Peptidases of the rumen bacterium, Prevotella ruminicola

Comparative Analysis of Gut Bacterial Diversity in Wild and Domestic Yaks on the Qinghai-Tibetan Plateau

The gut microbiota is a diverse and complex population, and it has a key role in the host's health and adaptability to the environment. The present study investigated the fecal bacterial community of wild grazing (WG) and domestic grazing (DG) yaks on natural grazing pastures, analyzing the gut microbiota using 16S rRNA sequencing to assess bacterial diversity. A total of 48 yak fecal samples were selected from two different grazing habitats. The DG group had more crude proteins and non-fiber carbohydrates. The WG group had more OM, insoluble dietary fiber such as NDF, ADF, ether extract, and TC. There were 165 and 142 unique operational taxonomic units (OTUs) in the WG and DG groups, respectively. Shannon index analysis revealed a higher bacterial diversity in the WG group than in the DG group. At the phylum level, Firmicutes were the dominant bacterial taxa in both groups. The relative abundance of Firmicutes in the WG group was higher than in the DG group. At the family level, the WG group had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than the DG group. The abundances of Alloprevotella and Succinivibrio were more pronounced in the DG group than in the WG group at the genus level. This study presents a novel understanding of the bacterial communities of ruminants and their potential applications for livestock production.

Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM)

The role of the gut microbiota and its interplay with host metabolic health, particularly in the context of type 2 diabetes mellitus (T2DM) management, is garnering increasing attention. Dipeptidyl peptidase 4 (DPP4) inhibitors, commonly known as gliptins, constitute a class of drugs extensively used in T2DM treatment. However, their potential interactions with gut microbiota remain poorly understood. In this study, we employed computational methodologies to investigate the binding affinities of various gliptins to DPP4-like homologs produced by intestinal bacteria. The 3D structures of DPP4 homologs from gut microbiota species, including Segatella copri, Phocaeicola vulgatus, Bacteroides uniformis, Parabacteroides merdae, and Alistipes sp., were predicted using computational modeling techniques. Subsequently, molecular dynamics simulations were conducted for 200 ns to ensure the stability of the predicted structures. Stable structures were then utilized to predict the binding interactions with known gliptins through molecular docking algorithms. Our results revealed binding similarities of gliptins toward bacterial DPP4 homologs compared to human DPP4. Specifically, certain gliptins exhibited similar binding scores to bacterial DPP4 homologs as they did with human DPP4, suggesting a potential interaction of these drugs with gut microbiota. These findings could help in understanding the interplay between gliptins and gut microbiota DPP4 homologs, considering the intricate relationship between the host metabolism and microbial communities in the gut.

Metagenomic sequencing identified microbial species in the rumen and cecum microbiome responsible for niacin treatment and related to intramuscular fat content in finishing cattle

Introduction

Niacin is one of the essential vitamins for mammals. It plays important roles in maintaining rumen microecological homeostasis. Our previous study indicated that dietary niacin significantly elevated intramuscular fat content (IMF) in castrated finishing steers. Whether niacin affects fat deposition by regulating the microbial composition and functional capacities of gastrointestinal microbiome has been unknown yet.

Methods

In this study, 16 castrated Xiangzhong Black cattle were randomly assigned into either control group fed with a basal concentrate diet (n = 8) or niacin group fed with a basal concentrate diet added 1000 mg/kg niacin (n = 8). Seven rumen samples and five cecum content samples were randomly collected from each of control and niacin groups for metagenomic sequencing analysis.

Results

A total of 2,981,786 non-redundant microbial genes were obtained from all tested samples. Based on this, the phylogenetic compositions of the rumen and cecum microbiome were characterized. We found that bacteria dominated the rumen and cecum microbiome. Prevotella ruminicola and Ruminococcus flavefaciens were the most abundant bacterial species in the rumen microbiome, while Clostridiales bacterium and Eubacterium rectale were predominant bacterial species in the cecum microbiome. Rumen microbiome had significantly higher abundances of GHs, GTs, and PLs, while cecum microbiome was enriched by CBMs and AAs. We found a significant effect of dietary niacin on rumen microbiome, but not on cecum microbiome. Dietary niacin up-regulated the abundances of bacterial species producing lactic acid and butyrate, fermenting lactic acid, and participating in lipid hydrolysis, and degradation and assimilation of nitrogen-containing compounds, but down-regulated the abundances of several pathogens and bacterial species involved in the metabolism of proteins and peptides, and methane emissions. From the correlation analysis, we suggested that niacin improved nutrient digestion and absorption, but reduced energy loss, and Valine, leucine and isoleucine degradation of rumen microbiome, which resulted in the increased host IMF.

Conclusion

The results suggested that dietary manipulation, such as the supplementation of niacin, should be regarded as the effective and convenient way to improve IMF of castrated finishing steers by regulating rumen microbiome.

Enhancing rumen microbial diversity and its impact on energy and protein metabolism in forage-fed goats

Introduction

This study explores if promoting a complex rumen microbiota represents an advantage or a handicap in the current dairy production systems in which ruminants are artificially reared in absence of contact with adult animals and fed preserved monophyte forage.

Methods

In order to promote a different rumen microbial diversity, a total of 36 newborn goat kids were artificially reared, divided in 4 groups and daily inoculated during 10 weeks with autoclaved rumen fluid (AUT), fresh rumen fluid from adult goats adapted to forage (RFF) or concentrate (RFC) diets, or absence of inoculation (CTL). At 6 months of age all animals were shifted to an oats hay diet to determine their ability to digest a low quality forage.

Results and discussion

Early life inoculation with fresh rumen fluid promoted an increase in the rumen overall microbial diversity which was detected later in life. As a result, at 6 months of age RFF and RFC animals had higher bacterial (+50 OTUs) and methanogens diversity (+4 OTUs) and the presence of a complex rumen protozoal community (+32 OTUs), whereas CTL animals remained protozoa-free. This superior rumen diversity and presence of rumen protozoa had beneficial effects on the energy metabolism allowing a faster adaptation to the forage diet, a higher forage digestion (+21% NDF digestibility) and an energetically favourable shift of the rumen fermentation pattern from acetate to butyrate (+92%) and propionate (+19%) production. These effects were associated with the presence of certain rumen bacterial taxa and a diverse protozoal community. On the contrary, the presence of rumen protozoa (mostly Entodinium) had a negative impact on the N metabolism leading to a higher bacterial protein breakdown in the rumen and lower microbial protein flow to the host based on purine derivatives urinary excretion (-17% to -54%). The inoculation with autoclaved rumen fluid, as source of fermentation products but not viable microbes, had smaller effects than using fresh inoculum. These findings suggest that enhancing rumen microbial diversity represents a desirable attribute when ruminants are fed forages in which the N supply does not represent a limiting factor for the rumen microbiota.

Effects of grain-based diets on the rumen and fecal bacterial communities of the North American bison (Bison bison)

To overcome the challenges of pasture-finishing of bison, producers commonly feed them with higher energy, grain-based diets to reach the desired market weight. However, decades of research on domesticated ruminants have shown that such diets can have profound effects on the composition of gut microbial communities. To gain further insight, the 16S rRNA gene-based study described in this report aimed to compare the composition of ruminal and fecal bacterial communities from two herds of bison heifers (n = 20/herd) raised on different ranches that were both transitioned from native pasture to a grain-based, free-choice diet for ~100 days prior to slaughter. Comparative analyses of operational taxonomic unit (OTU) composition, either by alpha diversity indices, principal coordinate analysis (PCoA), or on the most abundant individual OTUs, showed the dramatic effect of a diet on the composition of both rumen and fecal bacterial communities in bison. Indeed, feeding a grain-based diet resulted in a lower number of rumen and fecal bacterial OTUs, respectively, compared to grazing on pasture (p < 0.05). PCoA revealed that the composition of the rumen and fecal bacterial communities from the two herds was more similar when they were grazing on native pastures compared to when they were fed a grain-based, free-choice diet. Finally, a comparative analysis of the 20 most abundant OTUs from the rumen and fecal communities further showed that the representation of all these species-level bacterial groups differed (p < 0.05) between the two dietary treatments. Together, these results provide further insights into the rumen and fecal microbiomes of grazing bison and their response to grain-based diet regimens commonly used in intensive ruminant production systems.

Application of different proportions of sweet sorghum silage as a substitute for corn silage in dairy cows

This experiment explored the effects of different proportions of sweet sorghum silage as a substitute for corn silage on dry matter intake (DMI), milk yield, milk quality, apparent digestibility, rumen fermentation parameters, serum amino acid profile, and rumen microbial composition of dairy cows. A total of 32 mid-lactation Holstein dairy cows with similar body weights and parities were randomly divided into four treatments: 100% corn silage +0% sorghum silage (CON), 75% corn silage +25% sorghum silage (CS1), 50% corn silage +50% sorghum silage (CS2), and 25% corn silage +75% sorghum silage (CS3). The milk yield was increased (linear, p = .048) as the proportion of sweet sorghum increased. Linear (p = .003) and quadratic (p = .046) increased effects were observed in milk fat as corn silage was replaced with sorghum silage. Compared with the CON diet group, the CS2 and CS3 diet groups had lower dry matter (DM) (linear, p < .001), ether extract (EE) (linear, p < .001), and gross energy (GE) (linear, p = .001) digestibility of the dairy cows. The ruminal fluid aspartate (Asp) level decreased (linear, p = .003) as the proportion of sweet sorghum increased. Linear (p < .05) and quadratic (p < .05) increased effects were observed for the contents of threonine (Thr), glycine (Gly), valine (Val), leucine (Leu), tyrosine (Tyr), and histidine (His) in rumen fluid with the replacement of corn silage with sorghum silage. Cows fed the CS3 diet had greater Faecalibacterium, Bacteroides, and Prevotella ruminicola content/copy number than those fed the CON diet (p < .05). In conclusion, feeding sorghum silage as a replacement for corn silage could increase the milk yield and fat, promote the growth of rumen microbes, and provide more rumen fluid amino acids for the body and microbial utilization. We believe that sorghum silage is feasible for dairy cows, and it is reasonable to replace corn silage with 75% sorghum silage.

Metabolome and microbiome analysis revealed the effect mechanism of different feeding modes on the meat quality of Black Tibetan sheep

Introduction

Black Tibetan sheep is one of the primitive sheep breeds in China that is famous for its great eating quality and nutrient value but with little attention to the relationship between feeding regimes and rumen metabolome along with its impact on the muscle metabolism and meat quality.

Methods

This study applies metabolomics-based analyses of muscles and 16S rDNA-based sequencing of rumen fluid to examine how feeding regimes influence the composition of rumen microbiota, muscle metabolism and ultimately the quality of meat from Black Tibetan sheep. Twenty-seven rams were randomly assigned to either indoor feeding conditions (SG, n = 9), pasture grazing with indoor feeding conditions (BG, n = 9) or pasture grazing conditions (CG, n = 9) for 120 days.

Results

The results showed that, compared with BG and CG, SG improved the quality of Black Tibetan sheep mutton by preventing a decline in pH and increasing fat deposition to enhance the color, tenderness and water holding capacity (WHC) of the Longissimus lumborum (LL). Metabolomics and correlation analyses further indicated that the feeding regimes primarily altered amino acid, lipid and carbohydrate metabolism in muscles, thereby influencing the amino acid (AA) and fatty acid (FA) levels as well as the color, tenderness and WHC of the LL. Furthermore, SG increased the abundance of Christensenellaceae R-7 group, [Eubacterium] coprostanoligenes group, Methanobrevibacter, Ruminococcus 2 and Quinella, decreased the abundance of Lactobacillus, Prevotella 1 and Rikenellaceae RC9 gut group, and showed a tendency to decrease the abundance of Succinivibrio and Selenomonas 1. Interestingly, all of these microorganisms participated in the deposition of AAs and FAs and modified the levels of different metabolites involved in the regulation of meat quality (maltotriose, pyruvate, L-ascorbic acid, chenodeoxycholate, D-glucose 6-phosphate, glutathione, etc.).

Discussion

Overall, the results suggest that feeding Black Tibetan sheep indoors with composite forage diet was beneficial to improve the mouthfeel of meat, its color and its nutritional value by altering the abundance of rumen bacteria which influenced muscle metabolism.

Can dietary magnesium sources and buffer change the ruminal microbiota composition and fermentation of lactating dairy cows?

Magnesium oxide (MgO) is one of the most used Mg supplements in livestock. However, to avoid relying upon only one Mg source, it is important to have alternative Mg sources. Therefore, the objective of this study was to evaluate the effects of the interaction of two Mg sources with buffer use on the ruminal microbiota composition, ruminal fermentation, and nutrient digestibility in lactating dairy cows. Twenty lactating Holstein cows were blocked by parity and days in milk into five blocks with four cows each, in a 2 × 2 factorial design. Within blocks, cows were assigned to one of four treatments: 1) MgO; 2) MgO + Na sesquicarbonate (MgO+); 3) calcium-magnesium hydroxide (CaMgOH); 4) CaMgOH + Na sesquicarbonate (CaMgOH+). For 60 d, cows were individually fed a corn silage-based diet, and treatments were top-dressed. Ruminal fluid was collected via an orogastric tube, for analyses of the microbiota composition, volatile fatty acids (VFA), lactate, and ammonia nitrogen (NH3-N). The microbiota composition was analyzed using V4/16S rRNA gene sequencing, and taxonomy was assigned using the Silva database. Statistical analysis was carried out following the procedures of block design analysis, where block and cow were considered random variables. Effects of Mg source, buffer, and the interaction between Mg Source × Buffer were analyzed through orthogonal contrasts. There was no interaction effect of the two factors evaluated. There was a greater concentration of NH3-N, lactate, and butyrate in the ruminal fluid of cows fed with CaMg(OH)2, regardless of the buffer use. The increase in these fermentation intermediates/ end-products can be explained by an increase in abundance of micro-organisms of the genus Prevotella, Lactobacillus, and Butyrivibrio, which are micro-organisms mainly responsible for proteolysis, lactate-production, and butyrate-production in the rumen, respectively. Also, dietary buffer use did not affect the ruminal fermentation metabolites and pH; however, an improvement of the apparent total tract digestibility of dry matter (DM), organic matter (OM), neutral fiber detergent (NDF), and acid fiber detergent (ADF) were found for animals fed with dietary buffer. In summary, there was no interaction effect of buffer use and Mg source, whereas buffer improved total tract apparent digestibility of DM and OM through an increase in NDF and ADF digestibility and CaMg(OH)2 increased ruminal concentration of butyrate and abundance of butyrate-producing bacteria.

Prevotella: A Key Player in Ruminal Metabolism

Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.

Characteristics of ruminal microbiota and metabolome in Holstein cows differing in milk protein concentrations

The rumen is a vital organ containing vast amounts of microbes that play a key role in the digestion of nutrients and affect the production performance of ruminants. However, few studies have focused on the characterization of the ruminal microbiota composition and function in cows with long-term difference milk protein concentrations, and the relationship between milk protein concentration and ruminal microbiota remains elusive. In this study, we collected the data of milk protein concentrations of 1,025 Holstein cows for 10 mo on a commercial farm. Based on the milk protein concentrations, 30 cows were selected and divided into three groups (n = 10 per group): low milk protein group (LMP, milk protein concentration < 3.1%), medium milk protein group (MMP, 3.1% ≤ milk protein concentration < 3.4%), and high milk protein group (HMP, milk protein concentration ≥ 3.4%). The ruminal microbiome, metabolome, VFA concentrations and proportions, and amino acid profiles of the three groups were analyzed. The data showed that free amino acid (FAA) levels were lower in the rumen and higher in the plasma of HMP cows (P < 0.05). In addition, lower NH3 concentrations were observed in the rumen, plasma, and milk of the HMP cows (P < 0.05). Protease activity and isobutyric acid molar proportion in the rumen were lower in the HMP group (P < 0.05). Microbiome analysis showed that HMP cows had lower microbial diversity (represented as Shannon and Simpson indices) than LMP cows. At the genus level, lower relative abundances of Prevotella_1 and Ruminococcaceae_UCG_005 were observed in the HMP group (P < 0.05). At the operational taxonomic unit (OTU) level, a lower relative abundance of OTU3 (Prevotella ruminicola) was observed in the HMP group (P < 0.05). We found that the relative abundances of ruminal Prevotella_1 and OTU3 (Prevotella ruminicola) were negatively correlated with milk protein concentration (P < 0.05). These findings suggested that the cows with long-term high milk protein concentrations had lower microbial diversity and weaker protein degradation ability in the rumen. Furthermore, our observations identified a correlation between the milk protein concentration and ruminal microbiota.

Microbiota and Serum Metabolic Profile Changes in Korean Native Hanwoo Steer in Response to Diet Feeding Systems

The diversity of bacteria and their function in cattle gastrointestinal tracts can influence animal welfare. Next-generation sequencing (NGS) was used to investigate microbial diversity in the feces of Hanwoo steers reared under natural grazing (GS) and housing (HS) systems. Additionally, serum metabolic parameters, such as liver and kidney markers and mineral and lipid content changes, as well as their correlation with pyrotags, were studied. A total of 6468 ± 87.86 operational taxonomic units (OTUs) were identified in both steer groups, of which 3538 ± 38.17 OTUs were from grazing steer and 2930 ± 94.06 OTUs were from GS. Chao1 index analysis revealed a higher bacterial richness in GS. The dominant bacterial taxa were Bacteroidetes and Firmicutes. GS showed lower Bacteroidetes and higher Firmicutes abundance than HS. The serum of HS showed consistent increases in gamma-glutamyl transpeptidase (γGTP), glucose (GLU), total cholesterol (T-CHO), and triglyceride (TG) levels. The impact of GS on animal health and serum metabolic markers was strongly correlated with microbiota. As shown in this study, grazing has a significant impact on the fecal microbiota at the phylum and family levels, as well as the serum biochemical metabolites of Hanwoo steers.

Residual feed intake in peripartal dairy cows is associated with differences in milk fat yield, ruminal bacteria, biopolymer hydrolyzing enzymes, and circulating biomarkers of immunometabolism

Residual feed intake (RFI) measures feed efficiency independent of milk production level, and is typically calculated using data past peak lactation. In the current study, we retrospectively classified multiparous Holstein cows (n = 320) from 5 of our published studies into most feed-efficient (M-eff) or least feed-efficient (L-eff) groups using performance data collected during the peripartal period. Objectives were to assess differences in profiles of plasma biomarkers of immunometabolism, relative abundance of key ruminal bacteria, and activities of digestive enzymes in ruminal digesta between M-eff and L-eff cows. Individual data from cows with ad libitum access to a total mixed ration from d -28 to d +28 relative to calving were used. A linear regression model including dry matter intake (DMI), energy-corrected milk (ECM), changes in body weight (BW), and metabolic BW was used to classify cows based on RFI divergence into L-eff (n = 158) and M-eff (n = 162). Plasma collected from the coccygeal vessel at various times around parturition (L-eff = 60 cows; M-eff = 47 cows) was used for analyses of 30 biomarkers of immunometabolism. Ruminal digesta collected via esophageal tube (L-eff = 19 cows; M-eff = 29 cows) was used for DNA extraction and assessment of relative abundance (%) of 17 major bacteria using real-time PCR, as well as activity of cellulase, amylase, xylanase, and protease. The UNIVARIATE procedure of SAS 9.4 (SAS Institute Inc.) was used for analyses of RFI coefficients. The MIXED procedure of SAS was used for repeated measures analysis of performance, milk yield and composition, plasma immunometabolic biomarkers, ruminal bacteria, and enzyme activities. The M-eff cows consumed less DMI during the peripartal period compared with L-eff cows. In the larger cohort of cows, despite greater overall BW for M-eff cows especially in the prepartum (788 vs. 764 kg), no difference in body condition score was detected due to RFI or the interaction of RFI × time. Milk fat content (4.14 vs. 3.75 ± 0.06%) and milk fat yield (1.75 vs. 1.62 ± 0.04 kg) were greater in M-eff cows. Although cumulative ECM yield did not differ due to RFI (1,138 vs. 1,091 ± 21 kg), an RFI × time interaction due to greater ECM yield was found in M-eff cows. Among plasma biomarkers studied, concentrations of nonesterified fatty acids, β-hydroxybutyrate, bilirubin, ceruloplasmin, haptoglobin, myeloperoxidase, and reactive oxygen metabolites were overall greater, and glucose, paraoxonase, and IL-6 were lower in M-eff compared with L-eff cows. Among bacteria studied, abundance of Ruminobacter amylophilus and Prevotella ruminicola were more than 2-fold greater in M-eff cows. Despite lower ruminal activity of amylase in M-eff cows in the prepartum, regardless of RFI, we observed a marked linear increase after calving in amylase, cellulase, and xylanase activities. Protease activity did not differ due to RFI, time, or RFI × time. Despite greater concentrations of biomarkers reflective of negative energy balance and inflammation, higher feed efficiency measured as RFI in peripartal dairy cows might be associated with shifts in ruminal bacteria and amylase enzyme activity. Further studies could help address such factors, including the roles of the liver and the mammary gland.

Evaluation of a Colombian oregano oil (Lippia origanoides Kunth) and a novel yeast product from Pichia guilliermondii, alone or in combination, on rumen fermentation, methanogenesis and the microbiome in the rumen simulation technique

In this study, Lippia origanoides Kunth, native to the Alto Patía region in Southwest Colombia, and Pichia guilliermondii LV196, an inactivated yeast from the germplasm bank of Agrosavia (Colombian Agricultural Research Corporation), alone or combined, were tested for their long-term effect on rumen fermentation and methanogenesis whilst also characterising their effect on bacterial and methanogen communities. Whereas essential oils act through selective inhibition of microbial groups, yeasts are thought to work through the selective stimulation of key microbes in the rumen. We hypothesized that yeast supplementation could modulate the antimicrobial effect of a high thymol-containing oregano oil, allowing a more efficient feed utilization whilst decreasing methane production. When added to a rumen simulating fermentor (RUSITEC), L. origanoides Kunth at 132 µL/d had a detrimental effect on rumen fermentation which was accompanied by a reduction in the relative abundance of protozoa and fungi and a profound impact on the bacterial and archaeal communities. P. guilliermondii LV196 at 0.5 g/L, however, had no effect on fermentation parameters or nutrient utilization, and neither changes in microbial abundances or in the structure of bacterial and archaeal communities were observed. P. guilliermondii LV196 did not stimulate microbial numbers nor activity and, consequently we could not test whether it could have counterbalanced the antimicrobial effect of the essential oil. Future studies need to both investigate lower levels of essential oil addition, but also to re-examine the effects of P. guillermondii in the rumen and/or to replace it with other yeast of known biological activity when combined with oils extracted from L. origanoides Kunth.

Regulation of Dietary Protein Solubility Improves Ruminal Nitrogen Metabolism In Vitro: Role of Bacteria-Protozoa Interactions

Precision dietary interventions (e.g., altering proportions of dietary protein fractions) has significant implications for the efficiency of nutrient use in ruminants, as well as lowering their environmental footprint, specifically nitrogen (N) emissions. Soluble protein (SP) is defined as the protein fraction that is rapidly degraded in the rumen (e.g., non-protein N and true protein), and our previous study found that regulating SP levels could improve N efficiency in Hu sheep. Thus, the present study was conducted to explore in vitro how protein fractions with different SP levels modulate the rumen microbial community and its association with N metabolism. Four dietary treatments with different SP proportions and similar crude protein (CP) content (~14%) were formulated (% of CP): 20 (S20), 30 (S30), 40 (S40) and 50 (S50). Results showed that NH3-N content increased with increasing SP levels at 4, 12 and 24 h; TVFA, acetate, propionate and valerate were higher in S30 and S40 (p < 0.05) and had quadratic effects (p < 0.05). Moreover, dry matter digestibility (DMD) and N digestibility (ND) were all decreased with S20 and S50 (p < 0.05). The S30 and S40 treatments increased the abundance of Bacteroidetes and Prevotella (Prevotella_ruminicola) but decreased the abundance of Firmicutes and Proteobacteria (p < 0.05). Bacterial pathways related to amino acid and fatty acid metabolism also were enriched with S30 and S40. The abundance of Entodinium was increased with S30 and S40 and had a positive correlation with Prevotella, and these two genera also played an important role in N metabolism and VFA synthesis of this study. In conclusion, bacterial and protozoal communities were altered by the level of SP (% of CP), with higher SP levels (~50% of CP) increasing the microbial diversity but being detrimental to rumen N metabolism.

Characterization of a New Xylanase Found in the Rumen Metagenome and Its Effects on the Hydrolysis of Wheat

Wheat is the main ingredient of poultry diet, but its xylan has an adverse impact on poultry production. A novel xylanase from beef cattle rumen metagenome (RuXyn) and its effect on the wheat hydrolysis were investigated in the present study. The RuXyn coded for 377 amino acids and exhibited low identity (<40%) to previously reported proteins. The RuXyn was heterologously expressed in Escherichia coli and showed maximum activity at pH 6.0 and 40 °C. The activity of RuXyn could be increased by 79.8 and 36.0% in the presence of Ca²⁺ and Tween 20, respectively. The soluble xylan and insoluble xylan in wheat could be effectively degraded by RuXyn and xylooligosaccharides produced accounting for more than 80% of the products. This study demonstrates that RuXyn has substantial potential to improve the application of wheat in poultry production by degrading wheat xylan and the accompanying xylooligosaccharides produced.

Effects of Broussonetia papyrifera silage on rumen fermentation parameters and microbes of Holstein heifers

The structure and types of rumen microbes are closely related to host health. This study aimed to evaluate the effect of Broussonetia papyrifera silage (BPS) gradually replacing the whole crop maize silage (WCMS) on total tract digestibility, rumen fermentation parameters, serum biochemical indicators, and rumen microbes of Holstein heifers. The diet treatment consisted of four proportions of BPS (0%, 25%, 50% and 75%) as substitute for WCMS (designated as T0, T25, T50 and T75, respectively). Twenty heifers (body weight = 245 ± 24 kg) were randomly divided into four groups of five heifers, and randomly received one diet. The feeding adaption period was 7 days, and the experiment period was 30 days. Our findings suggested that the digestibility of neutral detergent fiber and crude protein increased linearly with the increased in BPS (P < 0.05). The concentrations of total protein and albumin increased quadratically with the increased in BPS (P < 0.05). The 16s high-throughput sequencing showed that feeding BPS did not change the diversity and structure of the rumen microbes of heifers. However, the relative abundances of Tenericutes and SR1-Absconditabacteria increased linearly with the increased in BPS (P < 0.05). The Weighted Correlation Network Analysis results suggested that ALT concentration was positively correlated with the abundance of Prevotella-1 (r = 0.73; P = 0.007). In general, Holstein heifers fed with BPS did not change the diversity and uniformity of rumen microbes, and enhanced the body protein metabolism.

Differential Effects of Natural Grazing and Feedlot Feeding on Yak Fecal Microbiota

Variation in food and diet shapes the diversity of the gut microbiota of ruminants. The present study investigated the microbial diversity in the fecal microbiota of yaks reared under natural grazing and feedlot system. A total of 48 domestic yaks with an average age of 7.5 years were selected from two different grazing habitats: one group grazed on natural pasture (grazing yaks—GY) while the other group was fed fodder and concentrate (feedlot yaks—FY). Crude protein, non-fiber carbohydrate, hemicelluloses, and digestible dry matter contents of natural pastures were higher than those in the feedlot. The lower insoluble fiber contents were found in grazing land. The 16S rRNA gene sequencing revealed 675 and 348 unique operational taxonomic units (OTUs) in the GY and FY, respectively, in addition to 1,778 common OTUs. Overall, a total of 9,891 OTUs were identified as a whole, of which 6,160 OTUs were from GY and 3,731 were from FY. Shannon index analysis revealed a higher bacterial diversity in GY than FY. At the phylum level, Firmicutes were dominant bacterial taxa in both groups. The relative abundance of Firmicutes in GY (56% ± 0.05) was higher than in FY (41% ± 0.08). At the family level, GY had a significantly higher abundance of Ruminococcaceae (p &lt; 0.001) and Rikenellaceae (p &lt; 0.001) than FY, but FY had a significantly higher abundance of Prevotellaceae than GY (p &lt; 0.001). At the genus level, abundances of Faecalibacterium, Alloprevotella, and Succinivibrio were higher in FY than in GY. This study presents novel information on fecal bacterial composition and diversity in yaks reared under two different production systems.

Genomic Insights into the Distribution of Peptidases and Proteolytic Capacity among Prevotella and Paraprevotella Species

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 MEROPS database. The phylogenetic relationships were also compared among the species based on 16S rRNA gene sequences and the occurrence of peptidases. A rich repertoire of peptidases was found that represents six catalytic types of peptidases (aspartic, cysteine, glutamic, metallo, mixed, and serine), together with some with unknown catalytic mechanisms, and 78 families. Metallopeptidases were the most predominant, followed by serine and cysteine peptidases. Considerable variations in peptidase occurrence and distribution were noted among the species and the different families of peptidases. A total of 48 different families of secretory peptidases were found in the genomes of the Prevotella and Paraprevotella species. Secretory peptidases in the families of S41 and M13 were ubiquitous, and S9, M16, C1, S13, and C69 were found in more than 95% of the species. Multivariate analysis of the peptidases indicated that species were mostly clustered except for a few species. Analysis using a bipartite association network showed that the majority of peptidase families were shared among the species. The relatedness of peptidase distributions among the species did not significantly correlate with their phylogenetic relationship based on the 16S rRNA genes. The genomic overview on the peptidases of Prevotella and Paraprevotella species provided new insights into their potential capacity to degrade proteins. IMPORTANCE Species of Prevotella are prevalent and predominant bacteria residing in animals and humans, and their proteolytic capacity and activity play important roles in nutrient utilization in animals (especially ruminants) and some anaerobic infections of the intestinal, respiratory, and urinary tracts in humans. This study reveals the large repertoire and wide distribution of metallo, serine, and cysteine peptidases, especially secretory peptidases, among the Prevotella species. The information presented here could aid in the identification of the Prevotella species and the peptidases to target to decrease the excessive protein degradation in the rumen and improve dietary nitrogen utilization by ruminant animals.

Amino acids metabolism by rumen microorganisms: Nutrition and ecology strategies to reduce nitrogen emissions from the inside to the outside

For the ruminant animal industry, the emission of nitrogenous substances, such as nitrous oxide (N₂O) and ammonia (NH₃), not only challenges environmental sustainability but also restricts its development. The metabolism of proteins and amino acids by rumen microorganisms is a key factor affecting nitrogen (N) excretion in ruminant animals. Rumen microorganisms that affect N excretion mainly include three types: proteolytic and peptidolytic bacteria (PPB), ureolytic bacteria (UB), and hyper-ammonia-producing bacteria (HAB). Microbes residing in the rumen, however, are influenced by several complex factors, such as diet, which results in fluctuations in the rumen metabolism of proteins and amino acids and ultimately affects N emission. Combining feed nutrition strategies (including ingredient adjustment and feed additives) and ecological mitigation strategies of N₂O and NH₃ in industrial practice can reduce the emission of nitrogenous pollutants from the ruminant breeding industry. In this review, the characteristics of the rumen microbial community related to N metabolism in ruminants were used as the metabolic basis. Furthermore, an effective strategy to increase N utilisation efficiency in combination with nutrition and ecology was reviewed to provide an inside-out approach to reduce N emissions from ruminants.

Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep

The cecum serves as an additional fermentation site for ruminants, but it lacks buffering capacity and has a relatively simple epithelial structure compared to the rumen. The role of high-grain (HG) diets in manipulating the rumen microbiome has been well elucidated, yet the microbial response to such diets in the cecum and the subsequent microbe-host interactions remain largely unexplored. Here, we describe the modification of the cecal microbiome and host epithelial gene expression based on data from 20 sheep grouped to feed an HG diet for 7, 14, and 28 days. Our data indicate that the alteration of cecal microbial fermentation was manifested by a decrease in luminal pH and an increase in acetate and butyrate concentrations following the diet change to HG. We further demonstrate that the alteration of the microbiome was driven by microbes that are likely acetate producers (e.g., Blautia spp. and Akkermansia spp.) and butyrate producers (e.g., Anaerostipes spp. and Roseburia spp.). Moreover, the core microbiota in the cecal microbiome was predominantly maintained after HG diet feeding, while the specific populations of the cecal microbiomes adaptively varied at the species and genomic levels time dependently. Association analysis suggests that the perturbations of the cecal microbiome under the HG diet were closely linked to the variations in the two key enzymes that catalyze the conversion of pyruvate to acetyl-CoA and urease enzymes that hydrolyze urea into ammonia, alongside mucosal inflammatory responses. Overall, our findings here provide novel insights into understanding microbiome-host interactions in the hindgut of ruminants.

IMPORTANCE High-grain (HG) diets are known to alter the rumen microbiome. However, the responses of the hindgut microbiota and its epithelial function need further investigation in ruminants. Using 20 sheep as the experimental model, we found that the microbial fermentation pattern of the cecum changed after switching to the HG diet. The taxa of the acetate and butyrate producers increased with the feeding time. Moreover, enzymes engaged in carbon and nitrogen metabolisms of the cecal microbiome are altered. The expression of epithelial genes related to volatile fatty acid (VFA) absorption and metabolism, cytokines, and tight junction proteins, alongside light microscopy visualization of epithelial tissue, suggested that the HG diet may induce cecal mucosal inflammatory responses. Our findings reveal cecal microbial and metabolic perturbations in response to HG diets in sheep and provide a new reference for the research on hindgut microbial homeostasis and host health in ruminants.

Adding polyethylene glycol to steer ration containing sorghum tannins increases crude protein digestibility and shifts nitrogen excretion from feces to urine

The objectives of the experiment were to study the effects of adding polyethylene glycol (PEG) to steer ration containing high sorghum tannins on rumen fermentation, nutrient digestion, nitrogen (N) balance and plasma biochemical parameters. Eight growing steers at 16 months of age were allotted to a replicated 4 × 4 Latin square design with 4 treatments and 4 periods (19 d each). Polyethylene glycol at 0, 1.75, 3.50 and 7.00 g/kg dry matter (DM) were added to a basal ration containing 27.82% DM of sorghum grain (total tannins 3.3 g/kg DM) as the treatments. The results indicated that adding PEG quadratically increased the ruminal pH (P = 0.049), tended to linearly increase the ruminal concentration of total volatile fatty acids (P = 0.070), increased the molar proportion of acetate (P = 0.016), linearly decreased the molar proportion of butyrate (P = 0.015), and tended to increase the molar proportion of iso-valerate (P = 0.061) and the ruminal concentration of ammonia N (P = 0.092). Adding PEG tended to quadratically decrease the relative abundance of methanogenic archaea (P = 0.082), linearly decreased the relative abundance of Fibrobacter succinogenes (P = 0.008) and decreased the relative abundance of Butyrivibrio fibrisolvens (P = 0.048) at 7.00 g/kg DM. Dietary addition with PEG increased the crude protein (CP) digestibility (P < 0.001) and tended to increase the neutral detergent fiber digestibility (P = 0.066) in a linear manner. Adding PEG to basal ration also increased the plasma globulin concentration (P = 0.029) and tended to linearly increase the plasma total protein concentration (P = 0.069). Adding PEG linearly decreased the fecal N excretion (P < 0.001) and the fecal N-to-total N excretion ratio (P = 0.004) and increased the urinary N-to-total N excretion ratio (P = 0.004) and urinary urea excretion (P = 0.010) without affecting the urinary N and total N excretions (P > 0.05). It was concluded that adding PEG effectively improved the CP digestibility of the ration containing high sorghum tannins but increased the urinary urea excretion without improving the N retention and N retention rate in steers.

The use of live yeast to increase intake and performance of cattle receiving low-quality tropical forages

The objective was to evaluate the effects of a specific strain of live yeast (LY) on growth performance, fermentation parameters, feed efficiency, and bacterial communities in the rumen of growing cattle fed low-quality hay. In experiment (exp.) 1, 12 Droughtmaster bull calves (270 ± 7.6 kg initial body weight [BW]) were blocked by BW into two groups, allocated individually in pens, and fed ad libitum Rhodes grass hay (8.4% of crude protein [CP]) and 300 g/bull of supplement (52% CP) without (Control) or with LY (8 × 109 colony-forming unit [CFU]/d Saccharomyces cerevisiae CNCM I-1077; Lallemand Inc., Montreal, Canada) for 28 d, followed by 7 d in metabolism crates. Blood and rumen fluid were collected before feeding and 4 h after feeding. In exp. 2, for assessment of growth performance, 48 Charbray steers (329 ± 20.2 kg initial BW) were separated into two blocks by initial BW and randomly allocated into 12 pens. The steers were fed Rhodes grass hay (7.3% CP) and 220 g/steer of supplement (60% CP) without or with LY (8 × 109 CFU/d) for 42 d, after a 2-wk adaptation period. In exp. 1, fiber digestibility was calculated from total fecal collection, and, in exp 2, indigestible neutral detergent fiber (NDF) was used as a marker. Inclusion of LY increased (P = 0.03) NDF intake by 8.3% in exp. 1, without affecting total tract digestibility. No changes were observed in microbial yield or in the efficiency of microbial production. There was a Treatment × Time interaction (P < 0.01) for the molar proportion of short-chain fatty acids, with LY increasing propionate before feeding. Inclusion of LY decreased rumen ammonia 4 h after feeding (P = 0.03). The addition of LY reduced rumen bacterial diversity and the intraday variation in bacterial populations. Relative populations of Firmicutes and Verrucomicrobia varied over time (P < 0.05) only within the Control group. At the genus level, the relative abundance of an unclassified bacterial genus within the order Clostridiales, a group of cellulolytic bacteria, was reduced from 0 to 4 h after feeding in the Control group (P = 0.02) but not in the LY group (P = 1.00). During exp. 2, LY tended to increase average daily gain (ADG) (P = 0.08) and feed efficiency (P = 0.10), with no effect on NDF intake or digestibility. In conclusion, S. cerevisiae CNCM I-1077 reduced the intraday variation of rumen bacteria and increased the amount of NDF digested per day. These observations could be associated with the tendency of increased ADG and feed efficiency in growing cattle fed a low-quality forage.

Rumen bacteria and meat fatty acid composition of Sunit sheep reared under different feeding regimens in China

BACKGROUND

Rumen bacteria play a critical role in feed degradation and productivity. This study evaluated the impact of feeding regimen on the rumen microbial populations and fatty acid composition of the meat of sheep. Twenty-four Sunit sheep were raised on a grass pasture from birth to 9 months of age, at which time they were randomly divided into two feeding groups: pasture feeding (PF) and barn feeding (BF). Sheep in the PF group were allowed to graze freely on wild grassland for 3 months. Sheep in the BF group were confined for 3 months to a dry barn, in which they roamed freely with corn straw and corn.

RESULTS

Sheep in the PF group had greater rumen bacteria diversity. The relative abundances of the genera Butyrivibrio_2, Saccharofermentans and Succiniclasticum were increased, and that of the genus RC9_gut_group was decreased, in the PF compared to the BF sheep. The n-3 polyunsaturated fatty acid contents were greater in meat from PF sheep than from BF sheep. In addition, the α-linolenic acid (C18:3 n-3, ALA) and conjugated linoleic acid (CLA) contents were positively correlated with the abundance of Butyrivibrio_2.

CONCLUSION

Grazing may improve the diversity of rumen bacteria and increase the proportion of ALA and CLA in sheep meat. © 2020 Society of Chemical Industry.

Effect of hay type on cecal and fecal microbiome and fermentation parameters in horses

The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split-plot design run as a crossover in two periods. The whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for the amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. The main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, and all possible interactions and random effect of horse. Alpha and beta diversities were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05), whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total VFA concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared with cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared with the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared with cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.

Comparative effects of two multispecies direct-fed microbial products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers

We examined the effects of two direct-fed microbials (DFM) containing multiple microbial species and their fermentation products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers. Nine ruminally cannulated Holstein steers (mean ± SD body weight: 243 ± 12.4 kg) were assigned to three treatments arranged in a triplicated 3 × 3 Latin square design with three 21-d periods. Dietary treatments were 1) control (CON; basal diet), 2) Commence (PROB; basal diet plus 19 g/d of Commence), and 3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both multispecies DFM products. From day 16 to 20 of each period, feed and fecal samples were collected daily to determine the apparent total tract digestibilities of nutrients using indigestible neutral detergent fiber method. On day 21 of each period, blood samples were collected for analysis of plasma glucose and nonesterified fatty acid. Ruminal contents were collected at approximately 1, 3, 6, 9, 12, and 18 h after feeding on day 21 for analysis of volatile fatty acids (VFA), lactate, ammonia-N concentrations, bacterial community, and metabolome profile. Total tract digestibilities of nutrients did not differ (P > 0.05) among treatments. Compared with CON, steers fed either supplemental PROB or SYNB had greater (P = 0.04) plasma glucose concentrations. Compared with CON, total ruminal VFA, propionate, isovalerate, and valerate concentrations increased (P ≤ 0.05) or tended to increase (P ≤ 0.10) with either supplemental PROB or SYNB, but were not different (P > 0.05) between PROB and SYNB. Compared with CON, PROB reduced (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Rikenellaceae RC9, Succinivibrionaceae UCG-001, Succiniclasticum, and Ruminococcaceae UCG-002. Supplemental SYNB decreased (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Prevotella 7, Succinivibrio, Succiniclasticum, and Ruminococcaceae UCG-014. Compared with CON, metabolome analysis revealed that some amino acids were increased (P ≤ 0.05) in steers fed PROB. This study demonstrated that, compared with CON, supplementation of either PROB or SYNB altered the ruminal bacterial community and metabolome differently; however, their effects on the ruminal VFA profile and energy status of the steers were not different from each other.

Effects of Thymol Supplementation on Goat Rumen Fermentation and Rumen Microbiota In Vitro

This study was performed to explore the predominant responses of rumen microbiota with thymol supplementation as well as effective dose of thymol on rumen fermentation. Thymol at different concentrations, i.e., 0, 100 mg/L, 200 mg/L, and 400 mg/L (four groups × five replications) was applied for 24 h of fermentation in a rumen fluid incubation system. Illumina MiSeq sequencing was applied to investigate the ruminal microbes in addition to the examination of rumen fermentation. Thymol doses reached 200 mg/L and significantly decreased (p < 0.05) total gas production (TGP) and methane production; the production of total volatile fatty acids (VFA), propionate, and ammonia nitrogen, and the digestibility of dry matter and organic matter were apparently decreased (p < 0.05) when the thymol dose reached 400 mg/L. A thymol dose of 200 mg/L significantly affected (p < 0.05) the relative abundance of 14 genera of bacteria, three species of archaea, and two genera of protozoa. Network analysis showed that bacteria, archaea, and protozoa significantly correlated with methane production and VFA production. This study indicates an optimal dose of thymol at 200 mg/L to facilitate rumen fermentation, the critical roles of bacteria in rumen fermentation, and their interactions with the archaea and protozoa.

Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition

Alfalfa (Medicago sativa L.) silage (AS) is an important feedstuff in ruminant nutrition. However, its high non-protein nitrogen content often leads to poor ruminal nitrogen retention. Various pre-ensiling treatments differing with respect to dry matter concentrations, wilting intensities and sucrose addition have been previously shown to improve the quality and true protein preservation of AS, and have substantial effects on in vitro ruminal fermentation of the resulting silages. However, it is unknown how these pre-ensiling treatments affect the ruminal microbiota composition, and whether alterations in the microbiota explain previously observed differences in ruminal fermentation. Therefore, during AS incubation in a rumen simulation system, liquid and solid phases were sampled 2 and 7 days after first incubating AS, representing an early (ET) and late (LT) time point, respectively. Subsequently, DNA was extracted and qPCR (bacteria, archaea, and anaerobic fungi) and prokaryotic 16S rRNA gene amplicon sequence analyses were performed. At the ET, high dry matter concentration and sucrose addition increased concentrations of archaea in the liquid phase (P = 0.001) and anaerobic fungi in the solid phase (P < 0.001). At the LT, only sucrose addition increased archaeal concentration in the liquid phase (P = 0.014) and anaerobic fungal concentration in the solid phase (P < 0.001). Bacterial concentrations were not affected by pre-ensiling treatments. The prokaryotic phylogenetic diversity index decreased in the liquid phase from ET to LT (P = 0.034), whereas the solid phase was not affected (P = 0.060). This is suggestive of a general adaption of the microbiota to the soluble metabolites released from the incubated AS, particularly regarding the sucrose-treated AS. Redundancy analysis of the sequence data at the genus level indicated that sucrose addition (P = 0.001), time point (P = 0.001), and their interaction (P = 0.001) affected microbial community composition in both phases. In summary, of the pre-ensiling treatments tested sucrose addition had the largest effect on the microbiota, and together with sampling time point affected microbiota composition in both phases of the rumen simulation system. Thus, microbiota composition analysis helped to understand the ruminal fermentation patterns, but could not fully explain them.

Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions

The complex microbial ecosystem within the bovine rumen plays a crucial role in host nutrition, health, and environmental impact. However, little is known about the interactions between the functional entities within the system, which dictates the community structure and functional dynamics and host physiology. With the advancements in high-throughput sequencing and mathematical modeling, in silico genome-scale metabolic analysis promises to expand our understanding of the metabolic interplay in the community. In an attempt to understand the interactions between microbial species and the phages inside rumen, a genome-scale metabolic modeling approach was utilized by using key members in the rumen microbiome (a bacteroidete, a firmicute, and an archaeon) and the viral phages associated with them. Individual microbial host models were integrated into a community model using multi-level mathematical frameworks. An elaborate and heuristics-based computational procedure was employed to predict previously unknown interactions involving the transfer of fatty acids, vitamins, coenzymes, amino acids, and sugars among the community members. While some of these interactions could be inferred by the available multi-omic datasets, our proposed method provides a systemic understanding of why the interactions occur and how these affect the dynamics in a complex microbial ecosystem. To elucidate the functional role of the virome on the microbiome, local alignment search was used to identify the metabolic functions of the viruses associated with the hosts. The incorporation of these functions demonstrated the role of viral auxiliary metabolic genes in relaxing the metabolic bottlenecks in the microbial hosts and complementing the inter-species interactions. Finally, a comparative statistical analysis of different biologically significant community fitness criteria identified the variation in flux space and robustness of metabolic capacities of the community members. Our elucidation of metabolite exchange among the three members of the rumen microbiome shows how their genomic differences and interactions with the viral strains shape up a highly sophisticated metabolic interplay and explains how such interactions across kingdoms can cause metabolic and compositional shifts in the community and affect the health, nutrition, and pathophysiology of the ruminant animal.

Temporal Stability of the Ruminal Bacterial Communities in Beef Steers

Nutritional studies involving ruminants have traditionally relied on relatively short transition or wash-out periods between dietary treatments, typically two to four weeks. However, little is known about adequate adaptation periods required to reach stabilization of the rumen microbiome that could provide more accurate results from nutritional studies in ruminants. This study determined the rumen bacterial communities and rumen environment parameters over ten weeks following transition from a forage-based to concentrate-based diet. Several α-diversity metrics, including observed OTUs and Simpson’s Evenness fluctuated throughout the trial, but were typically either greatest (observed OTUs) or lowest (Simpson’s) at week 5 of the trial contrasted from weeks 1 and 10 (P < 0.05). At week 4, several orders associated with the shift to the final bacterial community composition, including Pasteurellales, Aeromonadales, and Bacteroidales. At week 5, rumen pH was correlated with α-diversity (P = 0.005) and predictive of the rumen microbiome signature at week 10 (R² = 0.48; P = 0.04). Rumen microbiome stability did not occur until approximately 9 weeks following adaptation to the diet and was associated with changes in specific bacterial populations and rumen environment. The results of this study suggest that adaptation and wash-out periods must be re-evaluated in order to accommodate necessary rumen microbiome acclimation.

Host Gender and Androgen Levels Regulate Gut Bacterial Taxa in Pigs Leading to Sex-Biased Serum Metabolite Profiles

Gut microbiota regulates host metabolism and immunity. The phylogenetic composition of gut microbiota is influenced by diverse factors that include host gender. In this study, the effects of gender on gut microbial composition and its subsequent influence on serum metabolites in pigs were evaluated. The bacterial composition of feces samples was determined by 16S rRNA gene sequencing in 293 pure-bred Duroc pigs (108 gilts and 185 entire boars) and 64 validated pigs from an eight-breed mosaic F₆ population. Twenty-eight F₆ boars were castrated at 80 days of age to evaluate the effects of androgen on gut microbial composition. Untargeted serum metabolite features were determined in 45 boars and 26 gilts by an ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). The study observed an obvious influence of host gender on the gut microbial composition and identified numerous sex-biased bacterial taxa. These included Veillonellaceae, Roseburia, Bulleidia, and Escherichia which showed the higher abundance in boars, and Treponema and Bacteroides which were over-represented in gilts. Castration significantly shifted the fecal microbiota composition of the boars toward that of gilts. The predicted functional pathways of the gut microbiome related to obesity and energy harvest were enriched in gilts, and positively associated with gilt-enriched bacteria. Functional pathways related to peptidases and carbohydrate metabolism were enriched in boars and positively associated with boar-enriched bacteria. Serum metabolites related to androgen and cresol metabolism were identified as sex-biased metabolites. Correlation analysis between serum metabolites and sex-biased bacteria identified that the serum concentration of androgen-related metabolites was positively correlated with Bulleidia and Escherichia, but negatively associated with Treponema, suggesting a significant interaction between gut microbiota and host sex hormone metabolism. These results offer basic knowledge of how host gender and gut microbiota influence host metabolism.

Methane Emission, Rumen Fermentation, and Microbial Community Response to a Nitrooxy Compound in Low-Quality Forage Fed Hu Sheep

The effects of nitroglycerine (NG) on the rumen methane emission, fermentation, and microbial community of Hu sheep were investigated. Eight sheep were fed NG (100 mg/head/day); another eight sheep served as controls. NG decreased methane emission of Hu sheep by ~ 19.3% (P < 0.05) without adversely affecting the production performance or rumen fermentation (P > 0.05). The alpha and beta diversity indexes of the bacterial and archaeal community showed no significant differences (P > 0.05). The dominant methanogenic species was the Methanobrevibacter gottschalkii clade, accounting for ~ 60%, followed by the Methanobrevibacter boviskoreani and Methanobrevibacter ruminantium clades. Prevotella 1 was the most dominant bacterial genus, accounting for ~ 42%, followed by the Rikenellaceae RC9 and Bacteroidales BS11 gut groups. In addition, pearson correlation analysis showed a few Methanomassiliicoccales species significantly correlated with several bacterial genera (P < 0.05).

Distributions of Extracellular Peptidases Across Prokaryotic Genomes Reflect Phylogeny and Habitat

Proteinaceous compounds are abundant forms of organic nitrogen in soil and aquatic ecosystems, and the rate of protein depolymerization, which is accomplished by a diverse range of microbial secreted peptidases, often limits nitrogen turnover in the environment. To determine if the distribution of secreted peptidases reflects the ecological and evolutionary histories of different taxa, we analyzed their distribution across prokaryotic lineages. Peptidase gene sequences of 147 archaeal and 2,191 bacterial genomes from the MEROPS database were screened for secretion signals, resulting in 55,072 secreted peptidases belonging to 148 peptidase families. These data, along with their corresponding 16S rRNA sequences, were used in our analysis. Overall, Bacteria had a much wider collection of secreted peptidases, higher average numbers of secreted peptidases per genome, and more unique peptidase families than Archaea. We found that the distribution of secreted peptidases corresponded to phylogenetic relationships among Bacteria and Archaea and often segregated according to microbial lifestyles, suggesting that the secreted peptidase complements of microbial taxa are optimized for the environmental microhabitats they occupy. Our analyses provide the groundwork for examining the specific functional role of families of secreted peptidases in relationship to the organisms and the corresponding environments in which they function.

Bacterial Community Diversity Associated With Different Utilization Efficiencies of Nitrogen in the Gastrointestinal Tract of Goats

The objective of this study was to examine the association between bacterial community structure and the utilization efficiency of nitrogen (UEN) phenotypes by determining the bacterial community in the gastrointestinal tract (GIT) of goats that differ in UEN using high-throughput 16S rRNA gene sequencing. Thirty Nubian goats were selected as experimental animals, and their UEN was determined in a metabolic experiment. Subsequently, eight individuals were grouped into the high nitrogen utilization (HNU) phenotype, and seven were grouped into the low nitrogen utilization (LNU) phenotype. The bacterial 16S rRNA gene amplicons from the rumen, abomasum, jejunum, cecum and colon contents of these animals were sequenced using next-generation high-throughput sequencing technology. Two hundred thirty-nine genera belonging to 23 phyla in the rumen, 319 genera belonging to 30 phyla in the abomasum, 248 genera belonging to 36 phyla in the jejunum, 248 genera belonging to 25 phyla in the colon and 246 genera belonging to 23 phyla in the cecum were detected, with Bacteroidetes and Firmicutes predominating. In addition, a significant correlation was observed between the UEN and the genera Succiniclasticum, Bacteroides, Ruminobacter, Methanimicrococcus, Mogibacterium, Eubacterium_hallii_group and Ruminococcus_1 in the rumen; Bacteroidales_S24-7_group, Bacteroidales_RF16_group, Bacteroidales_UCG-001 and Anaerovibrio in the abomasum; Ruminococcus_2, Candidatus_Saccharimonas, Candidatus_Arthromitus and Coprococcus_1 in the jejunum; Erysipelotrichaceae_UCG-004, Akkermansia, Senegalimassilia, Candidatus_Soleaferrea and Methanocorpusculum in the colon; and Ruminococcaceae_UCG-002, Anaerovibrio and Ruminococcaceae_UCG-007 in the cecum. Furthermore, the real-time PCR results showed that the ruminal copies of Fibrobacter_succinogenes, Butyrivibrio_fibrisolvens, Ruminococcus_sp._HUN007, Prevotella ruminicola and Streptococcus bovis in the HNU animals were significantly higher than those in the LNU animals. This study suggests an association of GIT microbial communities as a factor that influences UEN in goats.

The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health

The Dipeptidyl peptidase-4 (DPP-4) activity influences metabolic, behavioral and intestinal disorders through the cleavage of key hormones and peptides. Some studies describe the existence of human DPP-4 homologs in commensal bacteria, for instance in Prevotella or Lactobacillus. However, the role of the gut microbiota as a source of DPP-4-like activity has never been investigated. Through the comparison of the DPP-4 activity in the cecal content of germ-free mice (GFM) and gnotobiotic mice colonized with the gut microbiota of a healthy subject, we bring the proof of concept that a significant DPP-4-like activity occurs in the microbiota. By analyzing the existing literature, we propose that DPP-4-like activity encoded by the intestinal microbiome could constitute a novel mechanism to modulate protein digestion as well as host metabolism and behavior.

Tucumã Oil Shifted Ruminal Fermentation, Reducing Methane Production and Altering the Microbiome but Decreased Substrate Digestibility Within a RUSITEC Fed a Mixed Hay - Concentrate Diet

Tucumã oil is sourced from the fruit pulp of the tucumã tree and contains high concentrations of unsaturated fatty acids and carotenoids. Due to these properties it may have the potential to decrease enteric methane (CH4) from ruminants when included in the diet. The objective of this study was to determine the effect of oil mechanically extracted from the fruit pulp of tucumã on fermentation characteristics, CH4 production and the microbial community using the rumen stimulation technique. Treatments consisted of a control diet (forage:concentrate; 70:30), and tucumã oil included at 0.5 or 1.0% (v/v). Addition of tucumã oil linearly decreased (P < 0.01) dry matter disappearance. Total gas (mL/d) and carbon dioxide (CO2) production (mL/d, mL/g DM) were unaffected (P ≥ 0.36) to increasing addition of tucumã oil where 0.5% (v/v) of Tucumã oil numerically increased both variables. Acetate and butyrate percentages of total VFA were linearly decreased (P ≤ 0.01) and propionate and valerate percentages of total VFA were linearly increased (P < 0.01) by increasing concentrations of tucumã oil added to the substrate. The ratio of acetate to propionate was linearly decreased (P < 0.01) with increasing concentration of tucumã oil. Methane production (mL/d) was linearly decreased (P = 0.04) with increasing addition of tucumã oil to the substrate. Tucumã oil reduced the bacterial richness and diversity when included at 1.0% (v/v) in both solid- and liquid- associated microbes. The abundance of the genera Fibrobacter and Rikenellaceae RC9 gut group were decreased and Pyramidobacter, Megasphaera, Anaerovibrio, and Selenomonas were enriched by the addition of 1.0% tucumã oil. In conclusion, tucumã oil resulted in the favorable shift in fermentation products away from acetate toward propionate, decreasing the production of CH4 when tucumã oil was included at 1.0% (v/v), however, substrate digestibility was also inhibited. The rumen microbiota was also altered by the addition of tucumã oil.

Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation

Nitrogenous emissions from ruminant livestock production are of increasing public concern and, together with methane, contribute to environmental pollution. The main cause of nitrogen-(N)-containing emissions is the inadequate provision of N to ruminants, leading to an excess of ammonia in the rumen, which is subsequently excreted. Depending on the size and molecular structure, various bacterial, protozoal and fungal species are involved in the ruminal breakdown of nitrogenous compounds (NC). Decelerating ruminal NC degradation by controlling the abundance and activity of proteolytic and deaminating microorganisms, but without reducing cellulolytic processes, is a promising strategy to decrease N emissions along with increasing N utilization by ruminants. Different dietary options, including among others the treatment of feedstuffs with heat or the application of diverse feed additives, as well as vaccination against rumen microorganisms or their enzymes have been evaluated. Thereby, reduced productions of microbial metabolites, e.g. ammonia, and increased microbial N flows give evidence for an improved N retention. However, linkage between these findings and alterations in the rumen microbiota composition, particularly NC-degrading microbes, remains sparse and contradictory findings confound the exact evaluation of these manipulating strategies, thus emphasizing the need for comprehensive research. The demand for increased sustainability in ruminant livestock production requests to apply attention to microbial N utilization efficiency and this will require a better understanding of underlying metabolic processes as well as composition and interactions of ruminal NC-degrading microorganisms.

Lactobacilli Are Prominent Members of the Microbiota Involved in the Ruminal Digestion of Barley and Corn

The chemical composition of barley grain can vary among barley varieties (Fibar, Xena, McGwire, and Hilose) and result in different digestion efficiencies in the rumen. It is not known if compositional differences in barley can affect the microbiota involved in the ruminal digestion of barley. The objective of this study was to characterize the in situ rumen degradability and microbiota of four barley grain varieties and to compare these to corn. Three ruminally cannulated heifers were fed a low (60% barley silage, 37% barley grain, and 3% supplement) or high grain (37% barley silage, 60% barley grain, and 3% supplement) diet. One set of bags was used to estimate dry matter (DM), starch and crude protein (CP) degradability. A second set was used to extract DNA from the adherent microbiota and visualize grain after incubation using scanning electron microscopy (SEM). DNA was subjected to amplicon 16S rRNA gene sequencing followed by analysis using QIIME. In the low grain diet, McGwire had the highest effective degradability (ED) of DM (P < 0.01). The ED of starch was highest (P < 0.01) for Fibar, McGwire, and Xena, but the ED of CP was not affected by variety. For the high grain diet, Xena and McGwire had the highest ED of DM (P < 0.01). The ED of starch was highest (P < 0.01) for Xena and Fibar. The ED of protein was highest (P < 0.01) for Xena and McGwire. Although the microbiota did not differ among barley varieties, they did differ from corn and with incubation time. Lactobacilli were dominant members of the mature biofilms associated with corn and barley and were accompanied by a notable increase in the lactic acid utilizing genera, Megasphaera. As none of the cattle exhibited subclinical or clinical acidosis during the study, our results suggest that lactobacilli play a more prominent role in routine starch digestion than presently surmised.

Dietary Alfalfa and Calcium Salts of Long-Chain Fatty Acids Alter Protein Utilization, Microbial Populations, and Plasma Fatty Acid Profile in Holstein Freemartin Heifers

This study presented the effects of alfalfa and calcium salts of long-chain fatty acids (CSFA) on feed intake, apparent digestibility, rumen fermentation, microbial community, plasma biochemical parameters, and fatty acid profile in Holstein freemartin heifers. Eight Holstein freemartin heifers were randomly divided into a 4 × 4 Latin Square experiment with 2 × 2 factorial diets, with or without alfalfa or CSFA. Dietary supplementation of CSFA significantly increased the apparent digestibility of dry matter, crude protein, neutral detergent fiber, organic matter, and significantly reduced N retention (P < 0.05). CSFA increased the concentration of ammonia nitrogen in the ruminal fluid (P < 0.05), but alfalfa increased the concentration of valerate and isovalerate (P < 0.05). CSFA increased the concentration of ammonia nitrogen and the relative population of Streptococcus bovis in the rumen (P < 0.05) and inhibited the relative population of Ruminococcus flavefaciens, methanogens, and protozoa (P < 0.05). Alfalfa instead of Leymus chinensis increased the relative population of Butyrivibrio fibrisolvens and Ruminobacter amylophilus in the rumen (P < 0.05) and reduced the relative population of the Ruminococcus albus and Megasphaera elsdenii (P < 0.05). Supplemental CSFA increased the concentration of cholesterol and low-density lipoprotein cholesterol in the plasma (P < 0.05). And it also altered the composition of fatty acids in the plasma, which was expressed in reducing saturated fatty acid (ΣSFA) ratio and C14-C17 fatty acids proportion except C16:0 (P < 0.05) and increasing the proportion of polyunsaturated fatty acid (ΣPUFA) and unsaturated fatty acid (ΣUFA) (P < 0.05). The results showed that alfalfa and CSFA had interaction effect on the apparent digestibility of ether extracts, plasma triglyceride concentration, isobutyrate concentration, and Ruminococcus albus relative abundance in the rumen. It was concluded that alfalfa substituting Leymus chinensis did not change the apparent digestibility of nutrients in the final stage of fattening Holstein freemartin heifers, while CSFA increased the cholesterol and the proportion of unsaturated fatty acids in plasma. Alfalfa and CSFA had mutual interaction effect on fat digestion and plasma triglycerides.

Metabolic networks for nitrogen utilization in Prevotella ruminicola 23

Nitrogen metabolism in gut systems remains poorly studied in spite of its importance for microbial growth and its implications for the metabolism of the host. Prevotella spp. are the most predominant bacteria detected in the rumen, but their presence has also been related to health and disease states in the human gut and oral cavity. To explore the metabolic networks for nitrogen assimilation in this bacterium, changes in gene expression profiles in response to variations in the available nitrogen source and to different concentrations of ammonium were analyzed by microarray and reverse transcription quantitative PCR, and linked with function by further proteomic analysis. The observed patterns of transcript abundances for genes involved in ammonium assimilation differed from the classical “enteric paradigm” for nitrogen utilization. Expression of genes encoding high substrate affinity nitrogen assimilation enzymes (GS-GOGAT system) was similar in growth-limiting and non-limiting nitrogen concentrations in P. ruminicola 23, whereas E. coli and Salmonella spp. responses to excess nitrogen involve only low substrate affinity enzymes. This versatile behavior might be a key feature for ecological success in habitats such as the rumen and human colon where nitrogen is rarely limiting for growth, and might be linked to previously reported Prevotella spp. population imbalances relative to other bacterial species in gut systems.

Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau

Yak and Tibetan sheep are the major indigenous ruminants on the Qinghai-Tibetan Plateau in China. The aim of this work was to study the differences in ruminal fermentation parameters and rumen prokaryotic community composition between hosts and feeding paradigms. The 16S rRNA genes targeting bacteria and archaea were sequenced using the MiSeq platform. The results showed that the prokaryotic community structure between yak and Tibetan sheep was significantly different (P<0.01). A significant difference in structure was also found between groups of yaks barn fed with a total mixed ration (TMR) and those naturally grazing (NG) (P=0.034), as well as for Tibetan sheep of the two groups (P=0.026). The core prokaryotic populations that existed in the rumen mostly dominated the structure. There was an obvious correlation of the prokaryotic community composition at the phylum and genus levels with the host or the feeding pattern. In addition, Tibetan sheep showed significantly higher yields of volatile fatty acids (VFAs) than yak, as did the NG group compared with the TMR group. In conclusion, both the host and feeding pattern may influence rumen microbial ecology system, with host effects being more important than those of the feeding pattern.

In vitro fermentation of key dietary compounds with rumen fluid: A genome-centric perspective

The anaerobic decomposition of organic substrates leads to the generation of gases, such as methane, which can either be a valuable energy carrier in industrial applications or can be considered as a main greenhouse gas when it is naturally emitted. In this study we investigated in vitro the effect of dietary compounds, such as starch and proteins, on the microbial community present in the rumen fluid. High throughput shotgun sequencing, followed by metagenomic assembly and binning allowed the extraction of 18 genome bins. A composite bioinformatic analysis led to the prediction of metabolic pathways involved in the degradation of dietary compounds and in the biosynthesis of crucial products like propionate, methane and ammonia. The identification of genomes belonging to poorly characterized phyla such as Thermoplasmata and Elusimicrobia shed light on their putative role. The high abundance of methylotrophic archaea in the inoculum suggests a relevant role in methane production.

Temperature affects microbial abundance, activity and interactions in anaerobic digestion

Temperature is a major factor determining the performance of the anaerobic digestion process. The microbial abundance, activity and interactional networks were investigated under a temperature gradient from 25°C to 55°C through amplicon sequencing, using 16S ribosomal RNA and 16S rRNA gene-based approaches. Comparative analysis of past accumulative elements presented by 16S rRNA gene-based analysis, and the in-situ conditions presented by 16S rRNA-based analysis, provided new insights concerning the identification of microbial functional roles and interactions. The daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. Increased methanogenesis and hydrolysis at 50°C were main factors causing higher methane production which was also closely related with more well-defined methanogenic and/or related modules with comprehensive interactions and increased functional orderliness referred to more microorganisms participating in interactions. This research demonstrated the importance of evaluating functional roles and interactions of microbial community.

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus)

The quantification and community of bacteria in the gastrointestinal (GI) tract (stomach, jejunum, ileum, cecum, colon and rectum) of red kangaroos (Macropus rufus) were examined by using real-time PCR and paired-end Illumina sequencing. The quantification of bacteria showed that the number of bacteria in jejunum and rectum was significantly lower than that in colon and cecum (P < 0.05). A total of 1,872,590 sequences was remained after quality-filtering and 50,948 OTUs were identified at the 97 % similarity level. The dominant phyla in the GI tract of red kangaroos were identified as Actinobacteria, Bacteroidetes and Firmicutes. At the level of genus, the samples from different parts of GI tract clustered into three groups: stomach, small intestine (jejunum and ileum) and large intestine (cecum and rectum). Prevotella (29.81 %) was the most dominant genus in the stomach and significantly (P < 0.05) higher than that in other parts of GI tract. In the small intestine, Bifidobacterium (33.04, 12.14 %) and Streptococcus (22.90, 19.16 %) were dominant genera. Unclassified Ruminococcaceae was the most dominant family in large intestine and the total relative abundance of unclassified bacteria was above 50 %. In identified genera, Dorea was the most important variable to discriminate large intestine and it was significantly higher in cecum than in stomach, small intestine and colon (P < 0.05). Bifidobacterium (21.89 %) was the only dominant genus in colon. Future work on culture in vitro and genome sequencing of those unidentified bacteria might give us insight into the function of these microorganisms in the GI tract. In addition, the comparison of the bacterial community in the foregut of kangaroos and other herbivores and the rumen might give us insight into the mechanism of fiber degradation and help us exploit approaches to improve the feed efficiency and subsequently, reduce the methane emission from herbivores.

Metagenome of Mehsani buffalo rumen microbiota: an assessment of variation in feed-dependent phylogenetic and functional classification

AIM

To gain a greater understanding of the ecology and metabolic potential of the rumen microbiome with the changes in the animal diet.

METHODS

Diet composed of varying proportion of green and dry roughages along with grains was given to 8 Mehsani buffaloes, and rumen metagenome was sketched using shotgun semiconductor sequencing.

RESULTS

In the present study, the Bacteroidetes were found to be dominant at the phyla level and Prevotella at the genus level. The ratio of Firmicutes to Bacteroidetes was found to be higher in the solid fraction as compared to the liquid fraction. In the solid fraction of the dry roughage group, the significant increment (p < 0.05) in Bacteroidetes abundance was observed with increment of roughage concentration. At the genus level, Clostridium significantly increased with the increment in roughage concentration. A comparison of glycoside hydrolase and cellulosome functional genes revealed more glycoside hydrolase 3 encoding genes with higher fiber diet and significant difference in carbohydrate-active enzymes family composition between green and dry roughage groups of the liquid fraction.

CONCLUSION

The present study provides a base to understand the modulating behavior of microbiota which can be manipulated to improve livestock nutrient utilization efficiency and for targeting the efficient catabolism of complex carbohydrate molecules as well.

Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing

Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as ‘shared’ OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.