Composition of Fecal Microbiota in Grazing and Feedlot Angus Beef Cattle

This study is to investigate the difference in bovine fecal microbiota between grazing and feedlot Angus cattle. Fecal samples were collected from six Angus cattle grazed on grassland and six Angus cattle fed on a feedlot. The fecal bacterial community was analyzed by high-throughput sequencing of 16S rRNA gene. Sequencing of the V3–V4 region totally produced 1,113,170 effective tages that were computationally clustered into 775 operational taxonomic units (OTUs). These 775 OTUs were taxonomically assigned to bacterial 12 phyla, 19 classes, 25 orders, 54 families, 141 genera, and 145 species. The dominant phyla were Firmicutes and Bacteroidetes. There was similar species richness between grazing and feedlot Angus beef, while higher species diversity was observed in feedlot Angus beef. The relative abundance of Firmicutes, Cyanobacteria, Elusimicrobia and Patescibacteria was significantly different between grazing and feedlot Angus beef (p < 0.05). At a genus level, five microbiotas were significantly different between the two groups and all belonged to the Firmicutes phylum. These significant differences in microbiota composition between grazing and feedlot Angus beef may have an impact on the meat quality of Angus beef.

Fecal Bacterial Community of Allopatric Przewalski’s Gazelles and Their Sympatric Relatives

Mammal gastrointestinal tracts harbor diverse bacterial communities that play important roles in digestion, development, behavior, and immune function. Although, there is an increasing understanding of the factors that affect microbial community composition in laboratory populations, the impact of environment and host community composition on microbiomes in wild populations is less understood. Given that the composition of bacterial communities can be shaped by ecological factors, particularly exposure to the microbiome of other individuals, inter-specific interactions should impact on microbiome community composition. Here, we evaluated inter-population and inter-specific similarity in the fecal microbiota of Przewalski’s gazelle (Procapra przewalskii), an endangered endemic ruminant around Qinghai Lake in China. We compared the fecal bacterial communities of three Przewalski’s gazelle populations, with those of two sympatric ruminants, Tibetan gazelle (Procapra picticaudata) and Tibetan sheep (Ovis aries). The fecal bacterial community richness (Chao1, ACE) did not vary across the three Przewalski’s gazelle populations, nor did the composition vary between species. In contrast, the managed Przewalski’s gazelle population had higher bacterial diversity (Shannon and Simpson) and was more similar to its sympatric Tibetan sheep in beta diversity than the wild Przewalski’s gazelle populations. These results suggest that ecological factors like host community composition or diet affect Przewalski’s gazelle’s gastrointestinal bacterial community. The role of bacterial community composition in maintaining gastrointestinal health should be assessed to improve conservation management of endangered Przewalski’s gazelle. More broadly, captive breeding and reintroduction efforts may be impeded, where captive management results in dysbiosis and introduction of pathogenic bacteria. In free ranging populations, where wildlife and livestock co-occur, infection by domestic pathogens and diseases may be an underappreciated threat to wild animals.

Comparative study of growth performance, nutrient digestibility, and ruminal and fecal bacterial community between yaks and cattle-yaks raised by stall-feeding

The experiment was conducted to compare the growth performance, rumen fermentation, nutrient digestibility, and ruminal and fecal bacterial community between yaks and cattle-yaks. Ten male yaks (36-month-old) were used as the yak (YAK) group and 10 male cattle-yaks with similar age were selected as the cattle-yak (CAY) group. All the animals were fed same ration and the experiment lasted for 60 days. The results showed that the average daily gain and dry matter intake of CAY group were higher (P < 0.05) than those of YAK group. The ruminal concentrations of total volatile fatty acids, acetate, and butyrate were higher (P < 0.05) in CAY group than those in YAK group. However, the neutral detergent fiber and acid detergent fiber digestibility exhibited an opposite between two groups. In the rumen, the relative abundances of Prevotella 1 and Prevotellaceae UCG-001 were higher (P < 0.05) and Succiniclasticum and Butyrivibrio 2 were lower (P < 0.05) in YAK group compared to CAY group. In the feces, the unclassified Lachnospiraceae, Lachnospiraceae NK4A136 group, and Lachnospiraceae AC2044 group were significantly enriched (P < 0.05) in YAK group, whereas the Ruminococcaceae UCG-010, Ruminococcaceae UCG-013, and Succiniclasticum were significantly enriched (P < 0.05) in CAY group. Overall, under the same diet, the yaks have higher fiber utilization and cattle-yaks have higher energy utilization.

Dietary Supplementation with Fermented Brassica rapa L. Stimulates Defecation Accompanying Change in Colonic Bacterial Community Structure

Our previous studies have elucidated that oral administration of Brassica rapa L. extract, known as Nozawana in Japan, alters immune responses and gut microbiota composition, increasing the numbers of butyrate-producing bacteria. Therefore, further investigation would help elucidate the mechanism attributable for the changes and health-promoting effects observed after B rapa L. extract ingestion. To reveal the modulation effects of fermented B. rapa L. on immune function and intestinal bacterial community structure, we conducted an intervention study with healthy volunteers followed by a mouse feeding study. The pilot intervention study was conducted for healthy volunteers aged 40–64 years under the hypothesis that the number of subjects exhibiting any change in gut microbiota in response to fermented B. rapa L. consumption may be limited. In total, 20 volunteers consumed 30 g of fermented B. rapa L. per day for 4 weeks. The fecal bacterial community composition of the volunteers was characterized using terminal-restriction fragment length polymorphism patterning followed by clustering analysis. To evaluate the detailed changes in the immune responses and the gut bacterial composition, assessed by high-throughput sequencing, we fed healthy mice with freeze-dried, fermented B. rapa L. for 2 weeks. The fecal bacterial community composition of the volunteers before the intervention was divided into three clades. Regardless of the clade, the defecation frequency significantly increased during the intervention weeks compared with that before the intervention. However, this clustering detected a specific increase of Prevotella in one cluster (low to zero Prevotella and high occupation of Clostridium at clusters IV and XIVa) post-ingestion. The cytokine production of spleen cells significantly increased due to feeding fermented B. rapa L. to the mice. This supplementary in vivo trial provided comparable results to the volunteer study regarding the effects of ingestion of the material given the compositional change complying with that of dietary fiber, particularly in the increase of genera Prevotella, Lachnospira, and genera in the Ruminococcaceae family, and the increase in daily defecation amount during 2 weeks of administration. We conclude that feeding fermented B. rapa L. may be responsible for the observed modulation in gut microbiota to increase fiber-degrading bacteria and butyrate-producing bacteria which may be relevant to the improvement in bowel function such as defecation frequency.

The Liquid Diet Composition Affects the Fecal Bacterial Community in Pre-weaning Dairy Calves

Feeding a liquid diet to the newborn calf has considerable implications for developing the intestinal microbiota, as its composition can shift the population to a highly adapted microbiota. The present work evaluated 15 Holstein calves individually housed and fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9% CP; 16.2% fat; diluted to 14% solids; n = 5) and III – acidified whole milk to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at week 8 of life. Calves also had free access to water and starter concentrate. After weaning, all calves were grouped on pasture, fed with starter concentrate, and hay ad libitum. The fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8, and 10 of life. The bacterial community was assessed the through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. Diversity indices were not affected by the liquid diets, but by age (P &lt; 0.001) with weeks 1 and 2 presenting lower diversity, evenness, and richness values. The bacterial community structure was affected by diet, age, and the interaction of these factors (P &lt; 0.01). Twenty-eight bacterial phyla were identified in the fecal samples, and the most predominant phyla were Firmicutes (42.35%), Bacteroidota (39.37%), and Proteobacteria (9.36%). The most prevalent genera were Bacteroides (10.71%), Lactobacillus (8.11%), Alloprevotella (6.20%). Over the weeks, different genera were predominant, with some showing significant differences among treatments. The different liquid diets altered the fecal bacterial community during the pre-weaning period. However, differences in the initial colonization due to different liquid diets are alleviated after weaning, when animals share a common environment and solid diet composition.

Correction to: Dynamic changes of the fecal bacterial community in dairy cows during early lactation

An amendment to this paper has been published and can be accessed via the original article.

PSII-10 Dynamic changes of the fecal bacterial community in dairy cows from early to mid-lactation

The dynamics of the community structure and activity of the dairy cow fecal bacterial communities，therefore this study was conducted to characterize the fecal bacterial communities during gestation and lactation unclear. Here we aimed to characterize the fecal bacterial communities in dairy cows from early to mid-lactation. Feces were sampled from 20 healthy fresh Holstein dairy cows on day 1 (Fresh1d group) and day 14 (Fresh1d group) in milk, and from 10 mid-lactation dairy cows (mid group) from 45 to 60 days in milk (55.96 ± 6.51 days in milk). The early and mid-lactation ration was fed to fresh and mid-lactation cows. The relative abundance of microbial populations and operational taxonomic units revealed significant differences between the different lactation groups (P &lt; 0.05). The relative abundance of Ruminococcaceae_UCG-005 (P &lt; 0.01) and Rikenellaceae_RC9_gut_group (P = 0.02) increased, while that of Christensenellaceae_R-7_group (P &lt; 0.01) decreased as lactation progressed. Especially, low abundance of Bacillus, Escherichia-Shigella, Klebsiella and Streptococcus were detected in mid-lactation cows, this decreased further as lactation progressed, suggesting higher risk of these pathogenic infection during early lactation. Moreover, the relative abundance of predicted microbial genes involved in membrane transport, carbohydrate metabolism and amino acid metabolism were enriched, indicating an increase in the fermentation ability of hindgut microbiota as lactation progressed. Our study provides improved understanding of the dynamic composition and functional variation of the fecal microbiome from early to mid-lactation in dairy cows. The findings support the potential for microbial manipulation of the hindgut microbial community in dairy cows enabling the mitigation of environmental problems associated with dairy cows rearing and manure management.

PSVI-2 Effects of dietary supplementation of a Saccharomyces cerevisiae-based direct-fed microbial product on plasma carbonyl-metabolome and fecal bacterial community of beef steers

We examined the effects of dietary supplementation of a Saccharomyces cerevisiae-based direct-fed microbial on plasma carbonyl-metabolome and fecal bacterial community of beef steers during a 42-d receiving period. Forty newly-weaned beef steers were used in this study. The steers were stratified by BW and randomly assigned to receive a basal diet with no additive (CON; n = 20) or a basal diet supplemented with 19 g of CommenceTM (PROB; n = 20). CommenceTM (PMI, Arden Hills, MN) contains a blend of 6.2 × 1011 cfu/g of S. cerevisiae, 3.5 × 1010 cfu/g of a mixture of Enterococcus lactis, Bacillus subtilis, Enterococcus faecium, and L. casei. On d 0 and 40, rectal fecal samples were collected for bacterial community analysis via sequencing of the V3-V4 region of 16S rRNA gene. On d 42, blood was collected for analysis of carbonyl-containing metabolites in plasma using a chemical isotope labeling/liquid chromatography mass spectrometry-based untargeted metabolomics. The data were analyzed using the GLIMMIX procedure of SAS with treatment as a fixed effect) and (random effect). A total number of 812 unique plasma metabolites were detected. Up to 305 metabolites [fold change (FC) ≥ 1.5, FDR ≤ 0.01] including glucose, hippuric acid, glycoaldehyde, and 5-hydroxykynurenamine were increased by PROB supplementation, whereas 199 metabolites (FC ≤ 0.63, FDR ≤ 0.01) including acetoacetate were reduced. Correlation analysis showed that plasma concentrations of 5-oxopentanoate, 2-aceto-2-hydroxybutanoate, and 3-methyl-2-oxopentanoic acid were positively correlated (P ≤ 0.10) with average daily gain. Supplemental PROB increased (P ≤ 0.05) the relative abundance of Prevotellaceae, Megasphaera, Dorea, Acetitomaculum, and Blautia. In contrast, the relative abundance of Elusimicrobium, Moheibacter, and Stenotrophomonas were reduced (P ≤ 0.05). This study demonstrated that PROB altered the plasma carbonyl-metabolome and fecal bacterial community of the beef steers.

Effect of Broussonetia papyrifera silage on the serum indicators, hindgut parameters and fecal bacterial community of Holstein heifers

This study investigated the effects of substitution of whole corn silage (WCS) with Broussonetia papyrifera silage (BPS) in different ratios on the serum indicators, hindgut fermentation parameters (pH, ammoniacal nitrogen, and volatile fatty acids), and fecal bacterial community of Holstein heifers. Sixteen heifers (8-month-old, 220 ± 30 kg) were randomly divided into four treatments according to different BPS substitution ratios of feed basis (0%, 25%, 50%, and 75%). The experiment consisted of a 7-day preliminary feeding period and a 30-day experimental period. On the last day of the trial, the blood samples were collected from caudal vein, and the feces samples were collected from rectum. With the increasing of BPS content, the concentration of malondialdehyde (MDA) and interleukin-1β (IL-1β) in serum decreased (P < 0.05), and the immunoglobulin A (IgA) and IL-4 content of serum increased (P < 0.05); and the hindgut pH value increased (P < 0.05). 16S rRNA sequencing found that the dominant phyla were Firmicutes, Bacteroidetes, and Verrucomicrobia; and the dominant genera were Ruminococcaceae_UCG-005, Ruminococcaceae_UCG-010, and Rikenellaceae_RC9_gut_group. Linear Discriminant Analysis Effect Size (LEfSe) analysis found 12 differential operational taxonomic units (OTUs) which have strong correlation with some serum and hindgut indicators, and have the potential to be used as biomarkers. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) found that BPS have impacts on the pathways, such as carbohydrate transport and metabolism, and promotes amino acid transport and metabolism. To sum up, inclusion of BPS in heifer diets can affect serum anti-oxidant and immune indicators, fecal parameters, composition and function of fecal microorganisms in Holstein heifers.

Effect of Broussonetia papyrifera Silage on the Serum Indicators, Hindgut Parameters and Fecal Bacterial Community of Holstein Heifers

This study investigated the effects of substitution of whole corn silage (CS) with Broussonetia papyrifera silage (BPS) in different ratios on the serum indicators, hindgut fermentation parameters (pH, ammoniacal nitrogen, and volatile fatty acids), and fecal bacterial community of Holstein heifers. Sixteen heifers (8-month-old, 220±30 kg) were randomly divided into four treatments according to different BPS substitution ratios of feed basis (0%, 25%, 50%, and 75%). The experiment consisted of a 7-day preliminary feeding period and a 30-day experimental period. On the last day of the trial, the blood samples were collected from caudal vein, and the feces samples were collected from rectum. With the increasing of BPS content, the concentration of malondialdehyde (MDA) and interleukin-1β (IL-1β) in serum decreased (P<0.05), and the immunoglobulin A (IgA) and IL-4 content of serum increased (P<0.05); and the hindgut pH value increased (P<0.05). 16S rDNA sequencing found that the dominant phyla were Firmicutes, Bacteroidetes, and Verrucomicrobia; and the dominant genera were Ruminococcaceae_UCG-005, Ruminococcaceae_UCG-010, and Rikenellaceae_RC9_gut_group. Linear Discriminant Analysis Effect Size (LEfSe) analysis found 12 differential operational taxonomic units (OTUs) which have strong correlation with some serum and hindgut indicators. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) found that BPS have impacts on the pathways, such as carbohydrate transport and metabolism, and promotes amino acid transport and metabolism. To sum up, inclusion of BPS in heifer diets can affect the fecal bacterial community, and further improve serum anti-oxidant and immune indicators in Holstein heifers.