Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows

Temporal Changes in Faecal Microbiota Composition and Diversity in Dairy Cows Supplemented with a Lactobacillus-Based Direct-Fed Microbial

The rumen microbiota of dairy cows plays a crucial role in fermenting fibrous material, essential for nutrient extraction and overall productivity, detoxification of anti-nutritional toxic compounds, synthesis of vital nutrients, and is essential for optimal animal health. This study investigated the impact of Lentilactobacillus-, Lactocaseibacillus-, and Lacticaseibacillus-based direct-fed microbial (DFM) supplementation on dairy cows' faecal microbial composition and diversity. The study was carried out on a commercial dairy farm using 50 Holstein-Friesian cows randomly assigned into control (CON) and treatment (TRT) groups. Faecal samples were collected directly from the rectum every two months from September 2021 to January 2023. The bacterial 16S rRNA gene and fungal ITS-1 regions were amplified, sequenced, and analysed. Microbial diversity was assessed through alpha- and beta-diversity metrics. Linear discriminant analysis effect size (LEfSe) was performed to identify which taxa were driving the changes seen in the microbiota over time and treatment. Bacteroidaceae were the most prevalent bacterial family, followed by Lachnospiraceae and Muribaculaceae in both CON and TRT cows. Ascomycota, Basidiomycota, and Mucoromycota were the dominant three fungal phyla in the faeces of both CON and TRT cows. Bacterial genera Fructilactobacillus was abundant in the CON and Absicoccus in the TRT groups. Fungal taxa Chaetothryriales_incertae_sedis and Pseudomentella were absent in the faeces of TRT cows. Significant temporal and specific taxonomic differences were observed between the CON and TRT groups. The study's findings underscore the dynamic nature of microbial communities and the importance of targeted dietary interventions. Further research is necessary to elucidate these microbial shifts, long-term impacts, and functional implications, aiming to optimise ruminant nutrition and enhance dairy cow performance.

Metagenomic analysis reveals a dynamic rumen microbiome with diversified adaptive functions in response to dietary protein restriction and re-alimentation

Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.

Metagenomic discovery of microbial eukaryotes in stool microbiomes

Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.

Animal board invited review: The effect of diet on rumen microbial composition in dairy cows

Ruminants play an important part in the food supply chain, and manipulating rumen microbiota is important to maximising ruminants' production. Rumen microbiota through rumen fermentation produces as major end products volatile fatty acids that provide animal's energy requirements, and microbial CP. Diet is a key factor that can manipulate rumen microbiota, and each variation of the physical and chemical composition creates a specific niche that selects specific microbes. Alteration in the chemical composition of forage, the addition of concentrates in the diet, or the inclusion of plant extract and probiotics, can induce a change in rumen microbiota. High-throughput sequencing technologies are the approaches utilised to investigate the microbial system. Also, the application of omics technologies allows us to understand rumen microbiota composition and these approaches are useful to improve selection programmes. The aim of this review was to summarise the knowledge about rumen microbiota, its role in nutrient metabolism, and how diet can influence its composition.

Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color

Using oral swabs to collect the remnants of stomach content regurgitation during rumination in dairy cows can replicate up to 70% of the ruminal bacterial community, offering potential for broad-scale population-based studies on the rumen microbiome. The swabs collected from dairy cows often vary widely with respect to sample quality, likely due to several factors such as time of sample collection and cow rumination behavior, which may limit the ability of a given swab to accurately represent the ruminal microbiome. One such factor is the color of the swab, which can vary significantly across different cows. Here, we hypothesize that darker-colored swabs contain more rumen contents, thereby better representing the ruminal bacterial community than lighter-colored swabs. To address this, we collected oral swabs from 402 dairy cows and rumen samples from 13 cannulated cows on a research farm in Wisconsin, United States and subjected them to 16S rRNA sequencing. In addition, given that little is known about the ability of oral swabs to recapitulate the ruminal fungal community, we also conducted ITS sequencing of these samples. To correlate swab color to the microbiota we developed and utilized a novel imaging approach to colorimetrically quantify each swab from a range of light to dark. We found that swabs with increasing darkness scores were significantly associated with increased bacterial alpha diversity (p < 0.05). Lighter swabs exhibited greater variation in their community structure, with many identified amplicon sequence variants (ASVs) categorized as belonging to known bovine oral and environmental taxa. Our analysis of the fungal microbiome found that swabs with increasing darkness scores were associated with decreased alpha diversity (p < 0.05) and were also significantly associated with the ruminal solids fungal community, but not with the ruminal liquid community. Our study refines the utility of oral swabs as a useful proxy for capturing the ruminal microbiome and demonstrates that swab color is an important factor to consider when using this approach for documenting both the bacterial and fungal communities.

Rumen microbiota succession throughout the perinatal period and its association with postpartum production traits in dairy cows: A review

The transition period for dairy cows usually refers to the 3 weeks pre-calving to the 3 weeks post-calving. During this period, dairy cows undergo metabolic and physiological adaptations because of their susceptibility to metabolic and infectious diseases. Poor feeding management under these circumstances may adversely affect the health and subsequent production performance of the cows. Owing to long-term adaptation and evolution, the rumen has become a unique ecosystem inhabited by a complex microbial community closely associated with its natural host. Dietary components are metabolized by the rumen microbiota, and volatile fatty acids and microbial protein products can be used as precursor substances for synthesizing meat and milk components. The successful transition of perinatal dairy cows includes changes in diet, physiology, and the rumen microbiota. Rumen microbial profiles have been confirmed to be heritable and repairable; however, adverse circumstances affect rumen microbial composition, host digestion and metabolism, as well as postpartum production traits of dairy cows for a certain period. Preliminary evidence indicates a close relationship between the rumen microbiota and animal performance. Therefore, changes in rumen microbes during the transition period and the intrinsic links between the microbiota and host postpartum phenotypic traits need to be better understood to optimize production performance in ruminants.

Fermented total mixed ration enhances nutrient digestibility and modulates the milk components and fecal microbial community in lactating Holstein dairy cows

Fermented total mixed ration (FTMR) is an effective method of preserving high-moisture byproducts with higher aerobic stability after fermentation. FTMR has the potential to fulfill the daily nutritional requirements of cattle and enhance their production performance. The objective of this research was to examine the influence of FTMR on lactation performance, total tract apparent digestibility, fecal microbiota communities, and fermentation profiles in lactating dairy cows. A total of 12 cows were randomly assigned into two groups: the TMR group and the FTMR group. The TMR group was fed a total mixed ration (TMR) diet, and the FTMR group was fed an FTMR diet. The FTMR did not impact milk yield in dairy cows despite a decrease in dry matter intake, which increased the efficiency of the feed. In contrast to that in the TMR group, the milk fat content in the FTMR group was greater. The FTMR group showed greater digestibility of neutral detergent fiber (NDF), organic matter (OM), dry matter (DM), crude protein (CP), and acid detergent fiber (ADF) in the total digestive tract than did the TMR group. The FTMR increased the concentration of butyrate in the fecal matter and reduced the pH of the feces. The Chao1, ACE, and Shannon indices of the archaeal community in dairy cow feces were significantly higher in cow fed the FTMR compared to those fed the TMR. LefSe analysis revealed higher levels of Oscillospira, Lactobacillus, Prevotella, and Dehalobacterium in the feces of dairy cows fed the FTMR than in those fed the TMR. However, the abundances of Roseburia, rc4-4, Bulleidia and Sharpea exhibited the opposite trend. The abundances of Halobacteria, Halobacteriales, and Halobacteriaceae, which are biomarkers for distinguishing fecal archaea in the TMR from the FTMR, were substantially greater in the feces of dairy cows that consumed the TMR than in those that consumed the FTMR. Therefore, FTMR can improve the milk fat content, total tract apparent feed digestibility efficiency, and diversity of archaea in the feces. Additionally, this work provides a theoretical basis for the feasibility of FTMR feeding for dairy cows.

Effect of Different Slow-Release Urea on the Production Performance, Rumen Fermentation, and Blood Parameter of Angus Heifer

This study investigated the effect of replacing part of the dietary soybean meal with either polymer-coated urea or gelatinized starch urea on the production performance, blood indexes, and ruminal fermentation of Angus heifers. A total of 210 purebred Angus cattle (BW = 314.26 kg) were divided into three groups: the no urea group (CON), the polymer-coated urea group (PCU), and the gelatinized starch urea group (GSU); 20 g/kg polymer-coated urea or 25 g/kg gelatinized starch urea was used to replace part of soybean meal in the concentrate feed, according to the principle of isometabolic energy and isonitrogenous. The result showed that the PCU group had higher ADG and ADF apparent digestibility, while it had a lower feed-weight ratio. On the 86th day, the serum albumin (ALB) content in the PCU group was significantly higher than that in the CON group. In rumen, compared with the CON group, the contents of acetic acid and total volatile fatty acid were significantly higher in the PCU group, whereas butyric acid and propionic acid were significantly higher in the PCU group and GSU group. Ruminal bacterial diversity analysis found that the abundance of Firmicutes was higher in the PCU group at the phylum level, and an inverse result was observed in Bacteroidetes. The abundance of Paraprevotella was higher in the PCU group, whereas higher abundance of Prevotella was found in the GSU group at the genus level. These results indicate that slow-release urea can replace part of soybean meal in the diet, and the amount of substitution in this trial had no diverse effect on the performance of Angus heifers.

Potential Role of Lauric Acid in Milk Fat Synthesis in Chinese Holstein Cows Based on Integrated Analysis of Ruminal Microbiome and Metabolome

The composition and metabolic profile of the ruminal microbiome have an impact on milk composition. To unravel the ruminal microbiome and metabolome affecting milk fat synthesis in dairy cows, 16S rRNA and internal transcribed spacer (ITS) gene sequencing, as well as ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) methods were used to investigate the significant differences in ruminal bacterial and fungal communities as well as metabolome among Chinese Holstein cows with contrasting milk fat contents under the same diet (H-MF 5.82 ± 0.41% vs. L-MF 3.60 ± 0.12%). Another objective was to culture bovine mammary epithelial cells (BMECs) to assess the effect of metabolites on lipid metabolism. Results showed that the acetate-to-propionate ratio and xylanase activity in ruminal fluid were both higher in H-MF. Microbiome sequencing identified 10 types of bacteria and four types of fungi differently abundant at the genus level. Metabolomics analysis indicated 11 different ruminal metabolites between the two groups, the majority of which were lipids and organic acids. Among these, lauric acid (LA) was enriched in fatty acid biosynthesis with its concentration in milk fat of H-MF cows being greater (217 vs. 156 mg per 100 g milk), thus, it was selected for an in vitro study with BMECs. Exogenous LA led to a marked increase in intracellular triglyceride (TG) content and lipid droplet formation, and it upregulated the mRNA abundance of fatty acid uptake and activation (CD36 and ACSL1), TG synthesis (DGAT1, DGAT2 and GPAM), and transcriptional regulation (SREBP1) genes. Taken together, the greater relative abundance of xylan-fermenting bacteria and fungi, and lower abundance of bacteria suppressing short-chain fatty acid-producing bacteria or participating in fatty acid hydrogenation altered lipids and organic acids in the rumen of dairy cows. In BMECs, LA altered the expression of genes involved in lipid metabolism in mammary cells, ultimately promoting milk fat synthesis. Thus, it appears that this fatty acid plays a key role in milk fat synthesis.

Alfalfa supplementation timing changes the rumen archaeal and fungal community composition and colonization in pre-weaning lambs

The establishment of the rumen microbiota plays an important role in the rumen development. However, little is known about the effects of alfalfa supplementation time on rumen microbiota establishment. Here, a total of 42 Hu lambs, seven-day-old, were chosen for the study. After a week of adjustment, six lambs were sacrificed to establish a baseline. The remaining 36 lambs were randomly split into two groups: one receiving alfalfa hay at 14 days (EAF), the other at 42 days (LAF), both groups received milk replacer and starter pellets. Introducing alfalfa at 14 days of age significantly improved total dry matter intake between 28 and 42 days (p = 0.04) and average daily gain from both 14 to 28 days (p = 0.04) and 28 to 42 days (p < 0.01), but this effect disappears from 56 to 70 days (p > 0.05). At 42 days, the abundances of Naganishia, Ascochyta, and Neosetophoma in the EAF group were significantly higher (p < 0.05) than those in the LAF group (17.8% vs. 3.97, 10.89% vs. 1.77, and 1.27% vs. 0.09%, respectively). At 56 days, the abundances of Ascochyta, Wallemia, and Aspergillus in the EAF group were significantly lower (p < 0.05) than in the LAF group (3.53% vs. 16.40, 8.78% vs. 18.89, and 2.14% vs. 4.69%). At 70 days, Aspergillus abundance in the EAF group was significantly higher (p < 0.05) than in the LAF group (2.69% vs. 0.85%). The LEfSe analysis showed that Methanobrevibacter_smithii was the archaeal biomarker at 14 days in both groups. Methanobrevibacter_sp_AbM4 was enriched at 56 days in the LAF group. Compared to the LAF group, the specific fungal biomarkers in the EAF group included Sporobolomyces and Bullera at 14 days, Naganishia, Didymella, Cleistothelebolus, and Alloleptosphaeria at 42 days, Ascochyta, Neoascochyta, and Alfaria at 70 days. Correlation analysis results showed strong patterns of association both within and between archaea and fungi, which were influenced by alfalfa supplementation time. In summary, alfalfa supplementation at 14 days of age promotes the growth performance of lambs before weaning, and alfalfa supplementation timing significantly affects rumen archaeal and fungal communities and dynamical changes.

Comparison of ruminal microbiota, IL-1β gene variation, and tick incidence between Holstein × Gyr and Holstein heifers in grazing system

Introduction

The variation in bacterial communities among breeds has been previously reported and may be one of the reasons why Holstein × Gyr dairy heifers have better development in grazing systems in tropical conditions. This study aimed to explore the ruminal microbiota composition, the IL-1β gene variation, tick incidence, and blood parameters of Holstein × Gyr (½ Holstein × ½ Gyr) and Holstein heifers grazing intensely managed Guinea grass (Panicum maximum Jacq. cv. Mombaça).

Methods

Sixteen heifers were divided into two groups consisting of 8 Holstein × Gyr and 8 Holstein heifers. The experimental period was comprised of 3 periods of 21 days. Ruminal samples were taken via the stomach tube technique. The sequencing of the V4 hypervariable region of the 16S rRNA gene was performed using the Illumina MiSeq platform. Counting and collection of ticks were conducted each 21 days. Blood and skeletal muscle tissue biopsies were performed at the end of the experiment.

Results

Firmicutes were the most abundant phyla present in both breed rumen samples and Bacteroidota showed differences in relative abundance between breed groups, with greater values for Holstein heifers (p < 0.05 with FDR correction). The 10 most abundant unique OTUs identified in each breed included several OTUs of the genus Prevotella. Holstein heifers had a greater tick count and weight (9.8 ticks/animal and 1.6 g/animal, respectively) than Holstein × Gyr (2.56 ticks/animal and 0.4 g/animal, respectively). We found nucleotide substitutions in the IL-1β gene that might be related to adaptation and resistance phenotypes to tick infestation in Holstein × Gyr heifers. Blood concentrations of urea, albumin, insulin-like growth factor 1, triiodothyronine, and thyroxine were greater in Holstein × Gyr than in Holstein heifers.

Conclusion

Adaptations in Holstein × Gyr heifers such as ruminal microbiota, tick resistance, nucleotide substitutions in IL-1β gene, and hormone concentration suggest a better energy metabolism and thermoregulation resulting in better performance in tropical grazing systems.

Yeoman C, Grace S, Borgogna JLC, Foote AP, Nagy YI, Kashef MT, Yassin AS, Elshahed MS, Youssef NH. Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores

The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces, NY9, and Piromyces) were present at >4% relative abundance. AGF diversity was higher in members of the families Antilocapridae and Cervidae compared to Bovidae. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%-19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (n = 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera Neocallimastix and Orpinomyces were present in higher abundance in rumen samples, while Cyllamyces and Caecomyces were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.IMPORTANCERuminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum Neocallimastigomycota. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (n = 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (Neocallimastix and Orpinomyces) present in higher abundance in rumen samples, and two others (Cyllamyces and Caecomyces) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.

Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon

Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.

Characterization of the ruminal microbiota in sheep and goats fed different levels of tannin-rich Sericea lespedeza hay

Understanding ruminal microbiota and diet-host breed interactions under forage feeding conditions is essential for optimizing rumen fermentation and improving feed efficiency in small ruminants. This study aimed to investigate the effects of different ratios of condensed tannin-rich Sericea lespedeza (SL; Lespedeza cuneata) in the diets on changes and interactions of ruminal microbiota and host species (i.e., sheep and goats). Katahdin sheep (n = 12) and Alpine goats (n = 12) at approximately 10 to 12 mo of age were blocked by body weight (BW = 30.3 and 25.5 kg, respectively) and randomly assigned to one of the 3 treatments. Diets contained 75% coarsely ground forage and 25% concentrate. The forages were 1) 100% alfalfa hay (AL), 2) 100% SL, and 3) 50% AL + 50% SL (ASL). In the present study, the diversity and composition of ruminal microbiota differed between sheep and goats fed similar diets. Based on the taxonomic analysis, there was a distinct clustering pattern (P < 0.05) for sheep by diets, but such a pattern was not observed for goats (P > 0.1). The most predominant phyla were Firmicutes, Bacteroidetes, Ascomycota, and methanogen species of Methanobrevibactor sp. in the rumen of sheep and goats, regardless of diets. The Bacteroidetes and Ascomycota were enriched in sheep fed AL and ASL. In contrast, these microbial phyla were enhanced in goats fed tannin-rich SL diets, with the diet-by-host species interaction (P < 0.02) for the Bacteroidetes phylum. Sheep rumen fluid samples showed a higher degree of variability in microbial community composition compared to goat rumen fluid samples. The relative proportion of the Aspergillus fungi population was reduced to 90.7% in the SL group compared with the AL group, regardless of host species. The antimicrobial activity of tannins and greater sensitivities of selected microbiota species to these tannin compounds during SL feeding in sheep and goats perhaps caused this difference. The results from this study suggest that differences in the microbiota were associated with differences in diets and host species. Therefore, this study provides a better understanding of ruminal microbiota and diet-host species interactions under various tannin-rich diets, which could advance consolidative information on rumen microbiome community diversity changes and may improve sheep and goat production.

Forage lignocellulose is an important factor in driving the seasonal dynamics of rumen anaerobic fungi in grazing yak and cattle

Anaerobic fungi (AF) inhabit the gastrointestinal tract of ruminants and play an important role in the degradation of fiber feed. However, limited knowledge is available on seasonal dynamics and inter-species differences in rumen AF community in yak and cattle under natural grazing systems. Using the random forests model, the null model, and structural equation model, we investigated the seasonal dynamics and key driving factors of fiber-associated rumen AF in grazing yak and cattle throughout the year on the Qinghai-Tibet Plateau (QTP). We found that the richness and diversity of rumen AF of grazing yak and cattle in cold season were significantly higher than those in warm season (P < 0.05). We identified 12 rumen AF genera, among which , Cyllamyces, and Orpinomyces were predominant in the rumen of both grazing yak and cattle. LEfSe and random forest analysis showed that Feramyces, Tahromyces, and Buwchfawromyces were important seasonal indicator of rumen AF in grazing yak (P < 0.05), and Caecomyces, Cyllamyces, and Piromyces in grazing cattle (P < 0.05). Null model analysis revealed that the dynamic changes of rumen AF community structure were mainly affected by deterministic factors. Notably, mantel test and structural equation model revealed that forage physical-chemical properties, including dry matter (DM), neutral detergent fiber (NDF), and hemicellulose contents (HC) were the key factors driving the seasonal variations of the rumen AF community (P < 0.05). The results revealed that forage lignocellulose was probably an important factor affecting the seasonal dynamics and inter-species differences of the rumen AF community under natural grazing conditions. IMPORTANCE The seasonal dynamics of rumen anaerobic fungi in nature grazing yak and cattle were determined during cold and warm seasons based on pasture nutritional quality and environmental data sets. The main driving factors of anaerobic fungi in yak and cattle rumen were explored by combining random forest and structural equation models. In addition, the dynamic differences in the composition of the anaerobic fungi community in the yak and cattle in different seasons were characterized. It was found that some rumen anaerobic fungi have contributed to high fiber degradation rate in yak. These novel findings improve our understanding of the association of environmental and dietary seasonal variations with anaerobic fungal community, facilitating yak adaptation to high altitude.

Exploring the temporal dynamics of rumen bacterial and fungal communities in yaks (Bos grunniens) from 5 days after birth to adulthood by full-length 16S and 18S rRNA sequencing

The rumen of ruminants is inhabited by complex and diverse microorganisms. Young animals are exposed to a variety of microorganisms from their mother and the environment, and a few colonize and survive in their digestive tracts, forming specific microflora as the young animals grow and develop. In this study, we conducted full-length sequencing of bacterial and fungal communities in the rumen of pastured yaks of different ages (from 5  days after birth to adulthood) using amplified sequencing technology. The results showed that the rumen microflora of Zhongdian yaks changed gradually from 5 to 180  days after birth and tended to stabilize at 2  years of age. The rumen of adult yaks was the most suitable for the growth and reproduction of most bacteria. Bactria diversity of the yak rumen increased gradually from 5  days after birth to adulthood. With the growth of yaks, different dominated bacteria were enriched in different groups, but Prevotella remained highly abundant in all groups. The yak rumen at 90  days of age was the most suitable for the growth and reproduction of most fungi, and 90 days of age could be a cut-off point for the distribution of fungal communities. Fungal Thelebolus was the firstly reported in yak rumen and was enriched in the yak rumen of 90  days after birth. The most abundant and balanced fungal genera were found in adult yaks, and most of them were only detected in adult yaks. Our study reported on the rumen bacterial and fungal communities of Zhongdian yaks grazed at different ages and provided insights into the dynamic changes of dominant microflora with yak growth.

Fermented Total Mixed Ration Alters Rumen Fermentation Parameters and Microbiota in Dairy Cows

This study aimed to determine changes and interactions of ruminal microbiota and chemical parameters in dairy cows fed FTMR. Twelve multiparous Holstein dairy cows (Body weight = 616 ± 13.4 kg; day in milk = 106 ± 7.55 d; and parity = 2.31 ± 0.49; mean ± standard deviation) were divided randomly into two treatments depending on the day in milk, milk production, and parity. The two treatments were: (1) total mixed ration (TMR) and (2) FTMR. Illumina MiSeq sequencing was used to explore the changes in the ruminal microbiota. The results revealed that the bacterial and fungal diversity of the FTMR group were significantly higher than the TMR group. The predominant microbiota phyla in the bacteria and fungi showed significant differences between TMR and FTMR, as follows: Verrucomicrobia (p = 0.03) and Tenericutes (p = 0.01), Ascomycota (p = 0.04) and Basidiomycota (p = 0.04). The dominant bacterial genera in the bacteria, fungi, protozoan, and archaea that showed significant differences between TMR and FTMR were Unclassified_Bacteroidales (p = 0.02), Unclassified_RFP12 (p = 0.03), Candida (p = 0.0005), Bullera (p = 0.002), Cryptococcus (p = 0.007), and Ostracodinium (p = 0.01). LefSe analysis was performed to reveal the biomarker genera of the rumen microbiota community (bacteria, fungi, protozoan, and archaea) in the TMR and FTMR were the genera Shuttleworthia, Ruminococcus, Cryptococcus, Mycosphaerella, Bullera, Candida, and Ostracodinium. NH3-N concentration (p < 0.0001), total VFA concentration (p = 0.003), and molar proportion in total VFA of acetate (p = 0.01) were higher for the cows fed FTMR compared with the cows fed the TMR. Several bacterial genera showed significant correlations with rumen fermentation parameters. The genus Unclassified_Bacteroidales and Bullera were positively correlated with total volatile fatty acids (VFA) and acetate, whereas Candida and Ostracodinium showed negative correlations. Meanwhile, propionate was positively correlated with Candida and negatively correlated with Bullera. The PICRUSt functional profile prediction indicated that the xenobiotics biodegradation and metabolism, the lipid, amino acid, terpenoids, and polyketides metabolisms of the FTMR group were significantly higher than that of the TMR group. The results imply that FTMR can increase lipid and amino acid metabolism, and modulate the rumen microbiome and improve ruminal fermentation.

Characterization of the Dynamic Changes of Ruminal Microbiota Colonizing Citrus Pomace Waste during Rumen Incubation for Volatile Fatty Acid Production

Rumen microorganisms are promising for efficient bioconversion of lignocellulosic wastes to biofuels and industrially relevant products. Investigating the dynamic changes of the rumen microbial community colonizing citrus pomace (CtP) will advance our understanding of the utilization of citrus processing waste by rumen fluid. Citrus pomace in nylon bags was incubated in the rumen of three ruminally cannulated Holstein cows for 1, 2, 4, 8, 12, 24, and 48 h. Results showed that total volatile fatty acids concentrations and proportions of valerate and isovalerate were increased over time during the first 12 h. Three major cellulose enzymes attached to CtP rose initially and then decreased during the 48-h incubation. Primary colonization happened during the initial hours of CtP incubation, and microbes compete to attach CtP for degrading easily digestible components and/or utilizing the waste. The 16S rRNA gene sequencing data revealed the diversity and structure of microbiota adhered to CtP were distinctly different at each time point. The increased abundance of Fibrobacterota, Rikenellaceae_RC9_gut_group, and Butyrivibrio may explain the elevated volatile fatty acids concentrations. This study highlighted key metabolically active microbial taxa colonizing citrus pomace in a 48-h in situ rumen incubation, which could have implications for promoting the biotechnological process of CtP. IMPORTANCE As a natural fermentation system, the rumen ecosystem of ruminants can efficiently degrade plant cellulose, indicating that the rumen microbiome offers an opportunity for anaerobic digestion to utilize biomass wastes containing cellulose. Knowledge of the response of the in situ microbial community to citrus pomace during anaerobic fermentation will help improve the current understanding of citrus biomass waste utilization. Our results demonstrated that a highly diverse rumen bacterial community colonized citrus pomace rapidly and continuously changed during a 48-h incubation period. These findings may provide a deep understanding of constructing, manipulating, and enriching rumen microorganisms to improve the anaerobic fermentation efficiency of citrus pomace.

Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study

The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH₄ produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH₄ emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH₄ emission.

Dynamic changes in the yak rumen eukaryotic community and metabolome characteristics in response to feed type

With diversification of yak breeding, it is important to understand the effects of feed type on the rumen, especially microbiota and metabolites. Due to the unique characteristics of yak, research on rumen microbes and metabolites is limited. In this study, the effects of two diet types on rumen eukaryotic microflora and metabolites were evaluated using the Illumina MiSeq platform and liquid chromatography-mass spectrometry (LC-MS). All identified protozoa belonged to Trichostomatia. At the genus level, the relative abundance of Metadinium and Eudiplodinium were significantly (p < 0.05) higher in the roughage group than that of concentrate group, while the concentrate group harbored more Isotricha. Ascomycota, Basidiomycota, and Neocallimastigomycota were the main fungal phyla, and the Wallemia, Chordomyces, Chrysosporium, Cladosporium, Scopulariopsis, and Acremonium genera were significantly (p < 0.05) more abundant in the roughage group than the concentrate group, while the concentrate group harbored more Aspergillus, Neocallimastix, Thermoascus, and Cystofilobasidium (p < 0.05). Metabolomics analysis showed that feed type significantly affected the metabolites of rumen protein digestion and absorption (L-proline, L-phenylalanine, L-tryosine, L-leucine, L-tryptophan, and β-alanine), purine metabolism (hypoxanthine, xanthine, guanine, guanosine, adenosine, and adenine), and other metabolic pathway. Correlation analysis revealed extensive associations between differential microorganisms and important metabolites. The results provide a basis for comprehensively understanding the effects of feed types on rumen microorganisms and metabolites of yaks. The findings also provide a reference and new directions for future research.

The association of hyperketonemia with fecal and rumen microbiota at time of diagnosis in a case-control cohort of early lactation cows

BACKGROUND

Many dairy cows experience a state of energy deficit as they transition from late gestation to early lactation. The aims of this study were to 1) determine if the development of hyperketonemia in early lactation dairy cows is indicated by their gut microbiome, and 2) to identify microbial features which may inform health status. We conducted a prospective nested case-control study in which cows were enrolled 14 to 7 days before calving and followed through their first 14 days in milk (DIM). Hyperketonemic cows (HYK, n = 10) were classified based on a blood β-hydroxybutyrate (BHB) concentration 1.2 mmol/L within their first 14 DIM. For each HYK cow, two non-HYK (CON, n = 20) cows were matched by parity and 3 DIM, with BHB < 1.2 mmol/L. Daily blood BHB measures were used to confirm CON cows maintained their healthy status; some CON cows displayed BHB 1.2 mmol/L after matching and these cows were reclassified as control-HYK (C-HYK, n = 9). Rumen and fecal samples were collected on the day of diagnosis or matching and subjected to 16S rRNA profiling.

RESULTS

No differences in taxa abundance, or alpha and beta diversity, were observed among CON, C-HYK, and HYK health groups for fecal microbiomes. Similar microbiome composition based on beta diversity analysis was detected for all health statuses, however the rumen microbiome of CON and HYK cows were found to be significantly different. Interestingly, highly similar microbiome composition was observed among C-HYK cow rumen and fecal microbiomes, suggesting that these individual animals which initially appear healthy with late onset of hyperketonemia were highly similar to each other. These C-HYK cows had significantly lower abundance of Ruminococcus 2 in their rumen microbiome compared to CON and HYK groups. Multinomial regressions used to compute log-fold changes in microbial abundance relative to health status were not found to have predictive value, therefore were not useful to identify the role of certain microbial features in predicting health status.

CONCLUSIONS

Lower relative abundance of Ruminococcus 2 in C-HYK cow rumens was observed, suggesting these cows may be less efficient at degrading cellulose although the mechanistic role of Ruminococcus spp. in rumen metabolism is not completely understood. Substantial differences in fecal or rumen microbiomes among cows experiencing different levels of energy deficit were not observed, suggesting that hyperketonemia may not be greatly influenced by gut microbial composition, and vice versa. Further studies using higher resolution -omics approaches like meta-transcriptomics or meta-proteomics are needed to decipher the exact mechanisms at play.

The physiological dissimilarities of Holstein dairy cows with different milk yields

BACKGROUND

Even if breed, parity, dietary and environmental management are same, dairy cows still have notable differences in milk yield that may be underpinned by physiologic differences.

OBJECTIVES

This study aimed to investigate the physiological dissimilarities of dairy cows with different milk yields.

METHODS

Thirty cows were sorted into high milk-yielding cows (group H: 58.93±2.31 kg/day), moderate milk-yielding cows (group M: 44.99±0.54 kg/day), and low milk-yielding cows (group L: 24.99±6.83 kg/day) according to milk yield. Blood was collected and serum parameters were assessed. Rumen fluid was collected for the evaluation of rumen fermentation parameters (RFPs) and bacterial community composition (BCC).

RESULTS

Serum prolactin, growth hormone, glutathione peroxidase, immunoglobulin A and non-esterified fatty acid had a significantly positive correlation with milk yield (p < 0.05), whereas serum glucagon and total antioxidant capacity had a significantly negative correlation with milk yield (p < 0.05). The concentration of valeric acid and the ratio of acetic acid to propionic acid in the rumen fluid in group H was significantly lower than that in group L (p < 0.05). The concentration of acetic acid and butyric acid in group H was significantly lower than that in groups M and L (p < 0.05). The relative abundances of Ruminococcaceae_NK4A214_group, Prevotella_1, Rikenellaceae_RC9_gut_group, Christensenellaceae_R-7_group, Muribaculaceae, and Ruminococcus_2 were negatively correlated with milk yield, whereas the relative abundance of Succinivibrionaceae_UCG-001, Lachnospiraceae_NK3A20_group, Shuttleworthia and Dialister were positively correlated with milk yield (p < 0.05).

CONCLUSIONS

This study indicates that dairy cows with different milk yields have clear divergence in serum indicators, RFPs, BCC and rumen microbial metabolism.

Rumen microbiota of indigenous and introduced ruminants and their adaptation to the Qinghai-Tibetan plateau

The grassland in the Qinghai-Tibetan plateau provide habitat for many indigenous and introduced ruminants which perform important ecological functions that impact the whole Qinghai-Tibetan plateau ecosystem. These indigenous Tibetan ruminants have evolved several adaptive traits to withstand the severe environmental conditions, especially cold, low oxygen partial pressure, high altitude, strong UV radiation, and poor forage availability on the alpine rangelands. Despite the challenges to husbandry associated with the need for enhanced adaptation, several domesticated ruminants have also been successfully introduced to the alpine pasture regions to survive in the harsh environment. For ruminants, these challenging conditions affect not only the host, but also their commensal microbiota, especially the diversity and composition of the rumen microbiota; multiple studies have described tripartite interactions among host-environment-rumen microbiota. Thus, there are significant benefits to understanding the role of rumen microbiota in the indigenous and introduced ruminants of the Qinghai-Tibetan plateau, which has co-evolved with the host to ensure the availability of specific metabolic functions required for host survival, health, growth, and development. In this report, we systemically reviewed the dynamics of rumen microbiota in both indigenous and introduced ruminants (including gut microbiota of wild ruminants) as well as their structure, functions, and interactions with changing environmental conditions, especially low food availability, that enable survival at high altitudes. We summarized that three predominant driving factors including increased VFA production, enhanced fiber degradation, and lower methane production as indicators of higher efficiency energy harvest and nutrient utilization by microbiota that can sustain the host during nutrient deficit. These cumulative studies suggested alteration of rumen microbiota structure and functional taxa with genes that encode cellulolytic enzymes to potentially enhance nutrient and energy harvesting in response to low quality and quantity forage and cold environment. Future progress toward understanding ruminant adaptation to high altitudes will require the integration of phenotypic data with multi-omics analyses to identify host-microbiota co-evolutionary adaptations enabling survival on the Qinghai-Tibetan plateau.

Effects of capsicum oleoresin supplementation on rumen fermentation and microbial abundance under different temperature and dietary conditions in vitro

This study aimed to determine the effect of capsicum oleoresin (CAP) on rumen fermentation and microbial abundance under different temperature and dietary conditions in vitro. The experimental design was arranged in a 2 × 2 × 3 factorial format together with two temperatures (normal: 39°C; hyperthermal: 42°C), two forage/concentrate ratios (30:70; 70:30), and two CAP concentrations in the incubation fluid at 20 and 200 mg/L with a control group. Regarding the fermentation characteristics, high temperature reduced short-chain fatty acids (SCFA) production except for molar percentages of butyrate while increasing acetate-to-propionate ratio and ammonia concentration. The diets increased total SCFA, propionate, and ammonia concentrations while decreasing acetate percentage and acetate-to-propionate ratio. CAP reduced acetate percentage and acetate-to-propionate ratio. Under hyperthermal condition, CAP could reduce acetate percentage and increase acetate-to-propionate ratio, lessening the negative effect of high heat on SCFA. Hyperthermal condition and diet altered the relative abundance of microbial abundance in cellulose-degrading bacteria. CAP showed little effect on the microbial abundance which only increased Butyrivibrio fibrisolvens. Thus, CAP could improve rumen fermentation under different conditions, with plasticity in response to the ramp of different temperature and dietary conditions, although hardly affecting rumen microbial abundance.

Age-dependent variations in rumen bacterial community of Mongolian cattle from weaning to adulthood

BACKGROUND

Rumen microbes play an important role in ruminant energy supply and animal performance. Previous studies showed that the rumen microbiome of Mongolian cattle has adapted to degrade the rough forage to provide sufficient energy to tolerate the harsh desert ecological conditions. However, little is known about the succession of rumen microbes in different developmental stages of post-weaning Mongolian cattle.

METHODS

Here, we examined the succession of the rumen microbial composition and structure of 15 post-weaning Mongolian cattle at three developmental stages i.e., 5 months (RM05), 18 months (RM18) and, 36 months (RM36) by using the 16S rRNA gene sequencing method.

RESULTS

We did not find any age-dependent variations in the ruminal concentrations of any volatile fatty acid (VFA) of Mongolian cattle. The diversity of the rumen bacterial community was significantly lower in RM05 group, which reached to stability with age. Bacteroidetes and Firmicutes were the two dominant phyla among all age groups. Phylum Actinobacteria was significantly higher in RM05 group, phyla Spirochaetes, and Tenericutes were highly abundant in RM18 group, and phyla Proteobacteria and Epsilonbacteraeota were enriched in RM36 group. Genera Prevotella_1, Bacteroides, and Bifidobacterium were abundant in RM05 group. The short chain fatty acid (SCFA) producing bacteria Rikenellaceae_RC9_gut_group showed high abundance in RM18 group and fiber degrading genus Alloprevotella was highly abundant in RM36 group. Random forest analysis identified Alloprevotella, Ileibacterium, and Helicobacter as important age discriminatory genera. In particular, the genera Ruminococcaceae_UCG-005, Bacteroides, Saccharofermentans, and Fibrobacter in RM05, genera [Eubacterium] coprostanoligenes_group, Erysipelotrichaceae_UCG-004, Helicobacter, Saccharofermentans, Papillibacter, and Turicibacter in RM18, and genera Rikenellaceae_RC9_gut_group, Lachnospiraceae_AC2044_group, and Papillibacter in RM36 showed the top interactions values in the intra-group interaction network.

CONCLUSIONS

The results showed that rumen microbiota of Mongolian cattle reached to stability and maturity with age after weaning. This study provides some theoretical evidence about the importance of functional specific rumen bacteria in different age groups. Further studies are needed to determine their actual roles and interactions with the host.

An Age Effect of Rumen Microbiome in Dairy Buffaloes Revealed by Metagenomics

Age is an important factor in shaping the gut microbiome. However, the age effect on the rumen microbial community for dairy buffaloes remains less explored. Using metagenomics, we examined the microbial composition and functions of rumen microbiota in dairy Murrah buffaloes of different ages: Y (1 year old), M (3−5 years old), E (6−8 years old), and O (>9 years old). We found that Bacteroidetes and Firmicutes were the predominant phyla, with Prevotella accounting for the highest abundance at the genus level. The proportion of Bacteroides and Methanobrevibacter significantly increased with age, while the abundance of genus Lactobacillus significantly decreased with age (LDA > 3, p < 0.05). Most differed COG and KEGG pathways were enriched in Y with carbohydrate metabolism, while older buffaloes enriched more functions of protein metabolism and the processing of replication and repair (LDA > 2, p < 0.05). Additionally, the functional contribution analysis revealed that the genera Prevotella and Lactobacillus of Y with more functions of CAZymes encoded genes of glycoside hydrolases and carbohydrate esterases for their roles of capable of metabolizing starch and sucrose-associated oligosaccharide enzyme, hemicellulase, and cellulase activities than the other three groups (LDA > 2, p < 0.05), thus affecting the 1-year-old dairy buffalo rumen carbohydrate metabolism. This study provides comprehensive dairy buffalo rumen metagenome data and assists in manipulating the rumen microbiome for improved dairy buffalo production.

Longitudinal Changes of the Ruminal Microbiota in Angus Beef Steers

The ruminal microbiota of Angus cows and steers were characterized using 16s rRNA gene sequencing, and the expression of their metabolic pathways was predicted. Samples were collected on weaning day from the steers and the cows, and subsequently on three other occasions from the steers. Results showed that microbial richness, evenness, and diversity decreased (p < 0.001) in the rumen of the steers as they were weaned and transitioned to a high-concentrate feedlot diet. However, on the day of weaning, microbial evenness was similar to that observed in the rumen of cows (p = 0.12). The abundance of archaea was similar (p = 0.59) between the cows and steers at weaning, but it decreased (p = 0.04) in the rumen of steers after weaning, and remained stable (p ≥ 0.44) for the remainder of their lives. Likewise, no difference (p = 0.51) in the abundance of Bacteroidetes was detected between the cows and the calves on the day they were weaned, but the abundance of this phylum increased (p = 0.001) and remained stable after that. These results suggest that cows may have a strong influence on the composition, and help modulate the ruminal microbiota of young calves; however, following weaning, their ruminal microbiotas tend to differentiate from that state observed at earlier ages.

The Remodeling Effects of High-Concentrate Diets on Microbial Composition and Function in the Hindgut of Dairy Cows

At present, research on high-concentrate (HC) diets mostly focused on the rumen, and there is a paucity of information on the hindgut microbiota of dairy cows. In the present study, a 2 × 2 crossover design with four healthy Holstein cows was used, and the metagenomics approach was adopted to reveal the remodeling effects of HC diets on hindgut microbiota and their metabolic functions. Results showed that, compared with the low-concentrate (LC) diets, HC diets have markedly decreased (p < 0.05) the abundance of cellulolytic bacteria (such as Fibrobacter, Ruminococcus, and Ruminiclostridium) and methanogens (such as Methanobrevibacter, Methanosarcina, and Methanosphaera); and correspondingly, HC diets have significantly reduced (p < 0.05) the abundance of carbohydrate-active enzymes (CAZy) related to hemicellulases (GH10, GH11, and GH54) and cellulases (GH1, GH44, and GH45) and increased the abundance of one oligosaccharide-degrading enzyme (GH32). Furthermore, 62 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of hindgut microbiota were affected (p < 0.05) by different dietary treatments, and the major pathways altered by HC diets were “Methane metabolism” (enriched in the LC group), “Lipid metabolism” (enriched in the HC group), and several sub-pathways in “Amino acid metabolism” (such as Phenylalanine metabolism, and Phenylalanine, tyrosine, and tryptophan biosynthesis). Also, the microbial genes involved in the pathways “Methane metabolism” (except 1 gene), “Tryptophan metabolism”, and “Phenylalanine metabolism” were all decreased (p < 0.05) in the present study. These findings suggested that HC diets caused the remodeling of hindgut microbiota and its potential functions, and these results may benefit in gaining a deeper understanding of the impact of HC diets on the hindgut microbiota of dairy cows.

Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

How Divergence for Feed Efficiency Traits Affects Body Measurements and Metabolites in Blood and Ruminal Parameters on Pre-Weaning Dairy Heifers

The objectives of this study were: (1) to evaluate feed efficiency indexes and their relationships with body measurements and blood and ruminal metabolites in the pre-weaning period; (2) to determine if such measurements can be used as feed-efficiency markers during the pre-weaning period. Holstein-Gyr heifer calves (n = 36), enrolled between 4 and 12 weeks of age, were classified into two residual feed intake (RFI) and residual body weight gain (RG) groups: high efficiency (HE; RFI, n = 10; and RG, n = 9), and low efficiency (LE; RFI, n = 10; and RG, n = 8). Calves were fed whole milk (6 L/day) and solid feed ad libitum. Body developments were measured weekly and feed intake (milk and solid feed) daily during the whole period. Blood samples were collected at 12 weeks of age and analyzed for glucose, insulin and β-hydroxybutyrate (BHB). Samples of ruminal content were collected on the same day and analyzed for pH, NH₃-N, and volatile fatty acids (VFA). Among the growth characteristics, only the initial hip width differed between the RFI groups, and withers height differed between the RG groups. Concentration of BHB was greater and glucose: insulin ratios tended to be greater in LE-RG animals. Butyric acid proportions were similar among RFI groups, but tended to be greater for HE-RG than for LE-RG. Overall, correlation coefficients between RFI or RG and blood, rumen, or morphometric markers were low. Thus, it is unlikely that measurements of metabolic indicators, per se, will be useful in the early identification of more efficient animals. Understanding the underlying physiological basis for improved feed efficiency in dairy heifers requires further investigation.

Investigating the Reciprocal Interrelationships among the Ruminal Microbiota, Metabolome, and Mastitis in Early Lactating Holstein Dairy Cows

Simple Summary

Dairy cow mastitis is an inflammatory disease often caused by bacterial infections. In the present study, we identified the ruminal microbial biomarkers and metabolites of mastitis in dairy cows. The investigation of the reciprocal interrelationships among the ruminal microbiota, metabolome, and mastitis revealed that short-chain fatty acid (SCFA)-producing microflora and the metabolites related to anti-inflammation and antibacterial activity were significantly higher in healthy cows than in those with mastitis. The identified potential species and metabolites might provide a novel perspective to assist in targeting the ruminal microbiota with preventive/therapeutic strategies against mastitis in the future.

Abstract

Mastitis in dairy cow significantly affects animal performance, ultimately reducing profitability. The reciprocal interrelationships among ruminal microbiota, metabolome, and mastitis combining early inflammatory factors (serum proinflammatory cytokines) in lactating dairy cows has not been explored, thus, this study evaluated these reciprocal interrelationships in early lactating Holstein dairy cows to identify potential microbial biomarkers and their relationship with ruminal metabolites. The ruminal fluid was sampled from 8 healthy and 8 mastitis cows for the microbiota and metabolite analyses. The critical ruminal microbial biomarkers and metabolites related to somatic cell counts (SCC) and serum proinflammatory cytokines were identified by the linear discriminant analysis effect size (LEfSe) algorithm and Spearman’s correlation analysis, respectively. The SCC level and proinflammatory cytokines positively correlated with Sharpea and negatively correlated with Ruminococcaceae UCG-014, Ruminococcus flavefaciens, and Treponema saccharophilum. Furthermore, the metabolites xanthurenic acid, and 1-(1H-benzo[d]imidazol-2-yl) ethan-1-ol positively correlated with microbial biomarkers of healthy cows, whereas, xanthine, pantothenic acid, and anacardic acid were negatively correlated with the microbial biomarkers of mastitis cows. In conclusion, Ruminococcus flavefaciens and Treponema saccharophilum are potential strains for improving the health of dairy cows. The current study provides a novel perspective to assist in targeting the ruminal microbiota with preventive/therapeutic strategies against inflammatory diseases in the future.

Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion

Microbial consortia efficiently degrade complex biopolymers found in the organic fraction of municipal solid waste (OFMSW). Through enzyme production and division of labor during anaerobic digestion, microbial communities break down recalcitrant polymers and make fermentation products, including methane. However, microbial communities remain underutilized for waste degradation as it remains difficult to characterize and predict microbial interactions during waste breakdown, especially as cultivation conditions change drastically throughout anaerobic digestion. This review discusses recent progress and opportunities in cultivating natural and engineered consortia for OFMSW hydrolysis, including how recalcitrant substrates are degraded by enzymes as well as the critical factors that govern microbial interactions and culture stability. Methods to measure substrate degradation are also reviewed, and we demonstrate the need for increased standardization to enable comparisons across different environments.

Effects of Age, Diet CP, NDF, EE, and Starch on the Rumen Bacteria Community and Function in Dairy Cattle

To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. Rumen fermentation profile, enzyme activity, and bacteria community in rumen fluid were measured. The acetate to propionate ratio (A/P) at M9, M18, and M23 was higher than other ages, and M6 was the lowest (p < 0.05). The total volatile fatty acid (TVFA) at M23 and M27 was higher than at other ages (p < 0.05). The urease at M18 was lower than at M1.5, M6, and M9, and the xylanase at M18 was higher than at M1.5, M23, and M27 (p < 0.05). Thirty-three bacteria were identified as biomarkers of the different groups based on the linear discriminant analysis (LDA) when the LDA score >4. The variation partitioning approach analysis showed that the age and diet had a 7.98 and 32.49% contribution to the rumen bacteria community variation, respectively. The richness of Succinivibrionaceae_UCG-002 and Fibrobacter were positive correlated with age (r > 0.60, p < 0.01) and positively correlated with TVFA and acetate (r > 0.50, p < 0.01). The Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans has a positive correlation (r > 0.80, p < 0.05) with diet fiber and a negative correlation (r < −0.80, p < 0.05) with diet protein and starch, which were also positively correlated with the acetate and A/P (r > 0.50, p < 0.01). The genera of Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans could be worked as the target bacteria to modulate the rumen fermentation by diet; meanwhile, the high age correlated bacteria such as Succinivibrionaceae_UCG-002 and Fibrobacter also should be considered when shaping the rumen function.

Addition of Activated Carbon into a Cattle Diet to Mitigate GHG Emissions and Improve Production

Globally, the most problematic greenhouse gas (GHG) emissions of ruminant livestock is methane (CH4), with a global warming potential 25 times that of carbon dioxide. This work considers the emissions and production effects of powdered activated carbon (PAC) at 0.5% by dry matter (DM) on methanogenic rumen flora as the major source of dairy cattle enteric methane emissions. In total, 180 dairy cattle located in Brymaroo, Queensland (QLD), Australia, were studied in a three-cycle repeated measures ANOVA format with a 4 week primary interval. Emissions eructated during milking and in faecal deposits were measured, and in addition, 16S rRNA gene sequencing was performed to determine the collective populations of prokaryotic bacteria and archaea as well methanogenic communities for each treatment. Moreover, 0.5% PAC addition reduced CH4 emissions by 30–40% and CO2 emissions by 10%, while improving daily milk production by 3.43%, milk protein by 2.63% and milk fat by 6.32%, on average for the herd (p < 0.001 in all cases). rRNA gene sequencing showed populations of methanogenic flora decreased by 30% on average with a corresponding increase in the nonmethanogenic species. We strongly advocate further on-farm trials with the dietary addition of PAC in ruminant diets to mitigate emissions while maintaining or improving productivity.

Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis

Simple Summary

The archaeal population, or ‘archaeome’, is comprised of unicellular microorganisms with a distinct biology compared with bacteria and has been shown to be an important component of host-associated microbes. While the impact of antimicrobial administration on gastrointestinal microbiota has been widely evaluated, no metagenomics-based analysis has been performed to assess the impact of an early life antimicrobials intervention on the fecal archaeome in swine. The aim of this study was therefore to investigate the impact of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Our results suggest that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets.

Abstract

The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.

Temporal changes in total and metabolically active ruminal methanogens in dairy cows supplemented with 3-nitrooxypropanol

The purpose of this study was to investigate the effect of 3-nitrooxypropanol (3-NOP), a potent methane inhibitor, on total and metabolically active methanogens in the rumen of dairy cows over the course of the day and over a 12-wk period. Rumen contents of 8 ruminally cannulated early-lactation dairy cows were sampled at 2, 6, and 10 h after feeding during wk 4, 8, and 12 of a randomized complete block design experiment in which 3-NOP was fed at 60 mg/kg of feed dry matter. Cows (4 fed the control and 4 fed the 3-NOP diet) were blocked based on their previous lactation milk yield or predicted milk yield. Rumen samples were extracted for microbial DNA (total) and microbial RNA (metabolically active), PCR amplified for the 16S rRNA gene of archaea, sequenced on an Illumina platform, and analyzed for archaea diversity. In addition, the 16S copy number and 3 ruminal methanogenic species were quantified using the real-time quantitative PCR assay. We detected a difference between DNA and RNA (cDNA)-based archaea communities, revealing that ruminal methanogens differ in their metabolic activities. Within DNA and cDNA components, methanogenic communities differed by sampling hour, week, and treatment. Overall, Methanobrevibacter was the dominant genus (94.3%) followed by Methanosphaera, with the latter genus having greater abundance in the cDNA component (14.5%) compared with total populations (5.5%). Methanosphaera was higher at 2 h after feeding, whereas Methanobrevibacter increased at 6 and 10 h in both groups, showing diurnal patterns among individual methanogenic lineages. Methanobrevibacter was reduced at wk 4, whereas Methanosphaera was reduced at wk 8 and 12 in cows supplemented with 3-NOP compared with control cows, suggesting differential responses among methanogens to 3-NOP. A reduction in Methanobrevibacter ruminantium in all 3-NOP samples from wk 8 was confirmed using real-time quantitative PCR. The relative abundance of individual methanogens was driven by a combination of dietary composition, dry matter intake, and hydrogen concentrations in the rumen. This study provides novel information on the effects of 3-NOP on individual methanogenic lineages, but further studies are needed to understand temporal dynamics and to validate the effects of 3-NOP on individual lineages of ruminal methanogens.

Stability Assessment of the Rumen Bacterial and Archaeal Communities in Dairy Cows Within a Single Lactation and Its Association With Host Phenotype

Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella, unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11, on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions.

Weaning Age Affects the Development of the Ruminal Bacterial and Archaeal Community in Hu Lambs During Early Life

Weaning plays an important role in many animal processes, including the development of the rumen microbiota in ruminants. Attaining a better understanding of the development of the rumen microbial community at different weaning stages can aid the identification of the optimal weaning age. We investigated the effects of weaning age on ruminal bacterial and archaeal communities in Hu lambs. Thirty male Hu lambs were randomly assigned to two weaning-age groups: a group weaned at 30 days of age (W30) and a group weaned at 45 days of age (W45), with each group having five replicate pens. On the weaning day (day 30 for W30 and day 45 for W45) and at 5 days postweaning [day 35 for W30 (PW30) and day 50 for W45 (PW45)], one lamb from each replicate was randomly selected and sacrificed. Rumen contents were collected to examine the ruminal microbiota. Compared to W30, PW30 had a decreased relative abundance of Bacteroidetes. At genus level, the extended milk replacer feeding (W45 vs. W30) increased the relative abundance of Ruminococcus while decreased that of Prevotella and Dialister. Compared to W30, PW30 exhibited decreased relative abundances of Prevotella, Dialister and Bacteroides but an increased unclassified Coriobacteriaceae. No significant difference was noted in the detected archaeal taxa among the animals. The function "biosynthesis of secondary metabolites" was less predominant in PW30 than in W30, whereas the opposite held true for "metabolism of cofactors and vitamins." Some bacterial genera were significantly correlated with rumen volatile fatty acid (VFA) concentration or other animal measures, including negative correlations between ruminal VFA concentration and unclassified Mogibacteriaceae and unclassified Veillonellaceae; positive correlations of ruminal papillae length with Fibrobacter and unclassified Lachnospiraceae, but negative correlations with Mitsuokella and Succiniclasticum; and negative correlations between plasma D-lactate concentration and Prevotella, unclassified Paraprevotellaceae, and Desulfovibrio. Our results revealed that the ruminal bacterial community underwent larger changes over time in lambs weaned at 30 days of age than in lambs weaned half a month later. Thus, extending milk replacer feeding to 45 days weaning was recommended from the perspective of the rumen microbial community in the Hu lamb industry.

The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition

The ruminal microbiota allows ruminants to utilize fibrous feeds and is in the limelight of ruminant nutrition research for many years. However, the overwhelming majority of investigations have focused on bacteria, whereas anaerobic fungi (AF) have been widely neglected by ruminant nutritionists. Anaerobic fungi are not only crucial fiber degraders but also important nutrient sources for the host. This review summarizes the current findings on AF and, most importantly, discusses their new application potentials in modern ruminant nutrition. Available data suggest AF can be applied as direct-fed microbials to enhance ruminal fiber degradation, which is indeed of interest for high-yielding dairy cows that often show depressed ruminal fibrolysis in response to high-grain feeding. Moreover, these microorganisms have relevance for the nutrient supply and reduction of methane emissions. However, to reach AF-related improvements in ruminal fiber breakdown and animal performance, obstacles in large-scale AF cultivation and applicable administration options need to be overcome. At feedstuff level, silage production may benefit from the application of fungal enzymes that cleave lignocellulosic structures and consequently enable higher energy exploitation from forages in the rumen. Concluding, AF hold several potentials in improving ruminant feeding and future research efforts are called for to harness these potentials.

Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials

Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber-degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interactions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate metabolic pathways in the fungal hydrogenosome. The ability of co-cultures of anaerobic fungi and methanogens to degrade fiber and produce methane could potentially be a valuable method for the degradation of lignocellulosic materials and methane production.

The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi

This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.

Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing

Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.

Interrelationships of Fiber-Associated Anaerobic Fungi and Bacterial Communities in the Rumen of Bloated Cattle Grazing Alfalfa

Frothy bloat is major digestive disorder of cattle grazing alfalfa pastures. Among the many factors identified to contribute to the development of frothy bloat, the disruption of rumen microbiota appears to be of central importance. Anaerobic rumen fungi (ARF) play an important role in sequential breakdown and fermentation of plant polysaccharides and promote the physical disruption of plant cell walls. In the present study, we investigated the dynamics of ARF during the development of alfalfa-induced frothy bloat and in response to bloat preventive treatments. By sequencing the internal transcribed spacer (ITS1) region of metagenomic DNA from the solid fraction of rumen contents, we were able to identify eight distinct genera of ARF, including Neocallimastix, Caecomyces, Orpinomyces, Piromyces, Cyllamyces, Anaeromyces, Buwchfawromyces, and unclassified Neocallimastigaceae. Overall, transition of steers from a baseline hay diet to alfalfa pastures was associated with drastic changes in the composition of the fungal community, but the overall composition of ARF did not differ (p > 0.05) among bloated and non-bloated steers. A correlation network analysis of the proportion of ARF and ruminal bacterial communities identified hub fungal species that were negatively correlated with several bacterial species, suggesting the presence of inter-kingdom competition among these rumen microorganisms. Interestingly, the number of negative correlations among ARF and bacteria decreased with frothy bloat, indicating a potential disruption of normal microbial profiles within a bloated rumen ecosystem. A better understanding of fungal-bacterial interactions that differ among bloated and non-bloated rumen ecosystem could advance our understanding of the etiology of frothy bloat.

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation

The anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tracts of herbivores where they play a central role in the breakdown of plant material. Here, we report on the development of the hypervariable domains D1/D2 of the large ribosomal subunit (D1/D2 LSU) as a barcoding marker for the AGF. We generated a reference D1/D2 LSU database for all cultured AGF genera, as well as the majority of candidate genera encountered in prior internal transcribed spacer 1 (ITS1)-based surveys. Subsequently, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing was conducted on faecal samples from 21 wild and domesticated herbivores. Twenty-eight genera and candidate genera were identified, including multiple novel lineages that were predominantly, but not exclusively, identified in wild herbivores. Association between certain AGF genera and animal lifestyles, or animal host family was observed. Finally, to address the current paucity of AGF isolates, concurrent isolation efforts utilizing multiple approaches to maximize recovery yielded 216 isolates belonging to 12 different genera, several of which have no prior cultured-representatives. Our results establish the utility of D1/D2 LSU and PacBio sequencing for AGF diversity surveys, the culturability of multiple AGF taxa, and demonstrate that wild herbivores represent a yet-untapped reservoir of AGF diversity.

Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions

BACKGROUND

The development and maturation of rumen microbiota across the lifetime of grazing yaks remain unexplored due to the varied lifestyles and feed types of yaks as well as the challenges of obtaining samples. In addition, the interactions among four different rumen microbial groups (bacteria, archaea, fungi and protozoa) in the rumen of yak are not well defined. In this study, the rumen microbiota of full-grazing yaks aged 7 days to 12 years old was assessed to determine the maturation patterns of these four microbial groups and the dynamic interactions among them during different growth stages.

RESULTS

The rumen microbial groups (bacteria, archaea, protozoa and fungi) varied through the growth of yaks from neonatal (7 days) to adult (12 years), and the bacterial and archaeal groups were more sensitive to changes in growth stages compared to the two eukaryotic microbial groups. The age-discriminatory taxa within each microbial group were identified with the random forest model. Among them, Olsenella (bacteria), Group 10 sp., belonging to the family Methanomassiliicoccaceae (archaea), Orpinomyces (fungi), and Dasytricha (protozoa) contributed the most to discriminating the age of the rumen microbiota. Moreover, we found that the rumen archaea reached full maturation at 5 approximately years of age, and the other microbial groups matured between 5 and 8 years of age. The intra-interactions patterns and keystone species within each microbial group were identified by network analysis, and the inter-interactions among the four microbial groups changed with growth stage. Regarding the inter-interactions among the four microbial groups, taxa from bacteria and protozoa, including Christensenellaceae R-7 group, Prevotella 1, Trichostomatia, Ruminococcaceae UCG-014 and Lachnospiraceae, were the keystone species in the network based on betweenness centrality scores.

CONCLUSIONS

This study depicted a comprehensive view of rumen microbiota changes in different growth stages of grazing yaks. The results revealed the unique microbiota maturation trajectory and the intra- and inter-interactions among bacteria, archaea, fungi and protozoa in the rumen of grazing yaks across the lifetime of yaks. The information obtained in this study is vital for the future development of strategies to manipulate rumen microbiota in grazing yaks for better growth and performance in the harsh Qinghai-Tibetan Plateau ecosystem.

Resveratrol affects in vitro rumen fermentation, methane production and prokaryotic community composition in a time- and diet-specific manner

This study aimed to investigate the effect of resveratrol on methane production, rumen fermentation and microbial composition under high-concentrate (HC) and high-forage (HF) diets using the in vitro fermentation system. A total of 25 mg of resveratrol was supplemented into 300 mg of either HC or HF diet. Methane production, total volatile fatty acid (VFA) concentration, molar proportion of VFA, metabolites of resveratrol and prokaryotic community composition were measured after 12 and 24 h of in vitro fermentation. Resveratrol reduced methane production (ml per mg of dry matter degraded) by 41% and 60% under both HC and HF diets (P < 0.001), respectively, and this result could be associated with the lower abundance of Methanobrevibacter (P < 0.001) in response to resveratrol. The molar proportion of propionate was significantly higher in the resveratrol group only under the HC diet (P = 0.045). The relative abundance of 10 bacterial genera was affected by the three-way interaction of treatment, diet and time (P < 0.05). Resveratrol was partly converted to dihydroresveratrol after 24 h of fermentation, and its degradation could be associated with microbes belonging to the order Coriobacteriales. Our results suggest that multiple factors (e.g. diet and time) should be considered in animal experiments to test the effect of polyphenol or other plant extracts on rumen fermentation, methane emission and microbial composition.