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Rumen microorganisms produce various fibrolytic enzymes and degrade lignocellulosic materials into nutrient sources for ruminants; therefore, the characterization of fibrolytic enzymes contributing to the polysaccharide degradation in the rumen microbiota is important for efficient animal production. This study characterized the fibrolytic isozyme activities of a rumen microbiota from four groups of housed cattle (1, breeding Japanese Black; 2, feedlot Japanese Black; 3, lactating Holstein Friesian; 4, dry Holstein Friesian). Rumen fluids in all cattle groups showed similar concentrations of total volatile fatty acids and reducing sugars, whereas acetic acid contents and pH were different among them. Predominant genera were commonly detected in all cattle, although the bacterial compositions were different among cattle groups. Zymograms of whole proteins in rumen fluids showed endoglucanase activities at 55 and 57 kDa and xylanase activity at 44 kDa in all cattle. Meanwhile, several fibrolytic isozyme activities differed among cattle groups and individuals. Treponema, Succinivibrio, Anaeroplasma, Succiniclasticum, Ruminococcus, and Butyrivibrio showed positive correlations with fibrolytic isozyme activities. Further, endoglucanase activity at 68 kDa was positively correlated with pH. This study suggests the characteristics of fibrolytic isozyme activities and their correlations with the rumen microbiota.

Traditionally, yaks graze only natural pasture all year round without supplements. Forage intake of lactating yaks is below energy and protein requirements, even in the summer, and suckling yaks lose a substantial amount of significant body weight. Today, to mitigate the loss in body weight, supplementary feed is being offered to lactating yaks. However, the effects of supplementary feed on ruminal bacterial communities in lactating yaks is unknown. In the current study, we examined the effect of supplementary feed on ruminal microbiota, using 16S rRNA sequencing, and on volatile fatty acids (VFAs). Twenty-four lactating yaks of similar body weight (218 ± 19.5 kg) and grazing natural pasture were divided randomly into four groups and received different supplements: (1) rumen-protected amino acids (RPA), (2) concentrate feed (C), (3) RPA plus C (RPA+C), and (4) no supplements (control-CON). The concentrations of total VFAs, acetate, and butyrate were greater (p &lt, 0.05) when supplemented with concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA). Bacteroidetes (B) and Firmicutes (F) were the dominant ruminal bacterial phyla in all groups. The ratio of relative abundance of F:B in RPA+C was greater than in the RPA group, while there was no difference between CON and RPC (interaction, p = 0.026). At the genus level, the relative abundances of Absconditabacteriales_SR1, Bacteroidales-RF16-group, Bacteroidales_BS11_gut_group, Prevotellaceae, and Rikenellaceae_RC9_gut_group were lesser (p &lt, 0.05) with supplementary concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA), whereas Butyrivibrio_2 and Pseudobutyrivibrio were greater (p &lt, 0.05) with supplementary rumen-protected amino acids (RPA and RPA+C) than without rumen-protected amino acids (CON and C). These results demonstrate that supplementary feed: (1) alters the composition of rumen microbiota and concentrations of ruminal VFAs in lactating yaks, and (2) can be used to manipulate the composition of rumen microbiota.

Background Digestive processes in the rumen lead to the release of methyl-compounds, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas. Methylamines are produced from plant phosphatidylcholine degradation, by choline trimethylamine lyase, while methanol comes from demethoxylation of dietary pectins via pectin methylesterase activity. We have screened rumen metagenomic and metatranscriptomic datasets, metagenome assembled genomes, and the Hungate1000 genomes to identify organisms capable of producing methyl-compounds. We also describe the enrichment of pectin-degrading and methane-forming microbes from sheep rumen contents and the analysis of their genomes via metagenomic assembly. Results Screens of metagenomic data using the protein domains of choline trimethylamine lyase (CutC), and activator protein (CutD) found good matches only to Olsenella umbonata and to Caecibacter, while the Hungate1000 genomes and metagenome assembled genomes from the cattle rumen found bacteria within the phyla Actinobacteria, Firmicutes and Proteobacteria. The cutC and cutD genes clustered with genes that encode structural components of bacterial microcompartment proteins. Prevotella was the dominant genus encoding pectin methyl esterases, with smaller numbers of sequences identified from other fibre-degrading rumen bacteria. Some large pectin methyl esterases (> 2100 aa) were found to be encoded in Butyrivibrio genomes. The pectin-utilising, methane-producing consortium was composed of (i) a putative pectin-degrading bacterium (phylum Tenericutes, class Mollicutes), (ii) a galacturonate-using Sphaerochaeta sp. predicted to produce acetate, lactate, and ethanol, and (iii) a methylotrophic methanogen, Methanosphaera sp., with the ability to form methane via a primary ethanol-dependent, hydrogen-independent, methanogenesis pathway. Conclusions The main bacteria that produce methyl-compounds have been identified in ruminants. Their enzymatic activities can now be targeted with the aim of finding ways to reduce the supply of methyl-compound substrates to methanogens, and thereby limit methylotrophic methanogenesis in the rumen.

The aim of the study was to evaluate the ruminal function and microbial community of lamb under different nutrient levels. Sixty-four lambs with similarity body weight were randomly assigned to four groups after weaning off ewe’s milk on the 17th day (6.2 ± 0.2 kg). The lambs of the control group (CON) were fed a basal diet, and the other three groups were subjected to a diet of decreased protein (PR), digestible energy (ER) or both of them at 20% (BR) of basal diet. The decrease of dietary protein or energy level decreased the average daily gain, ruminal weight and mucosal thickness of lambs (P Fibrobacteres, whereas at the genus level, increased the relative abundance of Butyrivibrio and Prevotellaceae. Under different dietary energy and protein levels, 14 genera exhibited significant correlation with ruminal fermentation. These findings supplied new perspective for the understanding of the dietary effect on ruminal microbial community interactions and are of great significance for establishing the optimal nutrient supply strategy for lambs.

Recently, the potential role of gut microbiome (GM) in cardiovascular diseases has been revealed. Heart failure (HF) is one of the most prevalent cardiovascular diseases worldwide; however, whether GM dysbiosis participates in the development of HF remains largely unknown. This study aimed to investigate the specific changes in GM composition and function in isoproterenol (ISO)-induced HF in rats.The rats were divided into C (control), 4w-HF (ISO, 2.5 mg/kg/day for 4 weeks, intraperitoneally), and 2w-HF (ISO, 2.5 mg/kg/day for 2 weeks, intraperitoneally) groups. The cardiac structure and function in rats were assessed, and metagenomic analyses were then performed. Compared with the healthy control group, we found that the Shannon diversity index and microbial gene count in the 4w-HF and 2w-HF groups was drastically decreased. High-throughput sequencing showed that the three groups differed in intestinal bacterial community composition. Overgrowth of bacteria, such as Prevotella, was observed in the 4w-HF group, with reduced growth of bacteria, such as Roseburia, Lactobacillus, and Butyrivibrio, associated with healthy status compared with the C group on the genus level. Concomitant with the alteration of GM composition, underrepresentation of health-linked microbial function was observed in both the 4w-HF and 2w-HF groups compared with the C group.Iso-induced HF rats showed a significant decrease in the diversity and richness of the intestinal microbiome, with a downregulation of the key intestinal bacterial groups and overgrowth of bacteria considered to be involved in inflammatory responses as well as a decrease in health-linked microbial function. Our data indicated that altered GM may be a potential player in the pathogenesis and progression of HF.

The ruminal microbiota of 15 dairy buffalo was characterized using high-throughput 16S rRNA gene amplicon sequencing. Results showed that Bacteroidetes was the dominant bacterial phylum in all rumen samples, followed by Firmicutes, Proteobacteria, Tenericutes and Verrucomicrobia. Butyrivibrio was positively correlated with average milk fat yield (R = 0.55; p = 0.03), average milk total solid yield (R = 0.56; p = 0.03) and standard milk yield (R = 0.52; p = 0.05). Acinetobacter were positively correlated with average milk protein yield (R = 0.56; p = 0.03), average milk total solid yield (R = 0.60; p = 0.02) and standard milk yield (R = 0.57; p = 0.03). Acetobacter was positively correlated with acetate (R = 0.63; p = 0.01), propionate content (R = 0.55; p = 0.03), butyrate content (R = 0.61; p = 0.02) and total VFA (R = 0.62; p = 0.01). The phyla Proteobacteria (R = 0.53; p = 0.04) and genus Prevotella (R = 0.52; p = 0.05) were positively correlated with butyrate content. Correlation analysis suggested that increased Butyrivibrio and Acinetobacter residing in the buffalo rumen could improve milk performance.

To investigate the metabolism of 18:2n-6 and 18:3n-3 by pure cultures of Sharpea azabuensis, two different strains (RL 1 and ST18) were each incubated in the presence of 40 µg ml-1 18:2n-6 or 18:3n-3. Pure cultures of Butyrivibriofibrisolvens D1 and Butyrivibrio proteoclasticus P18 were included as control treatments. Similar to the metabolism of B. fibrisolvens, both S. azabuensis strains converted 18:2n-6 or 18:3n-3 to cis-9, trans-11 CLA or cis-9, trans-11, cis-15 CLnA, after which it was further reduced to trans-11 18:1 or trans-11, cis-15 18:2, respectively. B. proteoclasticus additionally reduced trans-11 18:1 to 18:0. Trans-11, cis-15 18:2 was also further metabolized by B. proteoclasticus, although trans-11 18:1 did not accumulate, and only minor amounts of 18:0 were formed. The time frame of 18:2n-6 and 18:3n-3 biohydrogenation by S. azabuensis was comparable with B. fibrisolvens, indicating that S. azabuensis and B. fibrisolvens might be alternative biohydrogenators of 18:2n-6 and 18:3n-3 in the rumen.

The beneficial effects of dietary fiber on the reproductive performance and welfare of sows have been discussed broadly, but few researches examined the causal changes and the association of gut microbiota and the steroid hormones, the main regulators of reproductive function. To shed light on this, thirty-six Meishan sows were allocated into 2.5% crude fiber (CF) group and 7.5% CF group respectively for an entire farrowing interval. On the 90th day of gestation, the saliva and fresh stool of sows were individually collected in the morning (06:00–07:00) for steroid hormones, short-chain fatty acids (SCFAs) and microbiome analysis. In addition, the parameter of pregnant behavioral and farrowing performance was recorded and evaluated. We observed that, as compared with the 2.5% CF treatment, 7.5% CF significantly increased the litter size (p = 0.01), reduced the stereotypic behaviors including sham chewing, rolling tongue and licking ground (p = 0.02, 0.04, 0.01) at later gestation stage, but increased lying time (p = 0.00). In coincide with this, 7.5% CF diet increased the salivary progesterone (p = 0.00), fecal estradiol and progesterone (p = 0.01, 0.02) level, fecal water and SCFAs content (p = 0.02, 0.03), decreased the salivary and fecal cortisol (p = 0.01, 0.00) level. Further, 7.5% CF diet increased the fecal microbiota richness (ACE, p = 0.04; Chao, p = 0.07) and diversity (Shannon, p = 0.01; Simpson, p = 0.04), the proportion of genus Ruminococcus, Butyrivibrio, Lactobacillus and Fibrobacter (p = 0.02, 0.05, 0.04, 0.00), whereas reduced the proportion of genus Clostridium, Streptococcus, Bacteroides and Escherichia-Shigella (p = 0.00, 0.00, 0.04, 0.04). These results indicate that, fibrous diet can regulate the steroid hormones secretion and modulate the gut with more cellulose-degrading and probiotic bacterium, but less opportunistic pathogens, and this may contribute to the improvement of reproductive performance and welfare in sows.

Danshen (Salviae Miltiorrhizae Radix et Rhizoma, SMR) has been used as a traditional Chinese medicine in clinic for treatment of coronary heart diseases. Previous works have shown that the chronic renal failure (CRF) is closely related to changes of intestinal bacteria. The aim is to explore the interaction between active components of SMR and intestinal bacteria from normal and CRF rats. The changes of intestinal bacteria were evaluated among normal rats, CRF model rats and SMR-treated rats via 16S rRNA gene sequencing technology. UPLC-QTOF/MS was applied for the analysis and identification of metabolites. RESULTS: Results showed that the following intestinal bacteria varied significantly in CRF rats, including Mucispirillum, Kurthia, Clostridium, Blautia, Butyrivibrio, Shuttleworthia, Peptococcus, Ruminococcus, Bradyrhizobium, Methylobacterium, Azospirillum, Thalassospira, Methylophilus, Pseudomonas, peptostreptococcaceae and bacteroidales. The ethanol extract of SMR (DS) significantly regulated Shuttleworthia, peptostreptococcaceae and Pseudomonas, while the water extract (DSS) significantly affected Peptococcus, peptostreptococcaceae and Ruminococcus. Methylation, demethylation, dehydrogenation, hydrogenation and hydroxylation were the major metabolic transformation of tanshinones in vitro by intestinal bacteria. Glucuronidation, methylation and hydrogenation were the main metabolic transformation of salvianolic acids. These results showed that the bioactive components of SMR, including tanshinones and salvianolic acids, might exert the medical effect via regulation intestinal bacteria.

In this study, high-throughput gene amplicon sequencing was used to investigate the effects of 6 treatments [2 levels of hemp seed oil (HSO) × 3 levels of cysteamine (CS)] on bacterial and fungal communities in the rumen of 30 crossbred dairy buffalo. Our results indicate that the total numbers of bacterial and fungal taxa were unaffected regardless of diet (p > 0.05), while the total number of archaea was affected (p < 0.05) by the interaction of HSO and CS. Compared with control treatment, microbial composition of archaea was strongly influenced by CS (p < 0.05), while the addition of HSO, CS or both had a weak effect on fungus and bacteria. In addition, there was a significant increase in the lactic acid content with the addition of HSO, and the addition of CS to the feed caused a significant decrease in the ratio of acetic acid to propionic acid, compared with control treatment (p < 0.05). Correlation analysis showed that Acetobacter was significantly positively correlated with the genera Pichia, Klebsiella and Acinetobacter. pH was found to have a significant effect on the methanogens, and total volatile fatty acids (VFA) had a strong correlation with Butyrivibrio. The strong influence of CS on some methanogens shows that it may have potential in the development of methane reduction interventions.

This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mixture at a lower supplemental level (20 g/day) to increase milk fat (%) and unsaturated fatty acid content in buffalo.

The objectives were to evaluate the effects of fiber source and dietary starch level on growth performance, nutrient digestion, rumen parameters, and rumen bacteria in fattening Hu lambs. A total of 360 Hu lambs (BW = 24.72 ± 0.14 kg, 2 months old) were subjected to a 2 × 3 factorial arrangement. Lambs randomly assigned 6 treatments with 6 repetitions (10 lambs per repetition) of each treatment. Six treatments were formulated to include the fiber sources with three starch levels. The experiment lasted a 63 d. The amount of feed, orts, and total feces were sampled on the 42nd day of the experiment. Rumen fluid samples were collected after 2 h of morning feeding on day 56. Rumen contents were collected last day after the selected lambs were slaughtered. Increasing the starch content decreased the digestibility of neutral detergent fiber (NDF, P = 0.005). Increasing the starch level increased the proportions of propionate (P = 0.002) and valerate (P = 0.001) and decreased the proportion of acetate (P < 0.001) and the ratio of acetate to propionate (P = 0.005). The abundance of Fibrobacter succinogenes was affected by an interaction between the fiber source and the starch level (P < 0.001). Fibrobacter succinogenes tended to be greater in lambs fed SH than in lambs fed BP (P = 0.091), which was greater in lambs fed high starch levels than in lambs fed low starch levels (P = 0.014). Increasing the starch level increased Streptococcus bovis abundance (P = 0.029) and decreased total bacteria (P = 0.025). At the genus level, increasing the starch level reduced the abundance of Butyrivibrio_2 (P = 0.020). Nevertheless, the final body weight (BW) and acid detergent fiber (ADF) digestibility were greater (P < 0.01) in lambs fed soybean hull (SH) than in lambs fed BP. The proportion of butyrate was greater (P = 0.005), while the rumen pH was lower (P = 0.001) in lambs fed beet pulp (BP) than in those fed SH. The abundances of Succiniclasticum, Candidatus_Saccharimonas, Ruminococcus_1, and Christensenellaceae_R-7 were greater in lambs fed SH than in those fed BP (P < 0.050), whereas the abundance of Fibrobacter was lower (P = 0.011). The predominant microbial phyla in all of the groups were Firmicutes, Bacteroidetes, and Fibrobacteres. Changing the starch level for fiber sources mainly changed the rumen community in terms of the phylum and genus abundances. Lambs fed SH with low starch level increased the final BW without affecting total volatile fatty acids (TVFA) concentrations.

In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.

In our previous studies, we revealed the effect of lactose inclusion in calf starters on the growth performance and gut development of calves. We conducted the present study as a follow-up study to identify the shift in rumen microbiota and its relation to rumen fermentation when calves are fed a lactose-containing starter. Thirty Holstein bull calves were divided into 2 calf starter treatment groups: texturized calf starter (i.e., control; n = 15) or calf starter in which starch was replaced with lactose at 10% (i.e., LAC10; n = 15) on a dry matter basis. All calves were fed their respective treatment calf starter ad libitum from d 7, and kleingrass hay from d 35. Rumen digesta were collected on d 80 (i.e., 3 wk after weaning) and used to analyze rumen microbiota and fermentation products. There was no apparent effect of lactose feeding on the alpha-diversity and overall composition of rumen microbiota. Amplicon sequencing and real-time PCR quantification of the 16S rRNA gene confirmed that the abundance of butyrate producing bacteria (i.e., Butyrivibrio group and Megasphaera elsdenii) did not differ between the control and LAC10 groups. Conversely, the relative abundance of Mitsuokella spp., which produce lactate, succinate, and acetate, was significantly higher in the rumen of calves that were fed lactose, whereas the lactate concentration did not differ between the control and LAC10 groups. These findings suggest that the lactate production can be elevated by an increase of Mitsuokella spp. and then converted into butyrate, not propionate, since the proportion of propionate was lower in lactose-fed calves. In addition, we observed a higher abundance of Coriobacteriaceae and Pseudoramibacter-Eubacterium in the LAC10 group. Both these bacterial taxa include acetate-producing bacteria, and a positive correlation between the acetate-to-propionate ratio and the abundance of Pseudoramibacter-Eubacterium was observed. Therefore, the higher abundance of Coriobacteriaceae, Mitsuokella spp., and Pseudoramibacter-Eubacterium in the rumen of lactose-fed calves partially explains the increase in the proportion of rumen acetate that was observed in our previous study.

Fat rich microorganisms, such as microalgae Schizochytrium spp., are potential biotechnological tools in the modulation of rumen microbiome towards ecofriendly and high nutritional value end-products. However, limited in vivo trials have been reported on the topic. The aim of this study was to contribute to the knowledge on the effect of fat rich microalgae on the methanogenic and feed degrading particle-associated microbes in goats&rsquo, rumen content. For the trial, twenty-four goats were divided into four homogenous clusters (six goats/treatment) according to their fat corrected (4%) milk yield, body weight and age and individually were fed with alfalfa hay and concentrate feeds (F/C = 50/50). The concentrate of the control group (CON) contained no microalgae, while those of the treated groups were supplemented daily with 20 (ALG20), 40 (ALG40), and 60 (ALG60) g of Schizochytrium spp./goat. The relative abundances of total Archaea, methanogens, Methanomassiliicoccales, Methanobrevibacter spp., Methanosphaera stadmanae and Methanobacterium formicicum were significantly (p &lt, 0.05) decreased in microalgae-fed goats compared to the CON ones. Moreover, a significant decline in the relative abundances of Firmicutes, Ruminococcus flavefaciens, Butyrivibrio fibrosolvents, and Neocallimastigales in the rumen particle-associated microbiota of microalgae supplemented goats were observed. In conclusion, goats&rsquo, diets supplementation with Schizochytrium spp., could be considered a sustainable nutritional strategy for methanogens inhibition in their rumen particle-associated microbiota.

Background The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen. Method We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage’s chemical characteristics and community structure of biofilm-embedded microbiota. Results Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen. Conclusion Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.

Alternatives to antibiotic treatments are required owing to the ban on the use of these drugs as growth promoters in food animal production. Tributyrin appears to play a role in improving growth performance in pigs, albeit with varying degrees of effectiveness. So far, very little is known about its effects on gut microbiota composition. In this study, we investigated the gut microbiota changes of piglets receiving, at weaning, 0.2% tributyrin added to their basal diet. Microbiota composition was assessed through 16S-rRNA gene sequencing on stools collected from tributyrin and control groups. The functional profiles of microbial communities were predicted from amplicon abundance data. A comparison between dietary groups revealed that tributyrin strongly modulated gut microbiota composition in piglets, increasing the relative abundance of a number of bacterial genera such as Oscillospira, Oscillibacter, Mucispirillum and Butyrivibrio. These genera were positively correlated to animal average daily gain (ADG) and/or body weight (BW). Based on the function profile prediction, the gut microbiome of the tributyrin group possessed an enhanced potential for energy metabolism and a reduced potential for carbohydrate metabolism. In conclusion, our results indicated that tributyrin can promote changes to gut microbial communities, which could contribute to improving animal performance after weaning.

Tall fescue KY-31 is an important primary forage for beef cattle. It carries a fungal endophyte that produces ergovaline, the main cause of tall fescue toxicosis that leads to major revenue loss for livestock producers. The MaxQ, an engineered cultivar, hosts an ergovaline nonproducing strain of the fungus and consequently is nontoxic. However, it is less attractive economically. It is not known how rumen microbiome processes these two forages towards nutrient generation and ergovaline transformation. We have analysed the rumen microbiome compositions of cattle that grazed MaxQ with an intervening KY-31 grazing period using the 16S rRNA-V4 element as an identifier and found that KY-31 remodelled the microbiome substantially, encompassing both cellulolytic and saccharolytic functions. The effect was not evident at the whole microbiome levels but was identified by analysing the sessile and planktonic fractions separately. A move from MaxQ to KY-31 lowered the Firmicutes abundance in the sessile fraction and increased it in planktonic part and caused an opposite effect for Bacteroidetes, although the total abundances of these dominant rumen organisms remained unchanged. The abundances of Fibrobacter , which degrades less degradable fibres, and certain cellulolytic Firmicutes such as Pseudobutyrivibrio and Butyrivibrio 2, dropped in the sessile fraction, and these losses were apparently compensated by increased occurrences of Eubacterium and specific Ruminococcaceae and Lachnospiraceae . A return to MaxQ restored the original Firmicutes and Bacteroidetes distributions. However, several KY-31 induced changes, such as the low abundance of Fibrobacter and Butyrivibrio two remained in place, and their substitutes maintained significant presence. The rumen microbiome was distinct from previously reported faecal microbiomes. In summary, KY-31 and MaxQ were digested in the cattle rumen with distinct consortia and the KY-31-specific features were dominant. The study also identified candidate ergovaline transforming bacteria. It highlighted the importance of analysing sessile and planktonic fractions separately.

Antimicrobial and antioxidant properties of spent coffee grounds (SCG) make them a potential ingredient in a diet for ruminants. This study investigated the effects of SCG on rumen microbiota. For 51 days, 36 dairy ewes were assigned to the experimental treatments (0, 30, 50, and 100 g SCG/kg). Ruminal samples were collected on day 50. DNA was extracted and subjected to paired-end Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA genes. Bioinformatic analyses were performed using QIIME (v.1.9.0). SCG increased dose-dependently bacterial diversity and altered bacterial structure. Further, 60, 78, and 449 operational taxonomic unit (OUT) were different between control and 30, 50 and 100 g/kg SCG groups, respectively. Higher differences were observed between the control and 100 g/kg SCG group, where OTU of the genera Treponema, CF231, Butyrivibrio, BF331, Anaeroplasma, Blautia, Fibrobacter, and Clostridium were enriched with SCG. Correlations between volatile fatty acids (VFA) and bacterial taxa were sparser in the SCG groups and had little overlap. Certain bacterial taxa presented different signs of the correlation with VFA in SCG and control groups, but Butyrivibrio and Blautia consistently correlated with branched-chain VFA in all groups. SCG induced shifts in the ruminal bacterial community and altered the correlation networks among bacterial taxa and ruminal VFA.

Traveler’s diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in travelers’ diarrhea susceptibility. To this end we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to traveler’s diarrhea. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution towards identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.

Mycotoxins are important food contaminants that commonly co-occur with modified mycotoxins such as mycotoxin-glucosides in contaminated cereal grains. These masked mycotoxins are less toxic, but their breakdown and release of unconjugated mycotoxins has been shown by mixed gut microbiota of humans and animals. The role of different bacteria in hydrolysing mycotoxin-glucosides is unknown, and this study therefore investigated fourteen strains of human gut bacteria for their ability to break down masked mycotoxins. Individual bacterial strains were incubated anaerobically with masked mycotoxins (deoxynivalenol-3-&beta, glucoside, DON-Glc, nivalenol-3-&beta, glucoside, NIV-Glc, HT-2-&beta, glucoside, HT-2-Glc, diacetoxyscirpenol-&alpha, glucoside, DAS-Glc), or unconjugated mycotoxins (DON, NIV, HT-2, T-2, and DAS) for up to 48 h. Bacterial growth, hydrolysis of mycotoxin-glucosides and further metabolism of mycotoxins were assessed. We found no impact of any mycotoxin on bacterial growth. We have demonstrated that Butyrivibrio fibrisolvens, Roseburia intestinalis and Eubacterium rectale hydrolyse DON-Glc, HT-2 Glc, and NIV-Glc efficiently and have confirmed this activity in Bifidobacterium adolescentis and Lactiplantibacillus plantarum (DON-Glc only). Prevotella copri and B. fibrisolvens efficiently de-acetylated T-2 and DAS, but none of the bacteria were capable of de-epoxydation or hydrolysis of &alpha, glucosides. In summary we have identified key bacteria involved in hydrolysing mycotoxin-glucosides and de-acetylating type A trichothecenes in the human gut.

Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.

This study was aimed to evaluate the effect of a mixed phytogenic (MP) on rumen bacteria and their potential association with rumen fermentation and milk yield parameters in water buffaloes. Twenty Murrah buffaloes were fed a basal diet (consisting of maize silage, brewers' grains, and concentrate mixture) for 6 weeks supplemented with 0 (control), 15 (MP15), 25 (MP25), and 35 (MP35) g of mixed phytogenic/buffalo per d. The mixed phytogenic contained fennel (seeds), ajwain (seeds), ginger (tubers), Swertia chirata (leaves), Citrullus colocynthis (fruit), turmeric, fenugreek (seeds), Terminalia chebula (fruit), licorice (roots), and Phyllanthus emblica (fruit) in equal quantities. After 2 weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment (d 42), rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no change in dry matter intake, milk yield and rumen fermentation parameters except pH, which increased (P = 0.029) in response to MP supplementation. The mixed phytogenic increased (P < 0.01) milk fatty acids (C4 to C14:0) in MP15 only. The milk C16:1 content and its unsaturation index were higher (P < 0.05) in MP35 as compared to the control and other treatments. Furthermore, C18:3n3 was higher (P < 0.05) in the control, MP15, and MP25, as compared to MP35. Supplementation of MP tended to increase (P = 0.095) the Shannon index of bacterial alpha diversity and a difference (P < 0.05) among treatment groups was observed in beta diversity. Feeding MP increased the Firmicutes, Proteobacteria, and Spirochaetes but decreased Bacteroidetes numerically. In addition, the dominant genus Prevotella decreased in all treatment groups while Pseudobutyrivibrio, Butyrivibrio, and Succinivibrioanceae increased numerically in MP25 and MP35. The mixed phytogenic promoted groups of rumen bacteria positively associated with milk and fat yield. Overall, our study revealed 14 positive correlations of rumen bacteria with milk yield and eight with rumen fermentation parameters. Our findings reveal substantial changes in the rumen bacteriome composition and milk fatty acid content in response to MP but these results should be interpreted carefully, as the sample size of our study was relatively small.

Objective Differential alterations in gut microbiota and chronic low-grade inflammation play a critical role in the development of Type 2 diabetes (T2D). Here we aimed to investigate if dysbiosis of inflammation and anti-inflammation-associated gut bacterial communities in fecal samples of individuals had any influence on T2D using a 16S rRNA gene of V3 region sequencing at Illumina MiSeq platform. Results Our findings showed that a higher abundance of inflammatory bacteria such as Lactobacillus ruminis, Ruminococcus gnavus, Bacteroides caccae, Butyricimonas, and Collinsella aerofaciens, and lower abundance of anti-inflammatory bacteria such as Faecalibacterium prausnitzii, and Butyrivibrio that likely play a role in the development of T2D. Our findings hint the potential of indigenous microbiota in developing diagnostic markers and therapeutic targets in T2D.

Background: Most studies on gut microbiome of irritable bowel syndrome (IBS) have focused on fecal microbiota, instead of mucosa-associated microbiota (MAM). Aims: The aim of this study wasto investigate the MAM in IBS patients including the difference in subtypes of IBS, namely, diarrhea-predominant IBS (IBS-D) and constipation-predominant IBS (IBS-C). Methods: Endoscopic brush samples were taken from terminal ileum and sigmoid colon of patients with IBS (17 IBS-D patients and 7 IBS-C patients) and 10 healthy controls. The MAM of samples was profiled by 16S rRNA gene amplicon sequencing. Potential changes in the MAM at the functional level were evaluated using PICRUSt software and the KEGG database. Results: There were no differences in MAM composition between terminal ileum and sigmoid colon according to β-diversity based on the UniFrac distance. In view of α-diversity, Shannon (evenness) but not Chao1 (richness) or observed operational taxonomic units tended to be lower in sigmoid colon MAM of IBS-C and IBS-D than the control group. The abundance of 4 genera in the sigmoid colon and 7 genera in the terminal ileum was significantly different among the 3 groups. Linear discriminant analysis effect size (LEfSe) showed that the genera of Ruminococcus, Akkermansia, Butyrivibrio, Methylobacterium, and Microbacterium and the family Erysipelotrichaceae were significantly higher in the IBS-C group, and the abundance of the genera Streptococcus, Acidaminococcus, Butyricicoccus, and Parvimonas was significantly higher in the IBS-D group. In addition, the proportion of genes responsible for the secretion system and LPS biosynthesis was significantly higher and that for methane metabolism, lysine biosynthesis, and enzyme families was significantly lower in the IBS-D group than in the IBS-C group. Conclusion: Dysbiosis pattern and the function of the microbiome seem to be different among subtypes of IBS, and MAM may play a crucial role in IBS symptom generation.

Although the prokaryotic communities of the rumen microbiome are being uncovered through genome sequencing, little is known about the resident viral populations. Whilst temperate phages can be predicted as integrated prophages when analyzing bacterial and archaeal genomes, the genetics underpinning lytic phages remain poorly characterized. To the five genomes of bacteriophages isolated from rumen-associated samples sequenced and analyzed previously, this study adds a further five novel genomes and predictions gleaned from them to further the understanding of the rumen phage population. Lytic bacteriophages isolated from fresh ovine and bovine fecal and rumen fluid samples were active against the predominant fibrolytic ruminal bacterium Butyrivibrio fibrisolvens. The double stranded DNA genomes were sequenced and reconstructed into single circular complete contigs. Based on sequence similarity and genome distances, the five phages represent four species from three separate genera, consisting of: (1) Butyrivibrio phages Arian and Bo-Finn; (2) Butyrivibrio phages Idris and Arawn; and (3) Butyrivibrio phage Ceridwen. They were predicted to all belong to the Siphoviridae family, based on evidence in the genomes such as size, the presence of the tail morphogenesis module, genes that share similarity to those in other siphovirus isolates and phylogenetic analysis using phage proteomes. Yet, phylogenomic analysis and sequence similarity of the entire phage genomes revealed that these five phages are unique and novel. These phages have only been observed undergoing the lytic lifecycle, but there is evidence in the genomes of phages Arawn and Idris for the potential to be temperate. However, there is no evidence in the genome of the bacterial host Butyrivibrio fibrisolvens of prophage genes or genes that share similarity with the phage genomes.

Ruminants are essential for maintaining the global population and managing greenhouse gas emissions. In the rumen, bacterial species belonging to the genera rumen Butyrivibrio and Pseudobutyrivibrio constitute the core bacterial rumen microbiome and are important degraders of plant-derived complex polysaccharides. Pseudobutyrivibrio xylanivorans MA3014 was selected for genome sequencing in order to examine its ability to breakdown and utilize plant polysaccharides. The complete genome sequence of MA3014 is 3.58 Mb, consists of three replicons (a chromosome, chromid and plasmid), has an overall G+C content of 39.6% and encodes 3,265 putative protein-coding genes (PCGs). Comparative pan-genomics of all cultivated and currently available P. xylanivorans genomes has revealed highly open genomes and a strong correlation of orthologous genes within this species of rumen bacteria. MA3014 is metabolically versatile and capable of utilizing a range of simple mono-or oligosaccharides to complex plant polysaccharides such as pectins, mannans, starch and hemicelluloses for growth, with lactate, butyrate and formate as the principal fermentation end-products. The genes encoding these metabolic pathways have been identified and MA3014 is predicted to encode an extensive repertoire of Carbohydrate-Active enZYmes (CAZymes) with 80 Glycoside Hydrolases (GHs), 28 Carbohydrate Esterases (CEs) and 51 Glycosyl Transferases (GTs), that suggest its role as an initiator of primary solubilization of plant matter in the rumen.

Obesity is associated with gut microbiome dysbiosis. Our previous research has shown that highly branched rhamnogalacturonan type I (RG-I)-enriched pectin (WRP, 531.5 kDa, 70.44% RG-I, Rha/(Gal + Ara) = 20) and its oligosaccharide with less branched RG-I [DWRP, 12.1 kDa, 50.29% RG-I, Rha/(Gal + Ara) = 6] are potential prebiotics. The present study is conducted to uncover the impact of the content, molecular size, and branch degrees of RG-I on the inhibiting effect of high-fat diet (HFD)-induced obesity. The commercial pectin (CP, 496.2 kDa, 35.77% RG-I, Rha/(Gal + Ara) = 6), WRP, and DWRP were orally administered to HFD-fed C57BL/6J mice (100 mg kg-1 d-1) to determine their individual effects on obesity. WRP significantly prevented bodyweight gain, insulin resistance, and inflammatory responses in HFD-fed mice. No obvious anti-obesity effect was observed in either CP or DWRP supplementation. A mechanistic study revealed that CP and DWRP could not enhance the diversity of gut microbiota, while WRP treatment positively modulated the gut microbiota of obese mice by increasing the abundance of Butyrivibrio, Roseburia, Barnesiella, Flavonifractor, Acetivibrio, and Clostridium cluster IV. Furthermore, WRP significantly promoted browning of white adipose tissues in HFD-fed mice, while CP and DWRP did not. WRP can attenuate the HFD-induced obesity by modulation of gut microbiota and lipid metabolism. Highly branched RG-I domain enrichment is essential for pectin mitigating against the HFD-induced obesity.

Simple Summary The specific enzymes secreted by microorganisms in the gastrointestinal tract (GIT) of ruminants, such as phytase, can catalyze the decomposition of calcium compounds (e.g., phytic acid) and release bound calcium for the absorption of animals. Therefore, we speculate that gastrointestinal microbes could be a factor affecting digestion and absorption of dietary calcium. However, little related research has been reported. In the present study, we found that the true digestibility of calcium (TDC) in goats is related to gastrointestinal bacteria. Some gastro-intestinal bacteria, such as ruminal Prevotella, were beneficial for true host digestibility of dietary calcium. Abstract The current study was performed to examine the relationship between the true digestibility of calcium (TDC) in the diet and bacterial community structure in the gastrointestinal tract (GIT) of goats. Twenty-six Nubian healthy female goats were selected as experimental animals, and their TDC was determined using metabolic experiments. Eight goats were grouped into the high digestibility of Calcium (HC) phenotype, and another eight were grouped into the low digestibility of Calcium (LC) phenotype. Their bacterial 16S rRNA gene amplicons from the rumen, abomasum, jejunum, cecum, and colon contents were sequenced using next-generation high-throughput sequencing technology. In the rumen, 239 genera belonging to 23 phyla, 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. In addition, there was a significant correlation between the TDC and the relative abundance of Candidatus_Saccharimonas, Christensenellaceae_R-7_group, Mogibacterium, Prevotella_1, Prevotella_UCG_004, Ruminococcus_2, Saccharibacteria in the rumen, Eubacterium_coprostanoligens_group, Lachnospiraceae_ND3007_group, Lachnospiraceae_NK3A20_group, p-1088-a5_gut_group, and Planctomycetes in the abomasum, Butyrivibrio in the cecum, and Fibrobacter in the cecum were observed. This study suggests an association of GIT microbial communities as a factor influencing TDC in goats.

Background As an essential trace element for mammalian species, selenium (Se) possesses powerful antioxidant properties and is a potential regulator of intestinal microbiota. However, effects of Cardamine hupingshanensis aqueous extract (CE), rich in Se, on balancing the intestinal redox status and regulating gut microbiota have been neglected. Results An Se-deficient rat model was established by feeding a low-Se diet (LD) for 5 weeks and CE was then supplemented to LD or normal-Se-diet (ND) rats. Antioxidant enzyme activities and short-chain fatty acids (SCFA) concentration were increased by CE in both LD and ND rats. CE improved the intestinal morphology of LD rats impaired by deficient Se. Intestinal microbiota demonstrated various changes; for example, Butyrivibrio was increased in LD rats, while Bacteroides, Christensenellaceae, Clostridiaceae and Blautia were enhanced in ND rats. Conclusion Our findings provide evidence that CE shows potential in improving intestinal redox status and regulating gut microbiota. © 2020 Society of Chemical Industry.

In this study, we examined differences between the microbiota of the ruminal fluid (DR) and feces (DF) from five lactating dairy cows over three consecutive days using 16S rRNA gene sequence‐based analysis. Results showed significant differences between the microbial communities of the DR and DF. In particular, the relative abundance of the phyla Firmicutes and Actinobacteria was significantly lower (q, This study compared differences between the rumen fluid and fecal microbiota of dairy cows and further sought to determine whether differences exist between individual samples collected over three consecutive days. A significant difference was found between the rumen and fecal microbiota suggesting that dairy cows have different microbial communities between ruminal fluid and feces. Notably, no differences were observed over the three days sampling, indicating that the gut microbial community of dairy cows may be likely stable on a day‐to‐day basis.

A network analysis including relative abundances of all ruminal microbial genera (archaea, bacteria, fungi, and protists) and their genes was performed to improve our understanding of how the interactions within the ruminal microbiome affects methane emissions (CH4). Metagenomics and CH4 data were available from 63 bovines of a two-breed rotational cross, offered two basal diets. Co-abundance network analysis revealed 10 clusters of functional niches. The most abundant hydrogenotrophic Methanobacteriales with key microbial genes involved in methanogenesis occupied a different functional niche (i.e., "methanogenesis" cluster) than methylotrophic Methanomassiliicoccales (Candidatus Methanomethylophylus) and acetogens (Blautia). Fungi and protists clustered together and other plant fiber degraders like Fibrobacter occupied a seperate cluster. A Partial Least Squares analysis approach to predict CH4 variation in each cluster showed the methanogenesis cluster had the best prediction ability (57.3%). However, the most important explanatory variables in this cluster were genes involved in complex carbohydrate degradation, metabolism of sugars and amino acids and Candidatus Azobacteroides carrying nitrogen fixation genes, but not methanogenic archaea and their genes. The cluster containing Fibrobacter, isolated from other microorganisms, was positively associated with CH4 and explained 49.8% of its variability, showing fermentative advantages compared to other bacteria and fungi in providing substrates (e.g., formate) for methanogenesis. In other clusters, genes with enhancing effect on CH4 were related to lactate and butyrate (Butyrivibrio and Pseudobutyrivibrio) production and simple amino acids metabolism. In comparison, ruminal genes negatively related to CH4 were involved in carbohydrate degradation via lactate and succinate and synthesis of more complex amino acids by γ-Proteobacteria. When analyzing low- and high-methane emitters data in separate networks, competition between methanogens in the methanogenesis cluster was uncovered by a broader diversity of methanogens involved in the three methanogenesis pathways and larger interactions within and between communities in low compared to high emitters. Generally, our results suggest that differences in CH4 are mainly explained by other microbial communities and their activities rather than being only methanogens-driven. Our study provides insight into the interactions of the rumen microbial communities and their genes by uncovering functional niches affecting CH4, which will benefit the development of efficient CH4 mitigation strategies.

To estimate how native herbage of three different phenological periods modify rumen performance and milk quality of yak grazing alpine meadow. In this study, milk composition and the diversity of the rumen microbial community were measured in 12 full-grazing female yaks on the Qinghai-Tibet Plateau (QTP). The nutrient composition of three phenological periods was determined: Vegetative stage (VS), bloom stage (BS), and senescent stage (SS). High-throughput sequencing of the bacterial 16S rRNA gene was used. The results showed that crude protein (CP) content of herbage in BS was higher than that in vs. and SS (p &lt, 0.05), and neutral detergent fiber (NDF) content of herbage in SS was higher than that in vs. and BS (p &lt, 0.05). Milk solids and fat contents were higher in the vs. and SS than in BS (p &lt, 0.05). However, milk protein content was higher for the vs. and BS than those for SS (p &lt, 0.05). The total volatile fatty acid (VFA), acetate, and propionate concentrations were higher in vs. and BS than in SS (p &lt, 0.05). The community richness estimates (Chao1 estimator) of vs. were higher than that in BS and the SS (p &lt, 0.05). The diversity indices (Shannon index) of the BS were higher than that vs. and the SS (p &lt, 0.05). Spearman correlation analysis between the milk composition, ruminal fermentation parameters, and the relative abundances of the rumen bacteria showed that milk protein content, total VFA, acetate, and propionate concentrations were positively correlated with the relative abundances of the genera Desulfovibrio, Prevotella_1, and Butyrivibrio_2 and was negatively correlated with Olsenella, Ruminococcaceae_UCG.010, and Rikenellaceae_RC9_gut_group abundances. Collectively, the results revealed that there were significant differences in nutrient composition of herbage, chemical composition of yak milk, and microbial diversity in rumen at different phenological stages. The correlations between ruminal fermentation parameters, chemical constituents of yak milk, and some genera of ruminal bacteria might be indicative that the ruminal fermentation parameters and chemical constituents of yak milk are strongly influenced by the rumen bacterial community composition.

Urea is a cost-effective replacement for feed proteins in ruminant diets. However, its metabolism by the rumen microbiome is not fully understood. Here, rumen contents were collected from 18 male sheep fed one of the following three treatments: a low N basal diet with no urea (UC, 0 g/kg dry matter (DM)), low urea (LU, 10 g/kg DM) and high urea (HU, 30 g/kg DM). Principal coordinate analysis showed that the microbial composition and functional profiles of the LU treatment significantly differed from the UC and HU treatments. The genera Prevotella, Succinivibrio, Succinatimonas and Megasphaera were higher in the LU rumen, while the genera Clostridium, Ruminococcus and Butyrivibrio were enriched in the UC and HU rumen. The aspartate–glutamate and arginine–proline metabolic pathways and valine, leucine and isoleucine biosynthesis were higher in the LU rumen. The cysteine and methionine metabolism, lysine degradation and fructose and pentose phosphate metabolism pathways were higher in the UC and HU rumen. The protozoa population in the HU treatment was higher than in the UC and LU treatments. These findings suggest that the rumen microbiome of sheep fed low N diet with different urea supplementation are significantly different.

Feed intake is a major factor in maintaining the balance between ruminal fermentation and the microbial community of dairy cows. To explore the relationship among feed intake, microbial metabolism, and ruminal fermentation, we examined the combined signatures of the microbiome and metabolome in dairy cows with different feed intake levels. Eighteen dairy cows were allocated to high feed intake (HFI), medium feed intake (MFI), and low feed intake (LFI) groups according to their average daily feed intake. 16S rDNA sequencing results revealed that the relative abundance of Firmicutes in the HFI group was significantly higher than that in the MFI and LFI groups (P < 0.05). The ratio of Bacteroidetes to Firmicutes was significantly lower in the HFI group than in the MFI and LFI groups (P < 0.05). The relative abundance of Lachnospiraceae_unclassified, Veillonellaceae_unclassified, and Saccharofermentants was significantly higher in the HFI group than in the LFI and MFI groups (P < 0.05). The relative abundance of Erysipelotrichaceae_unclassified and Butyrivibrio was significantly higher in the HFI group than in the MFI and LFI groups (P < 0.05). Ultra high performance liquid chromatography-mass spectrometry revealed five key pathways, including the linoleic acid metabolism pathway, alpha-linolenic acid metabolism, arginine and proline metabolism, glutathione metabolism, and valine, leucine, and isoleucine biosynthesis, which are closely related to energy and amino acid metabolism. Linoleic acid, glutamate, alpha-linolenic acid, l-methionine, and l-valine levels were significantly lower in the HFI group than in the MFI and LFI groups (q < 0.05), while the relative content of glutamate was significantly lower in the MFI group than in the LFI group (q < 0.05). Stearic acid content was significantly higher in the HFI group than in the LFI group (q < 0.05). Our findings provide insight into the rumen microbiome of dairy cows with different feed intake and the metabolic pathways closely associated with feed intake in early-lactating cows. The candidates involved in these metabolic pathways may be useful for identifying variations in feed intake. The signatures of the rumen microbiome and metabolome in dairy cows may help make decisions regarding feeding.

This study aimed to assess the impact of two different feeding programs, including or not antimicrobials, on gut microbiota development at early ages in commercial pigs. For this, 21-day-old weaned piglets were distributed into 12 pens (6 replicates with 26 pigs each) and fed ad libitum until fattening with: standard commercial formula with antibiotics and zinc oxide (2400 ppm) (AB), and alternative unmedicated feed formula (UN). Subsequently, the animals were moved to the fattening unit (F) receiving a common diet. Pigs were weighed, and feed consumption and diarrhea scores registered. Feces were collected on days 9 (pre-starter), 40 (starter) and 72 (fattening) post-weaning and microbial DNA extracted for 16S rDNA sequencing. Piglets fed UN diets had a worse feed efficiency (p &lt, 0.05) than AB during nursery, however, UN pigs spent less time scouring after weaning (p = 0.098). The structure of fecal community evolved with the age of the animals (p = 0.001), and diet also showed to have a role, particularly in the starter period when UN microbiomes clustered apart from AB, resembling the ecosystems found in the fattening animals. Fibrolytic genera (Fibrobacter, Butyrivibrio, Christellansellaceae) were enriched in UN piglets whereas Lactobacillus characterized AB piglets (adjusted p &lt, 0.05). Overall, this alternative feeding program could anticipate the gut development of piglets despite a lower feed efficiency compared to standard medicalized programs.

Background The rumen contains a myriad of microbes whose primary role is to degrade and ferment dietary nutrients, which then provide the host with energy and nutrients. Rumen microbes commonly attach to ingested plant materials and form biofilms for effective plant degradation. Quorum sensing (QS) is a well-recognised form of bacterial communication in most biofilm communities, with homoserine lactone (AHL)-based QS commonly being used by Gram-negative bacteria alone and AI-2 Lux-based QS communication being used to communicate across Gram-negative and Gram-positive bacteria. However, bacterial cell to cell communication in the rumen is poorly understood. In this study, rumen bacterial genomes from the Hungate collection and Genbank were prospected for QS-related genes. To check that the discovered QS genes are actually expressed in the rumen, we investigated expression levels in rumen metatranscriptome datasets. Results A total of 448 rumen bacterial genomes from the Hungate collection and Genbank, comprised of 311 Gram-positive, 136 Gram-negative and 1 Gram stain variable bacterium, were analysed. Abundance and distribution of AHL and AI-2 signalling genes showed that only one species (Citrobacter sp. NLAE-zl-C269) of a Gram-negative bacteria appeared to possess an AHL synthase gene, while the Lux-based genes (AI-2 QS) were identified in both Gram-positive and Gram-positive bacteria (191 genomes representing 38.2% of total genomes). Of these 192 genomes, 139 are from Gram-positive bactreetteria and 53 from Gram-negative bacteria. We also found that the genera Butyrivibrio, Prevotella, Ruminococcus and Pseudobutyrivibrio, which are well known as the most abundant bacterial genera in the rumen, possessed the most lux-based AI-2 QS genes. Gene expression levels within the metatranscriptome dataset showed that Prevotella, in particular, expressed high levels of LuxS synthase suggesting that this genus plays an important role in QS within the rumen. Conclusion This is the most comprehensive study of QS in the rumen microbiome to date. This study shows that AI-2-based QS is rife in the rumen. These results allow a greater understanding on plant-microbe interactions in the rumen.

The objective of this experiment was to compare ruminal fluid samples collected through rumen cannula (RC) or using an oral stomach tube (ST) for measurement of ruminal fermentation and microbiota variables. Six ruminally cannulated lactating Holstein cows fed a standard diet were used in the study. Rumen samples were collected at 0, 2, 4, 6, 8, and 12 h after the morning feeding on two consecutive days using both RC and ST techniques. Samples were filtered through two layers of cheesecloth and the filtered ruminal fluid was used for further analysis. Compared with RC, ST samples had 7% greater pH; however, the pattern in pH change after feeding was similar between sampling methods. Total volatile fatty acids (VFA), acetate and propionate concentrations in ruminal fluid were on average 23% lower for ST compared with RC. There were no differences between RC and ST in VFA molar proportions (except for isobutyrate), ammonia and dissolved hydrogen (dH2) concentrations, or total protozoa counts, and there were no interactions between sampling technique and time of sampling. Bacterial ASV richness was higher in ST compared with RC samples; however, no differences were observed for Shannon diversity. Based on Permanova analysis, bacterial community composition was influenced by sampling method and there was an interaction between sampling method and time of sampling. A core microbiota comprised of Prevotella, S24-7, unclassified Bacteroidales and unclassified Clostridiales, Butyrivibrio, unclassified Lachnospiraceae, unclassified Ruminococcaceae, Ruminococcus, and Sharpea was present in both ST and RC samples, although their relative abundance varied and was influenced by an interaction between sampling time and sampling method. Overall, our results suggest that ruminal fluid samples collected using ST (at 180 to 200 cm depth) are not representative of rumen pH, absolute values of VFA concentrations, or bacterial communities >2 h post-feeding when compared to samples of ruminal fluid collected using RC. However, ST can be a feasible sampling technique if the purpose is to study molar proportions of VFA, protozoa counts, dH2, and ammonia concentrations., Frontiers in Microbiology, 11, ISSN:1664-302X

Previous study showed that low protein diet-fed pigs are characterized by lower histidine concentration in the serum and muscle, suggesting that histidine may involve in protein-restricted response. Thus, the current study mainly investigated the effects of dietary histidine on growth performance, blood biochemical parameters and amino acids, intestinal morphology, and microbiota communities in low protein diet-challenged-piglets. The results showed that protein restriction inhibited growth performance, blood biochemical parameters and amino acids, and gut microbiota but had little effect on intestinal morphology. Dietary supplementation with histidine markedly enhanced serum histidine level and restored tryptophan concentration in low protein diet-fed piglets, while growth performance and intestinal morphology were not markedly altered in histidine-treated piglets. In addition, histidine exposure failed to affect bacterial diversity (observed species, Shannon, Simpson, Chao1, ACE, and phylogenetic diversity), but histidine-treated piglets exhibited higher abundances of Butyrivibrio and Bacteroides compared with the control and protein-restricted piglets. In conclusion, dietary histidine in low protein diet enhanced histidine concentration and affected gut microbiota (Butyrivibrio and Bacteroides) but failed to improve growth performance and intestinal morphology.

Despite the body of research into Zn for human and animal health and productivity, very little work has been done to discern whether this benefit is exerted solely on the host organism, or whether there is some effect of dietary Zn upon the gastrointestinal microbiota, particularly in ruminants. We hypothesized that (i) supplementation with Zn would alter the rumen bacterial community in yearling rams, but that (ii) supplementation with either inorganically sourced ZnSO4, or a chelated Zn AA complex, which was more bioavailable, would affect the rumen bacterial community differently. Sixteen purebred Targhee yearling rams were utilized in an 84-d completely randomized design, and allocated to one of three pelleted dietary treatments: control diet without fortified Zn (~1 × NRC), a diet fortified with a Zn AA complex (~2 × NRC), and a diet fortified with ZnSO4 (~2 × NRC). Rumen bacterial community was assessed using Illumina MiSeq of the V4 to V6 region of the 16S rRNA gene. One hundred and eleven OTUs were found with > 1% abundance across all samples. The genera Prevotella, Solobacterium, Ruminococcus, Butyrivibrio, Olsenella, Atopobium, and the candidate genus Saccharimonas were abundant in all samples. Total rumen bacterial evenness and diversity in rams were reduced by supplementation with a Zn AA complex, but not in rams supplemented with an equal concentration of ZnSO4, likely due to differences in bioavailability between organic and inorganically sourced supplement formulations. A number of bacterial genera were altered by Zn supplementation, but only the phylum Tenericutes was significantly reduced by ZnSO4 supplementation, suggesting that either Zn supplementation formulation could be utilized without causing a high-level shift in the rumen bacterial community which could have negative consequences for digestion and animal health.

Functional dyspepsia (FD) is one of the most prevalent functional gastrointestinal disorders (FGIDs). Accumulated evidence has shown that FD is a metabolic disease that might relate to gut microbiota, but the relationship between microbiome and the host metabolic changes is still uncertain. To clarify the host–microbiota co-metabolism disorders related to FD, an integrated approach combining 1H NMR-based metabolomics profiles, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene sequencing was used to investigate the relationship among FD, metabolism of gut microbiota and the host. 34 differential urinary metabolites and 19 differential fecal metabolites, which affected the metabolism of energy, amino acids, nucleotides and short chain fatty acids (SCFAs), were found to have associated with FD. Based on the receiver operating characteristic (ROC) analysis, 10 biomarkers were screened out as diagnostic markers of FD. Meanwhile, the concentrations of Flintibacter, Parasutterella, Eubacterium and Bacteroides significantly increased in the FD group, whereas Eisenbergiella, Butyrivibrio, Intestinimonas, Saccharofermentans, Acetivibrio, Lachnoanaerobaculum and Herbinix significantly decreased. Furthermore, the above altered microbiota revealed a strong correlation with the intermediate products of the tricarboxylic acid (TCA) cycle, amino acids and SCFAs. In our study, it suggested that the energy metabolism was mainly disturbed in FD rats. Our findings also demonstrated that FD might be the result of gut microbiota and metabolism disorders, which was potentially valuable to enrich our understanding of the pathogenesis of FD.