The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet

Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats

BACKGROUND

Dietary fiber is crucial to animal productivity and health, and its dynamic utilization process is shaped by the gastrointestinal microorganisms in ruminants. However, we lack a holistic understanding of the metabolic interactions and mediators of intestinal microbes under different fiber component interventions compared with that of their rumen counterparts. Here, we applied nutritional, amplicon, metagenomic, and metabolomic approaches to compare characteristic microbiome and metabolic strategies using goat models with fast-fermentation fiber (FF) and slow-fermentation fiber (SF) dietary interventions from a whole gastrointestinal perspective.

RESULTS

The SF diet selected fibrolytic bacteria Fibrobacter and Ruminococcus spp. and enriched for genes encoding for xylosidase, endoglucanase, and galactosidase in the rumen and cecum to enhance cellulose and hemicellulose utilization, which might be mediated by the enhanced microbial ATP production and cobalamin biosynthesis potentials in the rumen. The FF diet favors pectin-degrading bacteria Prevotella spp. and enriched for genes encoding for pectases (PL1, GH28, and CE8) to improve animal growth. Subsequent SCFA patterns and metabolic pathways unveiled the favor of acetate production in the rumen and butyrate production in the cecum for SF goats. Metagenomic binning verified this distinct selection of gastrointestinal microorganisms and metabolic pathways of different fiber types (fiber content and polysaccharide chemistry).

CONCLUSIONS

These findings provide novel insights into the key metabolic pathways and distinctive mechanisms through which dietary fiber types benefit the host animals from the whole gastrointestinal perspective. Video Abstract.

Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and their Differences Compared to Other Ruminants

The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.

Temporal modulation of duodenal microbiota in dairy cows: effects of dietary shift from high forage to high concentration

Introduction

The duodenum and its resident microbiota play crucial roles in the process of nutrient digestion and absorption. However, the temporal dynamics of duodenal microbiota in response to different dietary regimes remain are not yet fully understood. The aim of the present study was to explore the effects of high-forage (HF) and high-concentration (HS) diets on the circadian rhythm variation of duodenal fermentation and microbial communities in dairy cattle.

Methods

Six duodenum-cannulated Holstein dairy cows were assigned to HF and HS diets according to a crossover design with two periods, with each period lasting 21 d (18 d for adaptation, 3 d for sampling). Duodenal content samples were collected at six time points (07:00, 11:00, 15:00, 19:00, 23:00, and 03:00) for the analysis of volatile fatty acids (VFA) and characterization of microbial characterization. The times of 11:00, 15:00, and 19:00 were recorded as the light phase and 23:00, 03:00 and 07:00 were recorded as the dark phase.

Results

The results showed that TVFA displayed a significant circadian rhythm following the introduction of the HS diet (p < 0.01). The concentration of TVFA (p < 0.01) and acetate (p < 0.01) were significantly higher during the light than the dark phase, regardless of diet type. PERMANOVA analysis revealed that diet and diet × time interaction strongly influenced the composition of duodenal microbiota. The relative abundance of Lachnospiraceae_ND3007_group showed a positive correlation with the propionate proportions under the HS diet during the light phase, while the HS diet significantly increased the abundance of Bifidobacterium and norank_f__Lachnospiraceae.

Conclusion

These findings provide novel insights into diet-dependent circadian regulation of duodenal fermentation in dairy cattle.

Oregano essential oil enhanced body weight and well-being by modulating the HPA axis and 23-nordeoxycholic acid of cecal microbiota in Holstein steers under cold stress

BACKGROUND

Prolonged exposure to cold stress in cattle increases basal energy consumption and impedes optimal production. Consequently, herds require adequate attention during cold, extended winters to alleviate cold stress and maintain profitability. This study investigated the effects of oregano essential oil (EO) on body weight (BW), well-being, blood parameters, and cecal microbiota. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CK) or the same diet supplemented with 20 g/(d·head) EO for 270 days.

RESULTS

EO increased BW by increasing cecal microbial abundance and carbohydrate metabolism CAZymes, leading to elevated the total volatile fatty acids (VFA) levels. Cold stress activated the HPA axis, and mitigated stress by reducing serum levels of cortisol (COR), corticosterone (CORT), adrenocorticotropic hormone (ACTH), and dopamine (DA). EO increased well-being by decreasing viral species without apparent contribution to drug or antibiotic resistance development, and cecal metabolites were primarily enriched in growth, carbohydrate metabolism, and amino acid metabolism pathways. Specifically, tryptophan metabolism (2-picolinic acid, quinolinic acid, and oxindole) enhanced steer well-being by increasing antioxidants (superoxide dismutase (SOD), peroxidases (POD), and glutathione (GSH)) and reducing inflammatory factors (interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α)) following EO treatment. Notably, low-abundance microorganisms (s_Streptomyces_gardneri, s_Paenibacillus_sp._S09, and s_Nocardia_sp._Root136) may play a significant role in growth and immunity.

CONCLUSION

These findings provide fundamental insights into how EO alleviates cold stress by modulating the HPA axis, promotes growth and well-being of steers under cold stress by influencing mediates tryptophan metabolism of cecal microbiota in Holstein steers.

Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle

Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.

Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems

Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M2 = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.

Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans

Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.

Beneficial microorganisms: Regulating growth and defense for plant welfare

Beneficial microorganisms (BMs) promote plant growth and enhance stress resistance. This review summarizes how BMs induce growth promotion by improving nutrient uptake, producing growth-promoting hormones and stimulating root development. How BMs enhance disease resistance and help protect plants from abiotic stresses has also been explored. Growth-defense trade-offs are known to affect the ability of plants to survive under unfavourable conditions. This review discusses studies demonstrating that BMs regulate growth-defense trade-offs through microbe-associated molecular patterns and multiple pathways, including the leucine-rich repeat receptor-like kinase pathway, abscisic acid signalling pathway and specific transcriptional factor regulation. This multifaceted relationship underscores the significance of BMs in sustainable agriculture. Finally, the need for integration of artificial intelligence to revolutionize biofertilizer research has been highlighted. This review also elucidates the cutting-edge advancements and potential of plant-microbe synergistic microbial agents.

The Effects of Milk and Posterior Intestinal Microorganisms on the Lactation Performance of Dual-Purpose Cattle (Bos taurus) Revealed by 16S rRNA Sequencing

The aim of this research was to employ 16S rRNA high-throughput sequencing to thoroughly explore the interplay between milk and hindgut microbial communities and the effects of microorganisms in milk and the hindgut on the dairy quality of XJBC and CSC. In this study, 96 XJBC milk samples, 94 XJBC hindgut samples, 100 CSC milk samples, and 93 CSC hindgut samples were collected for microbial community analysis. The 16S rRNA sequencing data revealed that the microbial species richness in the milk of CSC exceeded that of XJBC, whereas the opposite was true for the hindgut microbial communities. A chi-square test was conducted using SPSS 19.0. The milk and posterior intestinal microbiota between individuals were analyzed with the Pearson chi-square test, maximum likelihood ratio, and Fisher's exact test. Nongenetic factors substantially influenced microbial community dynamics in both milk and the hindgut. In the milk of dairy cows, a significant negative correlation was observed between one genus and milk protein production. Nine genera were significantly negatively correlated with milk fat production, whereas one genus was positively correlated. Additionally, six genera were negatively correlated with lactose production, and two genera exhibited positive correlations. Notably, Phascolarctobacterium and Turicibacter were identified as genera originating from the hindgut, which led to reduced milk quality. In the hindgut microbial community of dairy cows, seven genera were significantly negatively associated with milk fat production, whereas one genus was positively associated with milk fat production. These findings indicate that certain mammary microorganisms may migrate from the hindgut, either endogenously or exogenously, disrupting the equilibrium of the mammary microbial community in dairy cows and potentially leading to inflammation. By enhancing feeding conditions and standardizing production practices, the invasion of harmful flora into mammary tissues can be minimized, reducing the risk of inflammation and thereby preserving the health of dairy cows and enhancing milk quality.

The impact of rumen microbial composition on apparent digestibility, rumen fermentation and metabolism in Sanhe cows and Holstein cows of different parities under identical dietary conditions

Previous studies have discussed the association between serum metabolism and lactation performance among Sanhe and Holstein cows of different parities and found that the metabolic profiles of these two breeds vary differently with parity. Since the rumen is the central organ for nutrient absorption and production transformation in dairy cows, it remains unknown whether the differences observed under the same dietary conditions are related to the structure of the rumen microbiome. This study measured the apparent digestibility and rumen fermentation parameters of Sanhe cows (S1/S2/S3/S4) and Holstein cows (H1/H2/H3/H4) across four parities and generated a comprehensive rumen microbiome dataset using high-throughput sequencing technology. Significant differences in dry matter digestibility (p = 0.001) and ammonia nitrogen (p = 0.024) were observed among the S groups, with higher trends of various VFA contents in S1 (0.05 < p < 0.1). The H group showed significant differences in crude protein digestibility (p = 0.001), higher isovaleric acid content in H1 (p = 0.002), and the lowest acetate to propionate ratio (p = 0.002) in H3. Metagenomic sequencing results indicated consistency between rumen microbiome patterns and metabolic changes, with S1 distinctly different from S2/S3/S4, and H1 and H2 different from H3 and H4. The species composition of the rumen microbiome was similar between Sanhe and Holstein cows, but differences in abundance were noted. Rhizophagus , Neocallimastix, and Piromyces were more abundant in S1, H1, and H2, and pathways such as autophagy-animal, plant-pathogen interaction, and endocytosis were significantly enriched in these parities. Multiparous Sanhe cows had higher abundances of ATP-binding cassette transporters pathways. Additionally, CAZymes such as GH84 and GH37 were significantly associated with differential physiological indicators and milk traits. In conclusion, this study reveals the complex relationship between rumen microbiota and metabolic characteristics in Sanhe and Holstein cows of different parities, indicating that changes in the structure of the rumen microbiome may be key factors affecting lactation performance and metabolic differences in dairy cows.

Reductive acetogenesis is a dominant process in the ruminant hindgut

BACKGROUND

The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.

RESULTS

To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.

CONCLUSIONS

These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts. Video Abstract.

Hindguts of Kyphosus sydneyanus harbor phylogenetically and genomically distinct Alistipes capable of degrading algal polysaccharides and diazotrophy

The genus Alistipes (Bacteroidota) is most often associated with human clinical samples and livestock. However, Alistipes are also prevalent in the hindgut of the marine herbivorous fish Kyphosus sydneyanus (Silver Drummer), and analysis of their carbohydrate-active enzyme (CAZyme) encoding gene repertoires suggests Alistipes degrade macroalgal biomass to support fish nutrition. To further explore host-associated traits unique to K. sydneyanus-derived Alistipes, we compared 445 high-quality genomes of Alistipes available in public databases (e.g., human and ruminant associated) with 99 metagenome-assembled genomes (MAGs) from the K. sydneyanus gut. Analyses showed that Alistipes from K. sydneyanus are phylogenetically distinct from other hosts and comprise 26 species based on genomic average nucleotide identity (ANI) analyses. Ruminant- and fish-derived Alistipes had significantly smaller genomes than human-derived strains, and lower GC contents, possibly reflecting a symbiotic relationship with their hosts. The fish-derived Alistipes were further delineated by their genetic capacity to fix nitrogen, biosynthesize cobalamin (vitamin B12), and utilize marine polysaccharides (e.g., alginate and carrageenan). The distribution of CAZymes encoded by Alistipes from K. sydneyanus was not phylogenetically conserved. Distinct CAZyme gene compositions were observed between closely related species. Conversely, CAZyme gene clusters (operons) targeting the same substrates were found across diverse species. Nonetheless, transcriptional data suggest that closely related Alistipes target specific groups of substrates within the fish hindgut. Results highlight host-specific adaptations among Alistipes in the fish hindgut that likely contribute to K. sydneyanus digesting their seaweed diet, and diverse and redundant carbohydrate-degrading capabilities across these Alistipes species.IMPORTANCEDespite numerous reports of the Alistipes genus in humans and ruminants, its diversity and function remain understudied, and there is no clear consensus on whether it positively or negatively impacts host health. Given the symbiotic role of gut communities in the Kyphosus sydneyanus hindgut, where Alistipes are prevalent, and the diversity of carbohydrate-active enzymes (CAZymes) encoded that likely contribute to the breakdown of important substrates in the host diet, it is likely that this genus provides essential services to the fish host. Therefore, considering its metabolism in various contexts and hosts is crucial for understanding the ecology of the genus. Our study highlights the distinct genetic traits of Alistipes based on host association, and the potential of fish-associated Alistipes to transform macroalgae biomass into nutraceuticals (alginate oligosaccharides, β-glucans, sulfated galactans, and sulfated fucans).

Unveiling novel antimicrobial peptides from the ruminant gastrointestinal microbiomes: A deep learning-driven approach yields an anti-MRSA candidate

INTRODUCTION

Antimicrobial peptides (AMPs) present a promising avenue to combat the growing threat of antibiotic resistance. The ruminant gastrointestinal microbiome serves as a unique ecosystem that offers untapped potential for AMP discovery.

OBJECTIVES

The aims of this study are to develop an effective methodology for the identification of novel AMPs from ruminant gastrointestinal microbiomes, followed by evaluating their antimicrobial efficacy and elucidating the mechanisms underlying their activity.

METHODS

We developed a deep learning-based model to identify AMP candidates from a dataset comprising 120 metagenomes and 10,373 metagenome-assembled genomes derived from the ruminant gastrointestinal tract. Both in vivo and in vitro experiments were performed to examine and validate the antimicrobial activities of the AMP candidates that were selected through bioinformatic analysis and subsequently synthesized chemically. Additionally, molecular dynamics simulations were conducted to explore the action mechanism of the most potent AMP candidate.

RESULTS

The deep learning model identified 27,192 potential secretory AMP candidates. Following bioinformatic analysis, 39 candidates were synthesized and tested. Remarkably, all synthesized peptides demonstrated antimicrobial activity against Staphylococcus aureus, with 79.5% showing effectiveness against multiple pathogens. Notably, Peptide 4, which exhibited the highest antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), confirmed this effect in a mouse model with wound infection, exhibiting a low propensity for resistance development and minimal cytotoxicity and hemolysis towards mammalian cells. Molecular dynamics simulations provided insights into the mechanism of Peptide 4, primarily its ability to disrupt bacterial cell membranes, leading to cell death.

CONCLUSION

This study highlights the power of combining deep learning with microbiome research to uncover novel therapeutic candidates, paving the way for the development of next-generation antimicrobials like Peptide 4 to combat the growing threat of MRSA would infections. It also underscores the value of utilizing ruminant microbial resources.

Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle

Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.

The biogeography of gastrointestinal mucosal microbiota of beef cattle at harvest

Introduction

The gastrointestinal microbiota profoundly influences the health and productivity of animals. This study aimed to characterize microbial community structures of the mouth, gastrointestinal tract (GIT), and feces of cattle.

Methods

Samples were collected from 18 Akaushi crossbred steers at harvest from multiple locations, including the oral cavity, rumen, abomasum, duodenum, jejunum, ileum, cecum, spiral colon, distal colon, and feces. These cattle were raised without exposure to antimicrobial drugs or hormone implants. Total microbial abundance was assessed using qPCR targeting the V3-V4 region of the 16S rRNA gene, and microbial community composition was evaluated through 16S rRNA gene sequencing.

Results

Total microbial abundance was lesser in the small intestine than in other GIT regions (p ≤ 0.05). Additionally, microbial communities in the small intestine had lower richness and diversity than other regions (p ≤ 0.05). Microbial community compositions were measurably different along the GIT, with greater relatedness in adjacent GIT sections when progressing from oral to aboral locations. Firmicutes, Bacteroidota, and Actinobacteria were the dominant phyla in all samples. However, variations in composition were evident at lower taxonomic levels within these dominant phyla among samples from different regions. Genera previously associated with healthy gut microbiome communities were observed in low abundance across GIT regions. Taxa historically associated with liver abscesses (e.g., Fusobacterium and Trueperella) were detected in low abundance (≤0.02% relative abundance) throughout the GIT. In contrast, Bacteroides, which recently has been identified as a dominant feature in many liver abscesses, was observed in greater relative abundance (5.2% on average) in the hindgut.

Discussion

This study provides an in-depth evaluation of the GIT of harvest-ready Akaushi crossbred cattle of varying growth rates. Clear differences exist in the abundance and composition of microbial populations at different points of the GIT. Unfortunately, no single GIT location can adequately represent the microbial communities of the entire GIT, which has important implications for future research. Additionally, examining microbiome data only at the phylum level likely oversimplifies important complexities of the microbial community structures, and investigations of lower taxonomic ranks should be included.

The Impact of an Extended Bleed-to-evisceration Interval on the Microbiological Quality of On-farm Slaughtered Cattle Carcasses

The uncertainties surrounding the microbiological risks of an extended exsanguination-to-evisceration interval have limited the implementation of on-farm slaughter in Europe. On-farm slaughter is increasingly advocated by farmers, consumers, and policymakers as a humane alternative to traditional slaughterhouse operations. However, concerns about hygiene and food safety, particularly bacterial contamination, have led to stringent time limits imposed by Member States on the interval between bleeding and evisceration. Microbiological standards for bovine carcasses in the European Union are governed by Commission Regulation (EC) No 2073/2005, which sets process hygiene criteria for aerobic colony count and Enterobacteriaceae. To investigate whether extending the bleed-to-evisceration interval compromises meat safety, five Holstein dairy cattle were slaughtered on-farm, with samples collected from the internal paralumbar area in contact with the intestines for up to 4 h postmortem. The samples were analyzed for Enterobacteriaceae, aerobic colony count, and Escherichia coli. None of the samples exceeded the established thresholds of 1.5 and 3.5 log CFU/cm2 for aerobic colony count and Enterobacteriaceae, respectively, as defined by Belgian health authorities for the nondestructive sampling method. These preliminary findings suggest that on-farm slaughter with evisceration occurring up to 4 h post-mortem does not pose increased microbiological risks to human health. However, further research is necessary, particularly under warmer environmental conditions and with a larger sample size, to confirm these results and to explore additional factors that may influence bacterial translocation and digestive tract wall integrity.

Early-life supplementation with mannan-rich fraction to regulate rumen microbiota, gut health, immunity, and growth performance in dairy goat kids

Enhancing gastrointestinal health, immunity, and digestion are key factors to support dairy goat kid performance. Several additives have been studied in relation to these actions. This study investigated the impact of mannan-rich fraction (MRF) inclusion in goat milk on the growth performance, gut health, rumen fermentation, and microbial profiles of Xinong Saanen dairy goat kids. A total of 80 kids aged 14 d and 4.72 ± 0.33 kg BW were randomly assigned into 2 groups: control and MRF (1 g/d MRF mixed into milk). Each group consisted of 40 kids with 10 kids per pen. All kids were given milk individually and fed a starter diet by pen, with the trial lasting 10 wk. Body weight and blood samples were collected on the seventh day at 2, 6, 10 and 12 wk of age, and feed intake was determined daily. From the first to seventh day at 12 wk of age, fecal samples were collected from 4 kids in each group to analyze nutrient digestibility. On the seventh day of 12 wk of age, 4 kids from each group were slaughtered for evaluation of rumen fermentation, rumen microbiota, and gut morphology. The results indicated that MRF supplementation led to greater overall BW, overall starter DMI, and overall ADG, along with a lower overall diarrhea rate. However, no difference in overall feed efficiency and apparent digestibility of nutrients was observed. Furthermore, MRF supplementation resulted in increased ileal villus height; higher RNA expression of claudin-1 and occludin in the duodenum; higher expression of ZO-1, JAM-2, and occludin in the jejunum; and higher expression of claudin-1, JAM-2, and occludin in the ileum. Additionally, the concentrations of overall IgA, overall IgM, and overall IgG were higher in the MRF group. The concentrations of ruminal acetate and total volatile fatty acid were higher with MRF supplementation (P < 0.05). Meanwhile, supplementation with MRF resulted in higher abundance of Bacteroidetes and Succinivibrio and lower abundance of Firmicutes and Succiniclasticum in the rumen. Overall, the growth performance, gut health, immunity, and ruminal microbial structure of dairy goat kids benefited from MRF supplementation.

Ruminant microbiome data are skewed and unFAIR, undermining their usefulness for sustainable production improvement

The ruminant microbiome plays a key role in the health, feed utilization and environmental impact of ruminant production systems. Microbiome research provides insights to reduce the environmental footprint and improve meat and milk production from ruminants. However, the microbiome composition depends on the ruminant species, habitat and diet, highlighting the importance of having a good representation of ruminant microbiomes in their local environment to translate research findings into beneficial approaches. This information is currently lacking. In this study, we examined the metadata of farmed ruminant microbiome studies to determine global representativeness and summarized information by ruminant species, geographic location, body site, and host information. We accessed data from the International Nucleotide Sequence Database Collaboration via the National Center for Biotechnology Information database. We retrieved 47,628 sample metadata, with cattle accounting for more than two-thirds of the samples. In contrast, goats, which have a similar global population to cattle, were underrepresented with less than 4% of the total samples. Most samples originated in Western Europe, North America, Australasia and China but countries with large ruminant populations in South America, Africa, Asia, and Eastern Europe were underrepresented. Microbiomes from the gastrointestinal tract were the most frequently studied, comprising about 87% of all samples. Additionally, the number of samples from other body sites such as the respiratory tract, milk, skin, reproductive tract, and fetal tissue, has markedly increased over the past decade. More than 40% of the samples lacked basic information and many were retrieved from generic taxonomic classifications where the ruminant species was manually recovered. The lack of basic information such as age, breed or sex can limit the reusability of the data for further analysis and follow-up studies. This requires correct taxonomic assignment of the ruminant host and basic metadata information using accepted ontologies adapted to host-associated microbiomes. Repositories should require this information as a condition of acceptance. The results of this survey highlight the need to encourage studies of the ruminant microbiome from underrepresented ruminant species and countries worldwide. This shortfall in information poses a challenge for the development of microbiome-based strategies to meet sustainability requirements, particularly in areas with expanding livestock production systems.

Seasonal stability of the rumen microbiome contributes to the adaptation patterns to extreme environmental conditions in grazing yak and cattle

BACKGROUND

The rumen microbiome plays an essential role in maintaining ruminants' growth and performance even under extreme environmental conditions, however, which factors influence rumen microbiome stability when ruminants are reared in such habitats throughout the year is unclear. Hence, the rumen microbiome of yak (less domesticated) and cattle (domesticated) reared on the Qinghai-Tibetan Plateau through the year were assessed to evaluate temporal changes in their composition, function, and stability.

RESULTS

Rumen fermentation characteristics and pH significantly shifted across seasons in both cattle and yak, but the patterns differed between the two ruminant species. Ruminal enzyme activity varied with season, and production of xylanase and cellulase was greater in yak compared to cattle in both fall and winter. The rumen bacterial community varied with season in both yak and cattle, with higher alpha diversity and similarity (beta diversity) in yak than cattle. The diversity indices of eukaryotic community did not change with season in both ruminant species, but higher similarity was observed in yak. In addition, the similarity of rumen microbiome functional community was higher in yak than cattle across seasons. Moreover, yak rumen microbiome encoded more genes (GH2 and GH3) related to cellulose and hemicellulose degradation compared to cattle, and a new enzyme family (GH160) gene involved in oligosaccharides was uniquely detected in yak rumen. The season affected microbiome attenuation and buffering values (stability), with higher buffering value in yak rumen microbiome than cattle. Positive correlations between antimicrobial resistance gene (dfrF) and CAZyme family (GH113) and microbiome stability were identified in yak, but such relationship was negatively correlated in cattle.

CONCLUSIONS

The findings of the potential of cellulose degradation, the relationship between rumen microbial stability and the abundance of functional genes varied differently across seasons and between yak and cattle provide insight into the mechanisms that may underpin their divergent adaptation patterns to the harsh climate of the Qinghai-Tibetan Plateau. These results lay a solid foundation for developing strategies to maintain and improve rumen microbiome stability and dig out the potential candidates for manufacturing lignocellulolytic enzymes in the yak rumen to enhance ruminants' performance under extreme environmental conditions.

Maternal gastrointestinal microbiome shapes gut microbial function and resistome of newborns in a cow-to-calf model

BACKGROUND

The maternal gut microbiome is the direct and important source of early colonization and development of the neonatal gut microbiome. However, differences in unique and shared features between mothers with different physiological phenotypes and their newborns still lack exhaustive investigation. Here, using a cow-to-calf model, a comprehensive investigation was conducted to elucidate the pattern and characterization of microbial transfer from the maternal source to the offspring.

RESULTS

The microbiota in the rumen and feces of dairy cows were divided into two clusters via enterotype analysis. The cows from the enterotype distinguished by Prevotella in the rumen had better production performance, whereas no difference was observed in the cows classified by feces enterotype. Furthermore, through a pairwise combination of fecal and ruminal enterotypes, we screened a group of dairy cows with excellent phenotypes. The gastrointestinal microbiomes of cows with different phenotypes and their offspring differed significantly. The rumen was a more important microbial source for meconium than feces. Transmission of beneficial bacteria from mother to offspring was observed. Additionally, the meconium inherits advantageous metabolic functions of the rumen. The resistome features of the rumen, feces, and meconium were consistent, and resistome abundance from cows to calves showed an expanding trend. The interaction between antibiotic-resistance genes and mobile genetic elements from the rumen to meconium was the most remarkable. The diversity of core metabolites from cows to calves was stable and not affected by differences in phenotypes. However, the abundance of specific metabolites varied greatly.

CONCLUSIONS

Our study demonstrates the microbial taxa, metabolic function, and resistome characteristics of maternal and neonatal microbiomes, and reveals the potential vertical transmission of the microbiome from a cow-to-calf model. These findings provide new insights into the transgenerational transmission pattern of the microbiome. Video Abstract.

Assessment of microbial communities in a dairy farm from a food safety perspective

Microbial communities associated with dairy farm operations have a significant influence on food safety, dairy product quality, and animal health. This study aimed to create a microbial mapping at a dairy farm to learn about their bacterial diversity, distribution, and potential dissemination pathways. The investigation included the detection of key zoonotic pathogens, enumeration of Staphylococcus aureus and Escherichia coli as indicators of typical bacterial loads in a dairy production environment, and a microbiome analysis using metagenomics. A total of 160 samples (environmental, udder swabs, feed, feces, raw milk, and water) were collected during winter (N = 80) and spring (N = 80). In winter, Cronobacter spp. were detected in four feed and two water samples; L. monocytogenes was identified in two samples, one from feces and one from a cattle mat; E. coli O157:H7 was found in two feed samples. On the other hand, during spring, Cronobacter spp. were present in four feed samples and one hallway drain, with only one feed sample testing positive for E. coli O157:H7, while L. monocytogenes was absent during the spring season. Regarding microbial counts, there was no significant difference between the two seasons (p = 0.068) for S. aureus; however, a significant difference (p = 0.025) was observed for E. coli. Environmental microbiome analysis showed the presence of Proteobacteria (46.0 %) and Firmicutes (27.2 %) as the dominant phyla during both seasons. Moraxellaceae (11.8 %) and Pseudomonadaceae (10.62 %) were notable during winter, while Lactobacillaceae (13.0 %) and Enterobacteriaceae (12.6 %) were prominent during spring. These findings offer valuable insights into microbial distribution within a dairy farm and potential risks to animal and human health through environmental cross-contamination.

The Influence of High-Concentrate Diet Supplemented with Tannin on Growth Performance, Rumen Fermentation, and Antioxidant Ability of Fattening Lambs

This experiment aimed to study the effects of tannin supplementation on growth performance, rumen fermentation characteristics, apparent digestibility and serum biochemistry, and antioxidant and immune indexes in fattening lambs. A total of 36 male Hu sheep lambs (body weight = 15.83 ± 0.48 kg and days of age = 55 ± 2 d) were fed a high-concentrate diet and randomly divided into one of three groups of 12 animals each: control with no tannin (CON) and tannin treatments (TA1, 3 g/d per lamb; TA2, 6 g/d per lamb). The feeding experiment lasted for 60 d. The results showed that the average daily gain and ruminal propionate content of lambs in the TA1 group were higher (p < 0.05) than those in the CON group. Lambs fed tannin had significantly increased (p < 0.05) microbial protein and decreased (p < 0.05) ammonia nitrogen concentrations in the rumen. In addition, the crude protein and neutral detergent fiber digestibility of the TA2 group were significantly decreased (p < 0.05) as compared with the TA1 and CON groups, respectively. The serum concentrations of triglyceride, immunoglobulin A, and catalase and the total antioxidant capacity were higher (p < 0.05) in the TA1 group that those in the CON group, whereas an opposite trend of urea nitrogen, interleukin-1β, and malondialdehyde was found between the two groups. Also, tannin supplementation increased (p < 0.05) Lactobacillus and decreased (p < 0.05) Salmonella counts in the feces of lambs. Taken together, tannin supplementation can improve the growth performance, immunity, and antioxidant ability of fattening lambs fed a high-concentrate diet.

Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition

The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.

The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host

The dominant bacteria in the hindgut of calves play an important role in their growth and health, which could even lead to lifelong consequences. However, the identification of core probiotics in the hindgut and its mechanism regulating host growth remain unclear. Here, a total of 1045 fecal samples were analyzed by 16S rRNA gene sequencing from the 408 Holstein dairy calves at the age of 0, 14, 28, 42, 56, and 70 days to characterize the dynamic changes of core taxa. Moreover, the mechanisms of nutrient metabolism of calf growth regulated by core bacteria were investigated using multi-omics analyses. Finally, fecal microbiota transplantation (FMT) in mice were conducted to illustrate the potential beneficial effects of core bacteria. Four calf enterotypes were identified and enterotypes dominated by Bifidobacterium and Oscillospiraceae_UCG-005 were representative. The frequency of enterotype conversion shifted from variable to stable. The close relationship observed between phenotype and enterotype, revealing a potential pro-growth effect of Bifidobacterium, might be implemented by promoting the use of carbohydrate, activating the synthesis of volatile fatty acids, amino acids and vitamin B6, and inhibiting methane production in the hindgut. The FMT results indicated the beneficial effect of Bifidobacterium on host growth and hindgut development. These results support the notion that the Bifidobacterium-dominated fecal microbiome would be an important driving force for promoting the host growth in the early life. Our findings provide new insights into the potential probiotic mining and application strategies to promote the growth of young animals or improve their growth retardation.

Heat stress and feeding effects on the mucosa-associated and digesta microbiome and their relationship to plasma and digesta fluid metabolites in the jejunum of dairy cows

The intestinal microbiota plays a pivotal role in digestive processes and maintains gut health and intestinal homeostasis. These functions may be compromised by increased environmental heat, which in turn reduces feed intake and gut integrity and activates the intestinal immune system. It remains unknown whether high ambient temperatures, which cause heat stress (HS) in dairy cows, disturb the eubiosis of the microbial community, and if so, to which extent the reduction in feed intake and the impairment of circulating and intestinal metabolites account for the alterations of the jejunal microbiota. To address these questions, jejunal digesta, mucosa, and plasma samples were collected from cows exposed to heat stress (HS; 28°C, temperature-humidity index [THI] = 76, n = 10), control conditions (CON; 16°C, THI = 60, n = 10), or pair-fed (PF; 16°C, THI = 60, n = 10) for 7 d. Digesta fluids were examined for pH, acetate, nonesterified fatty acids (NEFA), glucose, and lactate, and plasma samples were analyzed for glucose, lactate, BHB, triglycerides, NEFA, creatinine, and urea. The microbiota of the digesta and mucosa samples were analyzed by 16S rRNA sequencing. The α-diversity was higher in mucosa than digesta but was not affected by high ambient temperatures. However, the mucosa-associated microbiota appeared more responsive to ambient heat than the digesta microbiome. The adaptive responses under HS conditions comprised an increased mucosal abundance of Bifidobacteriaceae, Succinivibrionaceae UCG-001, Clostridia and Lactobacillus. In the digesta, HS has exerted effects on microbial abundance of Colidextribacter, and Lachnospiraceae UCG-008. Several correlations between plasma or intestinal metabolites and microbiota were elucidated, including Methanobacteriaceae correlating positively with plasma BHB and digesta glucose concentrations. Moreover, the reduction in feed intake during HS had non-negligible effects on microbial diversity and the abundance of certain taxa, underpinning the importance of nutrient supply on maintaining intestinal homeostasis.

Comparative analysis of intestinal microbiota composition between free-ranged captive yak populations in Nimu County

The intestinal microbiota assumes a pivotal role in modulating host metabolism, immune responses, overall health, and additional physiological dimensions. The structural and functional characteristics of the intestinal microbiota may cause alterations within the host's body to a certain extent. The composition of the gut microbiota is associated with environmental factors, dietary habits, and other pertinent conditions. The investigation into the gut microbiota of yaks remained relatively underexplored. An examination of yak gut microbiota holds promise in elucidating the complex relationship between microbial communities and the adaptive responses of the host to its environment. In this study, yak were selected from two distinct environmental conditions: those raised in sheds (NS, n=6) and grazed in Nimu County (NF, n=6). Fecal samples were collected from the yaks and subsequently processed for analysis through 16S rDNA and ITS sequencing methodologies. The results revealed that different feeding styles result in significant differences in the Alpha diversity of fungi in the gut of yaks, while the gut microbiota of captive yaks was relatively conserved. In addition, significant differences appeared in the abundance of microorganisms in different taxa, phylum Verrucomicrobiota was significantly enriched in group NF while Firmicutes was higher in group NS. At the genus level, Akkermansia, Paenibacillus, Roseburia, Dorea, UCG_012, Anaerovorax and Marvinbryantia were enriched in group NF while Desemzia, Olsenella, Kocuria, Ornithinimicrobium and Parvibacter were higher in group NS (P<0.05 or P<0.01). There was a significant difference in the function of gut microbiota between the two groups. The observed variations are likely influenced by differences in feeding methods and environmental conditions both inside and outside the pen. The findings of this investigation offer prospective insights into enhancing the yak breeding and expansion of the yak industry.

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats

The gastrointestinal tract (GIT) is stationed by a dynamic and complex microbial community with functions in digestion, metabolism, immunomodulation, and reproduction. However, there is relatively little research on the composition and function of microorganisms in different GIT segments in dairy goats. Herein, 80 chyme samples were taken from ten GIT sites of eight Xinong Saanen dairy goats and then analyzed and identified the microbial composition via 16S rRNA V1-V9 amplicon sequencing. A total of 6669 different operational taxonomic units (OTUs) were clustered, and 187 OTUs were shared by ten GIT segments. We observed 264 species belonging to 23 different phyla scattered across ten GITs, with Firmicutes (52.42%) and Bacteroidetes (22.88%) predominating. The results revealed obvious location differences in the composition, diversity, and function of the GIT microbiota. In LEfSe analysis, unidentified_Lachnospiraceae and unidentified_Succinniclassicum were significantly enriched in the four chambers of stomach, with functions in carbohydrate fermentation to compose short-chain fatty acids. Aeriscardovia, Candidatus_Saccharimonas, and Romboutsia were significantly higher in the foregut, playing an important role in synthesizing enzymes, amino acids, and vitamins and immunomodulation. Akkermansia, Bacteroides, and Alistipes were significantly abundant in the hindgut to degrade polysaccharides and oligosaccharides, etc. From rumen to rectum, α-diversity decreased first and then increased, while β-diversity showed the opposite trend. Metabolism was the major function of the GIT microbiome predicted by PICRUSt2, but with variation in target substrates along the regions. In summary, GIT segments play a decisive role in the composition and functions of microorganisms. KEY POINTS: • The jejunum and ileum were harsh for microorganisms to colonize due to the presence of bile acids, enzymes, faster chyme circulation, etc., exhibiting the lowest α-diversity and the highest β-diversity. • Variability in microbial profiles between the three foregut segments was greater than four chambers of stomach and hindgut, with a higher abundance of Firmicutes dominating than others. • Dairy goats dominated a higher abundance of Kiritimatiellaeota than cows, which was reported to be associated with fatty acid synthesis.

Effects of grain intervention on hypothalamic function and the metabolome of blood and milk in dairy cows

BACKGROUND

The hypothalamus plays a crucial role in the health and productivity of dairy cows, yet studies on its functionality and its impact on peripheral circulation in these animals are relatively scarce, particularly regarding dietary interventions. Therefore, our study undertook a comprehensive analysis, incorporating both metabolomics and transcriptomics, to explore the effects of a grain-based diet on the functionality of the hypothalamus, as well as on blood and milk in dairy cows.

RESULTS

The hypothalamic metabolome analysis revealed a significant reduction in prostaglandin E2 (PGE2) level as a prominent response to the grain-based diet introduction. Furthermore, the hypothalamic transcriptome profiling showed a notable upregulation in amino acid metabolism due to the grain-based diet. Conversely, the grain-based diet led to the downregulation of genes involved in the metabolic pathway from lecithin to PGE2, including phospholipase A2 (PLA2G4E, PLA2G2A, and PLA2G12B), cyclooxygenase-2 (COX2), and prostaglandin E synthase (PTGES). Additionally, the plasma metabolome analysis indicated a substantial decrease in the level of PGE2, along with a decline in adrenal steroid hormones (tetrahydrocortisol and pregnenolone) following the grain-based diet introduction. Analysis of the milk metabolome showed that the grain-based diet significantly increased uric acid level while notably decreasing PGE2 level. Importantly, PGE2 was identified as a critical metabolic marker in the hypothalamus, blood, and milk in response to grain intervention. Correlation analysis demonstrated a significant correlation among metabolic alterations in the hypothalamus, blood, and milk following the grain-based diet.

CONCLUSIONS

Our findings suggest a potential link between hypothalamic changes and alterations in peripheral circulation resulting from the introduction of a grain-based diet.

Untargeted metabolomics and metagenomics reveal signatures for intramammary ceftiofur treatment and lactation stage in the cattle hindgut

The gut microbiota in cattle is essential for protein, energy, and vitamin production and hence, microbiota perturbations can affect cattle performance. This study evaluated the effect of intramammary (IMM) ceftiofur treatment and lactation stage on the functional gut microbiome and metabolome. Forty dairy cows were enrolled at dry-off. Half received IMM ceftiofur and a non-antibiotic teat sealant containing bismuth subnitrate (cases), while the other half received the teat sealant (controls). Fecal samples were collected before treatment at dry off, during the dry period (weeks 1 and 5) and the first week after calving (week 9). Shotgun metagenomic sequencing was applied to predict microbial metabolic pathways whereas untargeted metabolomics was used identify polar and nonpolar metabolites. Compared to controls, long-term changes were observed in the cows given ceftiofur, including a lower abundance of microbial pathways linked to energy production, amino acid biosynthesis, and other vital molecules. The metabolome of treated cows had elevated levels of stachyose, phosphatidylethanolamine diacylglycerol (PE-DAG), and inosine a week after the IMM ceftiofur application, indicating alterations in microbial fermentation, lipid metabolism, energy, and cellular signaling. Differences were also observed by sampling, with cows in late lactation having more diverse metabolic pathways and a unique metabolome containing higher levels of histamine and histamine-producing bacteria. These data illustrate how IMM ceftiofur treatment can alter the functionality of the hindgut metabolome and microbiome. Understanding how antibiotics and lactation stages, which are each characterized by unique diets and physiology, impact the function of resident microbes is critical to define normal gut function in dairy cattle.

Rumen fermentation parameters and papillae development in Simmental growing bulls with divergent residual feed intake

Residual feed intake (RFI), a widespread index used to measure animal feed efficiency, is influenced by various individual biological factors related to inter-animal variation that need to be assessed. Herein, 30 Simmental bulls, raised under the same farm conditions, were divided on the basis of RFI values into a high efficient group (HE, RFI =  - 1.18 ± 0.33 kg DM/d, n = 15) and a low efficient group (LE, RFI = 0.92 ± 0.35 kg DM/d, n = 15). Subsequently, bulls were slaughtered at an average BW of 734 ± 39.4 kg. Their ruminal fermentation traits were analysed immediately after slaughtering and after 24 h of in vitro incubation. Furthermore, ruminal micro-biota composition and ruminal papillae morphology were examined. The LE group exhibited a higher propionate concentration as a percentage of total volatile fatty acids (17.3 vs 16.1%, P = 0.04) in the rumen fluid collected during slaughtering, which was also confirmed after in vitro fermentation (16.6 vs 15.4% respectively for LE and HE, P = 0.01). This phenomenon resulted in a significant alteration in the acetate-to-propionate ratio (A:P) with higher values for the HE group, both after slaughter (4.01 vs 3.66, P = 0.02) and after in vitro incubation (3.78 vs 3.66, P = 0.02). Methane production was similar in both groups either as absolute production (227 vs 218 mL for HE and LE, respectively) or expressed as a percentage of total gas (approximately 22%). Even if significant differences (P < 0.20) in the relative abundance of some bacterial genera were observed for the two RFI groups, no significant variations were observed in the alpha (Shannon index) and beta (Bray-Curtis index) diversity. Considering the papillae morphology, the LE subjects have shown higher length values (6.26 vs 4.90 mm, P < 0.01) while HE subjects have demonstrated higher papillae density (46.4 vs 40.5 n/cm2, P = 0.02). Histo-morphometric analysis did not reveal appreciable modifications in the total papilla thickness, boundaries or surface between the experimental groups. In conclusion, our results contribute to efforts to analyse the factors affecting feed efficiency at the ruminal level. Propionate production, papillae morphology and a few bacterial genera certainly play a role in this regard, although not a decisive one.

Bacteroidia and Clostridia are equipped to degrade a cascade of polysaccharides along the hindgut of the herbivorous fish Kyphosus sydneyanus

The gut microbiota of the marine herbivorous fish Kyphosus sydneyanus are thought to play an important role in host nutrition by supplying short-chain fatty acids (SCFAs) through fermentation of dietary red and brown macroalgae. Here, using 645 metagenome-assembled genomes (MAGs) from wild fish, we determined the capacity of different bacterial taxa to degrade seaweed carbohydrates along the gut. Most bacteria (99%) were unclassified at the species level. Gut communities and CAZyme-related transcriptional activity were dominated by Bacteroidia and Clostridia. Both classes possess genes CAZymes acting on internal polysaccharide bonds, suggesting their role initiating glycan depolymerization, followed by rarer Gammaproteobacteria and Verrucomicrobiae. Results indicate that Bacteroidia utilize substrates in both brown and red algae, whereas other taxa, namely, Clostridia, Bacilli, and Verrucomicrobiae, utilize mainly brown algae. Bacteroidia had the highest CAZyme gene densities overall, and Alistipes were especially enriched in CAZyme gene clusters (n = 73 versus just 62 distributed across all other taxa), pointing to an enhanced capacity for macroalgal polysaccharide utilization (e.g., alginate, laminarin, and sulfated polysaccharides). Pairwise correlations of MAG relative abundances and encoded CAZyme compositions provide evidence of potential inter-species collaborations. Co-abundant MAGs exhibited complementary degradative capacities for specific substrates, and flexibility in their capacity to source carbon (e.g., glucose- or galactose-rich glycans), possibly facilitating coexistence via niche partitioning. Results indicate the potential for collaborative microbial carbohydrate metabolism in the K. sydneyanus gut, that a greater variety of taxa contribute to the breakdown of brown versus red dietary algae, and that Bacteroidia encompass specialized macroalgae degraders.

Effect of Dietary and Age Changes on Ruminal Microbial Diversity in Holstein Calves

Ruminal microorganisms play a crucial role in the energy supply of ruminants and animal performance. We analyzed the variations in rumen bacteria and fungi at 45 d, 75 d, and 105 d by using 16SrRNA and ITS sequencing data and investigated their correlation with rumen fermentation. According to the results, rumen microflora tended to gradually mature with age, and bacterial and fungal establishment gradually stabilized. Upon comparing the three periods, the concentration of propionic acid increased significantly (p < 0.05) after weaning, and weaning accompanied by a transition in diet remarkably decreased (p < 0.05) rumen diversity in the short term and induced a corresponding change in the rumen microbiota composition. Bacteroidota, Actinobacteriota, and Firmicutes were the core bacterial phyla for all age periods. Ruminococcus, NK4A214_group, Sharpea, Rikenellaceae_RC9_gut_group, and norank_f__Butyricicoccaceae were the markedly abundant bacterial genera in pre-weaning. After weaning, the relative abundance of Erysipelotrichaceae_ UCG-002, Eubacterium_ruminantium_group, and Solobacterium significantly increased (p < 0.05). The relative abundance of Acetitomaculum increased with age with the greatest abundance noted at 105 d (37%). The dominant fungal phyla were Ascomycota and Basidiomycota, and Aspergillus and Xeromyces were the most abundant fungal genera after weaning. Trichomonascus, Phialosimplex, and Talaromyces were enriched at 105 d. However, the low abundance of Neocallimastigomycota was not detected throughout the study, which is worthy of further investigation. In addition, correlations were observed between age-related abundances of specific genera and microbiota functions and rumen fermentation-related parameters. This study revealed that rumen microbiota and rumen fermentation capacity are correlated, which contributed to a better understanding of the effects of age and diet on rumen microbiology and fermentation in calves.

Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome

Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.

Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation

Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomach to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestines. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin

Dietary influence on the microbiome in algivorous sea urchins such as Tripneustes gratilla elatensis suggests a bacterial contribution to the digestion of fiber-rich seaweed. An ecological insight into the spatial arrangement in the gut bacterial community will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. Toward this goal, we investigated the bacterial communities in the esophagus, stomach, and intestine of Ulva-fed sea urchins through 16S rRNA amplicon sequencing, followed by the prediction of their functional genes. We revealed communities with distinct features, especially those in the esophagus and intestine. The esophageal community was less diverse and was poor in food digestive or fermentation genes. In contrast, bacteria that can contribute to the digestion of the dietary Ulva were common in the stomach and intestine and consisted of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. Bacteroidetes and Firmicutes were found as the main phyla in the gut and are presumably also necessary in food digestion. The abundant sulfate-reducing bacteria in the stomach and intestine from the genera Desulfotalea, Desulfitispora, and Defluviitalea may aid in removing the excess sulfate from the decomposition of the algal polysaccharides. Although these sea urchins were fed with Ulva, genes for the degradation of polysaccharides of other algae and plants were present in this sea urchin gut microbiome. We conclude that the succession of microbial communities along the gut obtained supports the hypothesis on bacterial contribution to food digestion. IMPORTANCE Alga grazing by the sea urchin Tripneustes gratilla elatensis is vital for nutrient recycling and constructing new reefs. This research was driven by the need to expand the knowledge of bacteria that may aid this host in alga digestion and their phylogeny, roles, and activity niches. We hypothesized alterations in the bacterial compositional structure along the gut and their association with the potential contribution to food digestion. The current spatial insight into the sea urchin's gut microbiome ecology is novel and reveals how distinct bacterial communities are when distant from each other in this organ. It points to keynote bacteria with genes that may aid the host in the digestion of the complex sulfated polysaccharides in dietary Ulva by removing the released sulfates and fermentation to provide energy. The gut bacteria's genomic arsenal may also help to gain energy from diets of other algae and plants.

An analysis of the cecum microbiome of three breeds of the guinea pig: Andina, Inti, and Peru

This study investigated the effect of host genetics on the structure and composition of the cecum microbiota of three breeds of guinea pigs: Andina, Inti, and Peru. Fifteen guinea pigs were distributed into three groups according to their breed: Andina (5), Inti (5), and Peru (5). We discovered that four main phyla were shared between the three breeds: Bacteroidota, Firmicutes, Spirochaetota, and Synergistota. Although there were no significant differences in the alpha and beta diversity analysis, we found that the Linear discriminant analysis effect size and the heat tree analysis showed significant differences between the abundance of several taxa present in the cecum microbiome of the three breeds. These results suggest that host genetics could be a factor in the structure and composition of the guinea pig cecum microbiome. In addition, we found unique genera for each breed that have fermentation capacity and, therefore can be analyzed in further studies to determine if there is a functional relationship between them and the breed and its industrial profile.

Fecal microbiota transplantation holds the secret to youth

Aging shows itself not just at the cellular level, with shortened telomeres and cell cycle arrest, but also at the organ and organismal level, with diminished brainpower, dry eyes, intestinal inflammation, muscular atrophy, wrinkles, etc. When the gut microbiota, often called the "virtual organ of the host," fails to function normally, it can lead to a cascade of health problems including, but not limited to, inflammatory bowel disease, obesity, metabolic liver disease, type II diabetes, cardiovascular disease, cancer, and even neurological disorders. An effective strategy for restoring healthy gut bacteria is fecal microbiota transplantation (FMT). It can reverse the effects of aging on the digestive system, the brain, and the vision by transplanting the functional bacteria found in the excrement of healthy individuals into the gut tracts of patients. This paves the way for future research into using the microbiome as a therapeutic target for disorders associated with aging.