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Introduction
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February 2001 - present
Publications
Publications (387)
Background
The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of...
Background
The conventional morphology-based classification of ciliates is often inaccurate and time-consuming. To address this issue, sequencing, and analysis of the 18S rRNA gene of ciliates have been used as an alternative. However, this method has limitations because the highly conserved nature of this gene makes it challenging to achieve speci...
The rumen microbiome digests plant feedstuff that would be otherwise indigestible and provides most of the metabolizable energy and protein the host animals need. Until recently, research efforts have primarily been directed to bacteria and archaea, leaving the protozoa, fungi, and viruses much less understood. Protozoa contribute to feed digestion...
Anaerobic digestion (AD) is a proven technology widely adopted to treat diverse organic wastes and produce energy in the form of heat, electricity and/or transportation fuels. The application of AD systems still faces challenges due to process stability, digestate management, high costs, and regulatory concerns and requirements among others. In man...
Methane (CH 4 ) emissions from ruminants are of a significant environmental concern, necessitating accurate prediction for emission inventories. Existing models rely solely on dietary and host animal-related data, ignoring the predicting power of rumen microbiota, the source of CH 4 . To address this limitation, we developed novel CH 4 prediction m...
The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-l...
Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida ) and holotrichs (order: Vestibuliferida ) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert...
1 Introduction
2 Direct-fed microbials commonly used in dairy cattle and their modes of action
3 Effects on the rumen and intestinal microbiomes and their functions
4 Effects on feed utilization and lactation performance
5 Effects on the immune system and health
6 Benefit to mitigation of methane emissions
7 Conclusion and future trends
8 Wh...
Ammonia is an important rumen internal environment indicator. In livestock production, feeding a large amount of non-protein nitrogen to ruminants will create high ammonia stress to the animals, which increases the risk of ammonia toxicity. However, the effects of ammonia toxicity on rumen microbiota and fermentation are still unknown. In this stud...
The maternal rumen microbiota can affect the infantile rumen microbiota and likely offspring growth, and some rumen microbes are heritable and are associated with host traits. However, little is known about the heritable microbes of the maternal rumen microbiota and their role in and effect on the growth of young ruminants. From analyzing the rumin...
Enteric methane (CH4) emissions from sheep contribute to global greenhouse gas emissions from livestock. However, as already available for dairy and beef cattle, empirical models are needed to predict CH4 emissions from sheep for accounting purposes. The objectives of this study were to: 1) collate an intercontinental database of enteric CH4 emissi...
Ruminal protozoa, especially entodiniomorphs, engulf other members of the rumen microbiome in large numbers; and they release oligopeptides and amino acids, which can be fermented to ammonia and volatile fatty acids (VFAs) by amino acid-fermenting bacteria (AAFB). Studies using defaunated (protozoa-free) sheep have demonstrated that ruminal protozo...
Obesity-related cardiometabolic disorders are driven by inflammation, oxidative stress, and gut dysbiosis. Green tea catechins protect against cardiometabolic disorders by anti-inflammatory, antioxidant, and prebiotic activities. However, whether obesity alters catechin bioavailability remains unknown. We hypothesized that obesity would decrease ca...
Manure nitrogen (N) from cattle contributes to nitrous oxide and ammonia emissions and nitrate leaching. Measurement of manure N outputs on dairy farms is laborious, expensive, and impractical at large scales; therefore, models are needed to predict N excreted in urine and feces. Building robust prediction models requires extensive data from animal...
Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the genus Entodinium has been consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that species such as Entodinium caudatum exert, their major biological and metabolic contri...
Measurement of enteric methane is expensive and not practical in most farms. Reliable prediction models have been developed recently for dairy and beef cattle based on intercontinental databases; however, equivalent sheep models are not yet available. This study aimed to: 1) collate an intercontinental database from individual sheep; 2) identify th...
Background
Heat stress (HS) affects the ruminal microbiota and decreases the lactation performance of dairy cows. Because HS decreases feed intake, the results of previous studies were confounded by the effect of HS on feed intake. This study examined the direct effect of HS on the ruminal microbiota using lactating Holstein cows that were pair-fed...
Significance
Agricultural methane emissions must be decreased by 11 to 30% of the 2010 level by 2030 and by 24 to 47% by 2050 to meet the 1.5 °C target. We identified three strategies to decrease product-based methane emissions while increasing animal productivity and five strategies to decrease absolute methane emissions without reducing animal pr...
Bacterial peptidases play important roles in health and nutrient digestion in both humans and animals, especially ruminant animals. In this study, we examined and compared the various peptidases (both total and secretory) among species of Prevotella (44 in total) and Paraprevotella (2) revealed in their sequenced genomes that were archived in the M...
Background
There is increasing research interest in using short-chain fatty acids (SCFAs) including butyrate as potential alternatives to antibiotic growth promoters in animal production. This study was conducted to evaluate the effects of supplementation of sodium butyrate (SB) in liquid feeds (milk, milk replacer, and the mixture of both) on the...
Using animal manure as organic fertilizer to grow fodder crops is causing public health concerns because animal manure is the major reservoir of veterinary antibiotics. In this study, we used a mathematical model to estimate the risk of human exposure to veterinary antibiotics when using swine manure as organic fertilizer to grow alfalfa (Medicago...
Citation: Ayemele, A.G.; Ma, L.; Li, X.; Yang, P.; Xu, J.; Yu, Z.; Bu, D. Identification of Bioactive Phytochemicals from Six Plants: Mechanistic Insights into the Inhibition of Rumen Protozoa, Ammoniagenesis, and α-Glucosidase. Biology 2021, 10, 1055. https://doi.org/ 10.3390/biology10101055
Rumen protozoa prey on feed-degrading bacteria synthesiz...
Calcium hydroxide (lime) treatment and solid-state anaerobic digestion (SSAD) of corn stover (CS) were carried out simultaneously with different lime doses (0, 2, 3.5, and 5%) and feedstock to seed sludge (F/S) ratios (6, 8, and 10). It was found that the addition of 3.5% lime improved CH 4 yield from 118 mL/g VS to 182 mL/g VS (54% increase) durin...
Rumen protozoa have a little contribution to the feed digestibility but Entodinium , the most predominant genus, is unfortunately culprit of the nitrogen utilization inefficiency. To bridge the gap, antibiotics have been used to inhibit the rumen protozoa but unfortunately, due to the health concern, this could not be really applied at the farm lev...
Weaning plays an important role in many animal processes, including the development of the rumen microbiota in ruminants. Attaining a better understanding of the development of the rumen microbial community at different weaning stages can aid the identification of the optimal weaning age. We investigated the effects of weaning age on ruminal bacter...
Entodinium caudatum is an anaerobic binucleated ciliate representing the most dominant protozoal species in the rumen. However, its biological features are largely unknown due to the inability to establish an axenic culture. In this study, we primally sequenced its macronucleus (MAC) genome to aid the understanding of its metabolism, physiology, ec...
Ruminant livestock enteric fermentation contributes approximately one-third of the global anthropogenic methane (CH 4 ) emissions and is projected to increase significantly to meet the increasing demand for animal-sourced protein. Methane, a short-lived greenhouse gas, needs to be reduced -24 to -47% by 2050 relative to 2010 to meet the 2.0°C targe...
Rumen protozoa, particularly the most predominant Entodinium spp., engulf rumen bacteria and subsequently recyle the microbial protein intraruminally, substantially lowering the nitrogen utilization efficiency in dairy cows. This study aimed to identify plants that can improve nitrogen utilization efficiency by inhibiting rumen protozoa, especially...
This study screened the leaves of six forest plants (Brassica rapa chinensis, Kalimeris indica, Calotropis procera, Portulara oleracea, Flemingia macrophylla, and Adansonia digitata) at 4 different doses (0, 0.7, 0.9 and 1.1 mg/ml) for their ability to inhibit rumen protozoa in vitro. Rumen fluid was collected from 3 different dairy cows and cultur...
Introduction
Rumen protozoa, particularly the most predominant Entodinium spp., engulf rumen bacteria and recycle the microbial protein intraruminally, substantially lowering the nitrogen utilization efficiency in dairy cows. This study aimed to use natural plants to improve nitrogen utilization efficiency through inhibiting rumen protozoa cultured...
Background:
Diet has a profound impact on the rumen microbiota, and the impact can vary among the different rumen ecological niches (REN). This study investigated the effects of dietary replacement of soybean meal (SBM) with dried distillers grains with solubles (DDGS) on the rumen microbiota occupying different REN of growing Hu lambs. After a 9-...
The complex rumen microbiota exhibits some degree of host specificity. The undeveloped simple rumen microbiota is hypothetically more amendable. The objective of this study was to investigate if the rumen prokaryotic microbial assemblage of young calves can be reprogrammed by oral inoculation with rumen microbiota of adult cows. Twenty newborn male...
Objectives
Green tea extract (GTE) protects against obesity in rodents by reducing gut permeability that otherwise provokes endotoxemia-mediated inflammation. However, whether obesity affects catechin bioavailability and microbial metabolism is unknown. We hypothesized that obesity will reduce catechin bioavailability by increasing microbial biotra...
Catechin-rich green tea extract (GTE) protects against nonalcoholic steatohepatitis (NASH) by alleviating gut-derived endotoxin translocation and hepatic TLR4-NFκB-inflammation. We hypothesized that intact GTE would attenuate NASH-associated responses along the gut-liver axis to a greater extent than purified (-)-epigallocatechin gallate (EGCG) or...
Background:
Dietary energy source and level in lactation diets can profoundly affect milk yield and composition. Such dietary effects on lactation performance are underpinned by alteration of the rumen microbiota, of which bacteria, archaea, fungi, and protozoa may vary differently. However, few studies have examined all the four groups of rumen m...
The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional gr...
Background
Short-chain fatty acids including butyrate have received increasing research interest as potential alternatives to antibiotic growth promoters (AGP) in animal production. This study was conducted to evaluate the effects of supplementation of sodium butyrate (SB) on the growth performance, rumen fermentation, antioxidant capacity, and imm...
Background: There is increasing research interest in using short-chain fatty acids (SCFAs) including butyrate as potential alternatives to antibiotic growth promoters in animal production. This study was conducted to evaluate the effects of supplementation of sodium butyrate (SB) in milk and/or milk replacer on the growth performance, rumen ferment...
Background: There is increasing research interest in using short-chain fatty acids (SCFAs) including butyrate as potential alternatives to antibiotic growth promoters in animal production. This study was conducted to evaluate the effects of supplementation of sodium butyrate (SB) in liquid feeds (milk, milk replacer, and the mixture of both) on the...
Background: There is increasing research interest in using short-chain fatty acids (SCFAs) including butyrate as potential alternatives to antibiotic growth promoters in animal production. This study was conducted to evaluate the effects of supplementation of sodium butyrate (SB) in liquid feeds (milk, milk replacer, and the mixture of both) on the...
Early life development and growth are critical in determining the lifelong growth performance and health of ruminants, and weaning poses the greatest challenge to young animals and has the most profound consequence. In this study, we aimed to investigate the effects of microbial intervention on the growth and development of young lambs and their ru...
Dr. Burk Dehority was an international expert on the classification and monoculture of ruminal ciliated protozoa. We have summarized many of the advancements in knowledge from his work but also in his scientific way of thinking about interactions of ruminal ciliates with the entire rumen microbial community and animal host. As a dedication to his l...
Background:
Many recent studies have gravitated towards manipulating the gastrointestinal (GI) microbiome of livestock to improve host nutrition and health using dietary interventions. Few studies, however, have evaluated if inoculation with rumen fluid could effectively reprogram the development of GI microbiota. We hypothesized that inoculation...
Defaunation studies have shown that rumen protozoa are one of the main causes of low nitrogen utilization efficiency due to their bacterivory and subsequent intraruminal cycling of microbial protein in ruminants. In genomic and transcriptomic studies, we found that rumen protozoa expressed lysozymes and peptidases at high levels. We hypothesized th...
Metabolic endotoxemia initiates low-grade chronic inflammation in metabolic syndrome (MetS) and provokes the progression towards more advanced cardiometabolic disorders. Our recent works in obese rodent models demonstrate that catechin-rich green tea extract (GTE) improves gut barrier integrity to alleviate the translocation of gut-derived endotoxi...
This study aimed to investigate the effects of two practically relevant doses of menthol-rich plant bioactive lipid compounds (PBLC) on fermentation, microbial community composition, and their interactions in sheep rumen. Twenty-four growing Suffolk sheep were divided into three treatments and were fed hay ad libitum plus 600 g/d of concentrate con...
This study investigated the effects of partially substituting soybean meal (SBM) with incremental amount of urea on rumen fermentation, nutrient digestion, plasma metabolites, and growth performance in fattening lambs. Seventy fattening male lambs were sorted into two blocks according to body weight (BW) and assigned to one of five dietary treatmen...
Nitrogen is a component of essential nutrients critical for the productivity of ruminants. If excreted in excess, N is also an important environmental pollutant contributing to acid deposition, eutrophication, human respiratory problems, and climate change. The complex microbial metabolic activity in the rumen and the effect on subsequent processes...
Enteric methane (CH4) production attributable to beef cattle contributes to global greenhouse gas emissions. Reliably estimating this contribution requires extensive CH4 emission data from beef cattle under different management conditions worldwide. The objectives were to: 1) predict CH4 production (g d−1 animal−1), yield [g (kg dry matter intake;...
Objectives
Green tea extract (GTE) alleviates nonalcoholic steatohepatitis (NASH) through a mechanism involving the gut-liver axis by limiting endotoxin-TLR4-NFκB inflammation, but the independent bioactivities of specific green tea catechins have not been defined. We hypothesized that epigallocatechin gallate (EGCG) and catechin (CAT) would protec...
The objective of this study was to evaluate the performance of existing models predicting enteric methane (CH4) emissions, using a large database (3183 individual data from 103 in vivo studies on dairy and beef cattle, sheep and goats fed diets from different countries). The impacts of dietary strategies to reduce CH4 emissions, and of diet quali...
Gut-derived endotoxin translocation provokes obesity by inducing TLR4/NFκB inflammation. We hypothesized that catechin-rich green tea extract (GTE) would protect against obesity-associated TLR4/NFκB inflammation by alleviating gut dysbiosis and limiting endotoxin translocation. Male C57BL/6J mice were fed a low-fat (LF) or high-fat (HF) diet contai...
Microbial fuel cells (MFCs) have potential to treat industrial wastewater containing organic compounds and simultaneously generate power. Organic compounds include textile dyes with various chromophore groups, which can be decolorized reductively by microorganisms under anaerobic conditions. In the present study, we examined the decolorization of R...
This study evaluated the effects of nitrogen source composition and monensin on the populations of proteolytic and amino acid-fermenting bacteria using in vitro enrichment culture. The experiment was designed with a 2 × 2 factorial arrangement: two nitrogen sources, casein (Cas) and tryptone (Try), and two levels of monensin, 0 (C) and 5 µmol/L (M)...
Rumen protozoa, primarily ciliates, are one of the important groups of strictly anaerobic microbes living in the rumen. Despite their ubiquitous occurrence in the rumen and significant contribution to host animals, it is still poorly understood why they live only in the rumen and similar environment. Because rumen protozoa require strict anaerobic...
Ruminal ciliates both preys on and form symbiotic relationships with other members of the ruminal microbiota for their survival. However, it remains elusive if they have selectivity over their preys or symbionts. In the present study, we investigated the above selectivity by identifying and comparing the free-living prokaryotes (FLP) and the ciliat...
Enteric methane (CH4) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CH4 is complex, expensive and impractical at large scales; therefore, models are commonly used to predict CH4 production. However, building robust prediction models requires extensive data from animals under different management syste...
Ruminant production systems are important contributors to anthropogenic methane (CH4) emissions, but there are large uncertainties in national and global livestock CH4 inventories. Sources of uncertainty in enteric CH4 emissions include animal inventories, feed dry matter intake (DMI), ingredient and chemical composition of the diets, and CH4 emiss...
The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, with the former producing much more methane than the latter. The objective of this study was to elucidate the microbial underpinning of such differential methane outputs between these two digestive organs. Methane production was measured from 5 adult sheep...</