaine blocked the germination of Aspergillus fumigatus, Aspergillus flavus and Aspergillus nig...

Invasive aspergillosis is one of the most common deep-seated fungal infections among patients with an impaired immune system. Albumin is a serum protein commonly administered to critical patients. Our objective was to evaluate the in vitro effect of human albumin upon germination and hyphal growth of Aspergillus species, especially the most pathoge...