Ruminal Microbiome Research Articles

PSVI-4 Effects of exogenous fibrolytic enzymes on beef cattle fed growing diets: Ruminal microbiome

Abstract The effect of pre-treatment with fibrolytic enzymes [cellulase/xylanase (Trichoderma ressie)] of growing diets (high quality and low-quality) on ruminal microbiome relative abundance (RA) were evaluated. Ruminally cannulated beef steers (n = 5; BW = 520 ± 30 kg) were used in a 5×4 unbalanced Latin square design using a 2×2 factorial arrangement of treatments: (a) growing diet quality [high (HQ) and low (LQ)] and (b) enzyme inclusion (0 or 0.75 mL/kg of diet DM). Steers were individually fed ad libitum throughout four 21-d periods consisting of 14-d of adaptation and 7-d of collections. Ruminal fluid samples (100 mL) were collected on d-5 of each collection-period, at 6 h post feeding for DNA extraction and determination of microbial RA. Microbiome data were sequenced by Illumnia® NovaSeq™ 6000 (16S rRNA). Regardless of enzyme×diet quality interaction (P ≥ 0.11) or pre-treatment with enzyme (P ≥ 0.12), Domain RA was affected (P ≤ 0.04), in which LQ diets increased RA of Bacteria (93.25 vs. 86.80%) and decreased Archaea (6.75 vs. 13.20%). In Phylum, LQ diets decreased RA (P ≤ 0.04) of Euryarchaeota (6.75 vs. 13.21%), and increased Bacteroidetes (11.22 vs. 2.26%). Within Class, LQ diets decreased RA (P ≤ 0.04) of Clostridia (38.66 vs. 51.40%), Methanobacteria (6.75 vs. 13.21%), and increased Bacteroidia (10.62 and 1.47%). Within Order LQ diets, decreased RA (P ≤ 0.04) of Clostridiales (38.47 vs. 51.29%), Methanobacteriales (6.75 vs. 13.21%), and increased Bacteroidales (10.62 vs. 1.47%). In Family, LQ diets showed decreased RA (P ≤ 0.04) of Methanobacteriaceae (6.75 vs. 13.21%), Ruminococcaceae (6.71 vs. 2.18%), and increased Prevotellaceae (9.83 vs. 1.17%). In Genus, LQ diets showed increased RA (P ≤ 0.03) of Prevotella (9.61 vs. 1.10%). The dietary pre-treatment with fibrolytic enzymes seems to not dramatically affect RA of ruminal microbiome, while growing diet quality greatly influenced ruminal microbiome RA.

PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

388 Nutrition and the Ruminal Microbiome: Emerging Frontiers from an Old Friend

Abstract Rumen, a pregastric anaerobic gut ecosystem, inhabits arguably the most diverse and complex microbial community, with a mutualistic relationship with the host. The relationship is best exemplified in the utilization of lignocellulosic material and non-protein nitrogen to provide energy and protein to the host. The microbial community of the rumen is composed of bacteria, archaea, protozoa, fungi and bacteriophages. Culture- or microscopy-based procedures have identified over 200 species of bacteria, methanogens, ciliated protozoa and zoosporic fungi. The community analysis based on the genetic material of all microbial cells, called microbiome, has vastly expanded our understanding of the ruminal ecosystem. Microbiome analysis is based on sequencing of the targeted amplicons (16S rDNA variable regions for bacteria and archaea, 18S rDNA for protozoa or Internal Transcribed Regions for fungi) or whole genome shotgun metagenomics analysis. Rapid advancements in nucleic acid sequencing technologies and bioinformatics pipelines have provided unprecedented opportunities to delineate the diversity and complexity of the microbial community in relation ruminal function and dysfunctions and link ruminal microbes to host nutrition and productivity. Culture-independent methods have identified thousands of microbial species in the rumen, suggesting that a major fraction of the microbiome has not been cultured and functionally identified. A core microbiome in bacterial and archaeal populations of the rumen has been identified across a wide geographical regions, but significant variations in diversity, abundance, and individual taxa do exist because of diet and host genetics. However, there is evidence of signature microbiome among individual animals on the same diet and environment. Microbiome-wide association studies in relation to dietary changes, ruminal function and dysfunctions have begun to link and define the complexity of the host-microbe relationships. Translation of the potential of the microbiome analysis is supported by emerging evidences that specific microbiota can be linked to ruminal activity and productivity.

PSIX-12 Inclusion of dried distillers grains with solubles in Lespedeza or alfalfa-based diets for meat goats is associated with a unique ruminal microbiome

Abstract This study evaluated the effect of replacement of corn and soybean meal with distillers dried grains with solubles (DDGS) in lespedeza or alfalfa-based diets on the ruminal microbiome of growing meat goats. A total of 36 meat goats with average body weight (BW) of 24 ± 1.8 kg were blocked by BW and randomly assigned to four isonitrogenous (18.0) and isocaloric (3.2 Mcal/ kg DM) diets in a completely randomized design for 60 days. The treatment diets were: (1) alfalfa-based diet (ALC; containing 40.5% alfalfa, 26% corn and 13% SBM), (2) alfalfa and DDGS (ALD; replacement of corn and SBM with DDGS), (3) Sericea lespedeza (SL)-based diet (SLC; containing 47.25% SL, 20% corn, 13% SBM), (4) SL and DDGS (SLD; replacement of corn and SBM with DDGS). At the end of the experiment, the goats were slaughtered and rumen contents were immediately sampled for 16S rRNA gene sequencing. Linear discriminant analysis (LDA) effect size (LEfSe) were used to detect differentially abundant taxa among treatments. The relative abundance of 11 taxa, including Ruminococcaceae UCG 002, Succinivibrionaceae UCG 002 and Prevotellaceae YAB2003 were reduced (LDA > 2; P < 0.05) while 62 taxa, including Ruminococcaceae UCG 013, Ruminococcaceae UCG 001, and Saccharofermentans were enriched (LDA > 2; P < 0.05) in ALD compared to ALC. Relative abundance of 35 taxa, including Ruminococcus YE281, Succinivibrio, and Lachnospiraceae ND3007 were reduced while 42 taxa, including Prevotellaceae UCG 003 and Ruminococcus were enriched (LDA > 2; P < 0.05) in SLD, compared to SLC. A total of 68, 35, 61, and 91 taxa were respectively detected ALC, SLC, SLD, and ALD, but not in other treatments. These results showed that inclusion of DDGS in lespedeza or alfalfa-based diet causes a shift in ruminal microbial community and is associated with a unique ruminal microbial community

PSXII-3 Rumen microbiome from beef steers undergoing grain adaptation with steam-flaked corn varying in bulk density

Abstract The effects of steam-flaked corn bulk density during grain adaptation phase on ruminal microbiome were evaluated. Crossbred-Angus ruminally cannulated steers (n = 6; BW = 405 ± 42 kg) were assigned to a randomized complete block design (block = body weight) to 1 of 2 grain adaptation strategies: 1) steam-flaked corn (SFC) bulk density of 335 g/L; and 2) 412 g/L. Steers were ad libitum fed, individually, during 6-7d phases, consisting of: HAY, followed by the STEP-UP1 through STEP-UP4, diets, respectively, in which roughage was gradually replaced with grain until FINISHER diet was fed. Respective SFC bulk densities were fed throughout STEP-UP diets, while the FINISHER diet consisted of 335 g/L strategy only for both groups. Ruminal fluid samples (100 mL) were collected on d-5 of each step, at 6h post-feeding for DNA extraction. Microbiome data were sequenced by Illumnia® NovaSeq™ 6000 (16S rRNA). The SFC bulk density did not affect (P > 0.50) the relative abundance (RA) for any taxonomy classification. Regardless of SFC bulk density, inclusion of grain throughout adaptation phases affected domain (P ≤ 0.03) when initial phases were compared to FINISHER. Phylum RA were affected (P ≤ 0.05) for Actinobacteria (27%), Bacteroidetes (11%), and Euryarchaeota (2%). Within Class RA were affected (P ≤ 0.04) for Clostridia (46%), Actinobacteria (27%), and Bacilli (5%). Order effects on RA were observed (P ≤ 0.04) for Clostridiales (45%), Coriobacteriales (25%), and Lactobacillales (4%). Within Family RA was affected (P ≤ 0.03) for Coriobacteriaceae (25%), Lachnospiraceae (27%), Ruminococcaceae (6%), and Lactobacillaceae (4%), while a tendency (P = 0.09) was observed for Veillonellaceae (1%). In Genus, RA was affected (P ≤ 0.01) for Olsenela (22%), Pediococcus (3%), and Butyrivibrio (3%). As steers advance through subsequent grain adaptation phases until the FINISHER, more meaningful ruminal microbiome changes are observed than SFC density change.

PSVIII-13 Evaluation of the effect of chlortetracycline on ruminal microbiome of ruminant against a background of plant extract

Abstract The limited use of antibiotics stimulates the search for alternatives or ways to reduce antibiotic resistance in order to prevent diseases and increase the productivity of ruminants. The aim of this study was to evaluate the effect of Quercus cortex (QC) extract (0.5 ml/kg body weight) together with chlortetracycline (Ch) (20%, 10 g/head/day) on cattle ruminal microbiome against the background of control (C), extract of QC and Ch. They were added separately as a substrate to the diets of bulls with rumen fistula (dairy breed, 12-months, diet - 80% hay, 20% grain feed, within 20 days). Microflora was analyzed using highly efficient sequencing of 16S rRNA gene (Illumina). QC was prepared by purification, grinding (1–2 mm), extraction in a water bath (30 min, 70 ° C). The taxonomic composition of ruminal microbiocenosis in control animals was represented by Bacteria and Fungi domains — 82.1 and 17.9%; QC - 99.8 and 0.2% was not classified; Ch - 10.4 and 89.6%; QC + Ch - 95.2 and 4.8%. Feeding with QC + Ch led to a decrease in phylums Bacteroidetes (P ≤ 0.05), Firmicutes (P ≤ 0.05), Proteobacteria compared to C. An increase in bacteria of Bacteroidia class (by 42.9% (P ≤ 0.05)) due to the species Prevotella and a decrease in the class of Gammaproteobacteria (by 6.9%) were registered. The species composition was characterized by a decrease in bacteria of Lactobacillus, Faecalibacterium, Escherichia, Fibrobacter genera. Ch group characterized by a decrease Fungi Ascomycota (P ≤ 0.05) and an increase in Chytridiomycota (P ≤ 0.05) and were not identified in QC and QC + Ch. Thus, this study highlights the potential use of plant extracts as an additional feed supplement, which can reduce the negative effects of chlortetracycline on the development of gram-positive bacteria and Fungi. This research was performed with financial support from the RSF (16-16-10048).

224 Epimural microbiota and rumen epithelial gene expression in healthy and liver-abscessed animals

Abstract Different dietary and feed additive strategies have been developed to reduce the liver abscess in feedlot cattle, but liver abscesses are still a major problem in beef production. We have limited knowledge about how rumen microbial communities interact with host epithelial gene expression in healthy and liver-abscessed animals. The objective of this study was to investigate the associations between the rumen content associated and rumen epimural microbiome and epithelial gene expression in liver-abscessed and healthy animals. To this end, we collected the ruminal contents and tissue samples from healthy (N=30; score=0, steers n=19 and heifers n=11) and liver-abscessed (N=30; score=A+, steers n=21 and heifers n=9) feedlot cattle at harvest. The bacterial community compositions in the ruminal contents and papillae were evaluated via 16S rDNA sequencing of the V4 region using the Illumina MiSeq platform. Additionally, total RNA was extracted from rumen epithelial tissues and sequenced using the Illumina NextSeq platform. The permutational analysis (PERMANOVA) on Bray Curtis distances matrices showed the microbial community in the ruminal contents was significantly different (P< 0.001) from the bacterial community observed in rumen papillae. The ruminal contents contained a higher abundance of Bacteroidetes and Proteobacteria while papillae contained higher abundance of Firmicutes. The epimural microbiota was different (P< 0.01) between healthy and liver abscessed animals while ruminal contents microbiome was not different between the two groups. The DeSeq2 algorithm identified differentially expressed genes (221) related to MAPK, NF-kappa B signaling pathway, immune and inflammatory response in liver-abscessed animals. Additionally, a wide range of epimural bacterial taxa were correlated (-0.52 to 0.67) with differentially expressed genes. These data demonstrate the interaction between epimural microbiota and the host and its effect on liver abscesses, and indicate the need to study the epimural microbiome for its impact on liver abscesses in feedlot cattle. USDA is an equal opportunity provider and employer.

141 Mineral Requirements of Dairy Cattle: Emphasis on organic minerals

Abstract Requirements for most minerals are expressed on an absorbed basis. The true absorption of minerals can vary widely because of source, presence of antagonists, dietary concentrations, and animal mineral status; therefore, expressing mineral requirements on an absorbed basis is theoretically sound. Unfortunately measuring true absorption of minerals is exceedingly difficult; available data is limited which means that often we are using constants. Requirements for lactation, growth, and conceptus growth are known with reasonable certainty; however establishing maintenance requirements is plagued with methodological difficulties, and the classical definition of maintenance (i.e., replenishment of inevitable fecal and urinary losses) ignores effects on water balance, acid-base balance in the rumen, and the ruminal and intestinal microbiome. For Na, Cl- and K, absorption is essentially 100% regardless of source. Lab methods are available to estimate absorption of P. Source of Ca accounts for the majority of the variation in Ca absorption and constants are available for feedstuffs and supplements. We have good data on absorption of Mg from basal diets and are able to estimate antagonism of Mg absorption caused by K. We are less able to estimate absorption of the various Mg supplements, some of which are highly variable. Except for the electrolytes (which affect water balance), requirements are known with reasonable certainty for macrominerals. Absorption coefficients for trace minerals (TM) are known with much less certainty. Source of supplemental TM (e.g., organic vs sulfates) can affect absorption but the effect depends on the mineral TM (e.g., source affects absorption of Cu more than that of Mn) and on interactions with basal diet. Maintenance requirements are generally poorly defined for TM and because of ‘non-factorial’ requirements such as effects on microbiome, source of TM likely affects requirements. This means that for some TM, the factorial approach to requirements may not be adequate.

PSVI-3 Effects of dietary supplementation of multi-species direct-fed microbial products on energy status, apparent nutrient digestibility, and rumen metatranscriptome of beef steers

Abstract This study evaluated the effects of two different multi-strain direct-fed microbial products on energy status, nutrient digestibility, and ruminal metatranscriptome of beef steers. Nine rumen-cannulated Holstein steers were assigned to 3 treatments arranged in a 3 × 3 Latin square design with three 21-d periods. Dietary treatments were (1) CON (basal diet without additive), (2) PROB (basal diet plus 19 g/d of Commence), and (3) SYNB (basal diet plus 28 g/d of RX3). Commence is a blend of S. cerevisiae, Enterococcus lactis, Bacillus subtilis, Enterococcus faecium, and L. casei. RX3 is a blend of S. cerevisiae and the fermentation products of S. cerevisiae, Enterococcus lactis, Bacillus licheniformis, and Bacillus subtilis. Rumen fluid (for metatranscriptomics analysis) and blood samples (for analysis of plasma glucose and non-esterified fatty acid) were collected on d 21 of each period. From d 16 – 20, TMR and fecal samples were collected daily to determine apparent total tract digestibility of nutrients using indigestible neutral detergent fiber (iNDF) method. The data were analyzed using the GLIMMIX procedure of SAS. The model included the effects of treatment, period, and random effects of cow and square. There were no effects on DMI and non-esterified fatty acid. Compared with CON, steers fed either additives had greater (P = 0.02) plasma glucose concentrations. Results of metatranscriptome analysis revealed no differentially expressed functional genes among the treatments. Apparent total-tract digestibility of nutrients were also similar among treatments. These results demonstrated that supplemental PROB and SYNB improved the plasma glucose concentration, but had no effects on the functional capacity of the ruminal microbiome and apparent digestibility of nutrients in beef steers.

Network analysis and functional estimation of the microbiome reveal the effects of cashew nut shell liquid feeding on methanogen behaviour in the rumen.

The effects of cashew nut shell liquid (CNSL) feeding on the methane (CH4 ) emission and the ruminal microbiome of Lai Sind beef cattle were investigated. Changes in the methane production and rumen microbiome by CNSL feeding were monitored by a respiration chamber and 16S rRNA gene amplicon sequencing respectively. The results demonstrated that CNSL feeding mitigated 20.2%-23.4% of the CH4 emission in vivo without apparent adverse effects on feed intake and feed digestibility. The rumen fluid analysis revealed a significant increase in the proportion of propionate in the total short-chain fatty acids. The relative abundance of methanogen (order Methanobacteriales) decreased significantly, indicating the direct inhibitory effect of CNSL on methanogens. The predicted function of the rumen microbiome indicated that carbohydrate and lipid metabolisms including propionate production were upregulated by CNSL feeding, whereas CH4 metabolism was downregulated. A network analysis revealed that methanogen changed its partner bacteria after CNSL feeding. The δ13 C of CH4 ranged from -74.2‰ to -66.6‰ with significant fluctuation by CNSL feeding, in agreement with the shift of the rumen microbiome. Our findings demonstrate that CNSL feeding can mitigate the CH4 emission from local cattle production systems in South-East Asia by modifying the rumen microbiome and its function.

Potential of Mulberry Leaf Biomass and Its Flavonoids to Improve Production and Health in Ruminants: Mechanistic Insights and Prospects.

Simple SummaryThe economics of livestock production depends upon the feasible feeding resources as feed costs constitute more than 70% of the total expenses of a livestock enterprise. In this regard, searching for alternative and cheaper feeding resources is imperative for economical and sustainable livestock production. Mulberry leaves are an important resource available for feeding livestock, as they possess quite high protein and energy contents as compared to other tree leaves and conventional forages. Moreover, polyphenolic compounds (mainly flavonoids) present in mulberry leaf (ML) possess excellent antioxidant and antimicrobial potential that can beneficially impact animal health and production. Mulberry leaves and its flavonoids have been shown to increase the feed digestibility and milk production in ruminants, while reducing methane emission. Moreover, mulberry flavonoids can positively influence body metabolism and alleviate oxidative stress in animals. This review highlights the importance of this unique feeding resource for ruminants to increase their performance while reducing methane emissions.Leaf biomass from the mulberry plant (genus Morus and family Moraceae) is considered a potential resource for livestock feeding. Mulberry leaves (MLs) contain high protein (14.0–34.2%) and metabolizable energy (1130–2240 kcal/kg) with high dry matter (DM) digestibility (75–85%) and palatability. Flavonoid contents of MLs confer unique antioxidant properties and can potentially help alleviate oxidative stress in animals during stressful periods, such as neonatal, weaning, and periparturient periods. In addition, mulberry leaf flavonoids (MLFs) possess antimicrobial properties and can effectively decrease the population of ruminal methanogens and protozoa to reduce enteric methane (CH4) production. Owing to its rich flavonoid content, feeding MLs increases fiber digestion and utilization leading to enhanced milk production in ruminants. Dietary supplementation with MLFs alters ruminal fermentation kinetics by increasing total volatile fatty acids, propionate, and ammonia concentrations. Furthermore, they can substantially increase the population of specific cellulolytic bacteria in the rumen. Owing to their structural homology with steroid hormones, the MLFs can potentially modulate different metabolic pathways particularly those linked with energy homeostasis. This review aims to highlight the potential of ML and its flavonoids to modulate the ruminal microbiome, fermentation, and metabolic status to enhance productive performance and health in ruminants while reducing CH4 emission.

Dietary Supplementation with Sodium Sulfate Improves Rumen Fermentation, Fiber Digestibility, and the Plasma Metabolome through Modulation of Rumen Bacterial Communities in Steers.

Six steers were used to study the effects of dietary supplementation with sodium sulfate (Na2SO4) on rumen fermentation, nutrient digestion, rumen microbiota, and plasma metabolites. The animals were fed a basal ration with Na2SO4 added at 0 g/day (sulfur [S] content of 0.115% dry matter [DM]), 20 g/day (S at 0.185% DM), or 40 g/day (S at 0.255% DM) in a replicate 3-by-3 Latin square design. The results indicated that supplementing with Na2SO4 increased the ruminal concentration of total volatile fatty acids, the molar proportions of acetate and butyrate, the ruminal concentrations of microbial protein, SO42--S, and S2--S, and the digestibility of fiber, while it decreased the molar proportion of propionate and the ruminal concentration of ammonia nitrogen. Supplementing with Na2SO4 increased the diversity and the richness of rumen microbiota and the relative abundances of the phylum Firmicutes and genera Ruminococcus 2, Rikenellaceae RC9 gut group, and Desulfovibrio, whereas it decreased the relative abundances of the phylum Bacteroidetes and genera Prevotella 1, Prevotellaceae UCG-001, and Treponema 2 Supplementing with Na2SO4 also increased the plasma concentrations of amino acids (l-arginine, l-methionine, l-cysteine, and l-lysine), purine derivatives (xanthine and hypoxanthine), vitamins (thiamine and biotin), and lipids (acetylcarnitine and l-carnitine). It was concluded that supplementing the steer ration with Na2SO4 was beneficial for improving the rumen fermentation, fiber digestibility, and nutrient metabolism through modulating the rumen microbial community.IMPORTANCE Essential elements like nitrogen and sulfur greatly affect rumen fermentation and metabolism in ruminants. However, little knowledge is available on the effects of sulfur on the rumen microbiota and plasma metabolome. The results of the present trial demonstrated that supplementing the steer ration with sodium sulfate markedly improved rumen fermentation, fiber digestibility, and metabolism of amino acids, purine derivatives, and vitamins through effects on the ruminal microbiome. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of sulfur on rumen fermentation and nutrient utilization.

Bioremediation: How to Decrease Greenhouse Gas Emissions Through Cattle

Introduction: The concentration of greenhouse gases within the atmosphere is currently on the rise. With the increase in human population comes a growing need for greater food security in order to support our population. The agricultural industry has a carbon footprint comparable to that of other extensive producers such as oil production facilities, waste sectors and industrial processors. This study aims to establish an experimental design to modify the current microbiome in cattle, as cattle farming practices account for a majority of agricultural methane production in North America. Methods: Young Canadian Holstein cattle with developing ruminal microbiomes will be placed into control and treatment groups and studied over the duration of 4 weeks. Ruminococcus hydrogenotrophicus will be inserted into the rumen of the experimental groups of cattle. Results: Results will generate findings on the basis of reducing methanogenic activity among the rumen of cattle, and therefore the results may propose a feasible answer towards the decreasing of the agricultural carbon footprint among the cattle industry. Discussion: The ability to decrease or eliminate the methane produced from agriculture would be a significant finding in current global studies. Through/by combining knowledge from environmental biology, agricultural science, microbiology and animal biology, solutions can be found for reducing the agricultural carbon footprint. Conclusion: The use of bioremediation methods to decrease methane production is a new area of research. By cultivating a microorganism that can compete with the methanogenic bacteria within the rumen of cows, less methane yield is plausible. Ultimately, leading to a proposed answer to curb climate change values to a decreasing end.

Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment.

Simple SummaryRecently, it has become apparent that the microbiome is essential to health and affects practically every aspect of physiology. The rumen contains highly dense and diverse microbial communities, which can impact health through their composition, diversity, and assembly. Nevertheless, the diversity and function of rumen microbes have not been fully described. Therefore, this study aims to identify differences in the functional attributes and metabolites of rumen microbiota to heat stress by metagenomics and metabolomics analyses. We observed differences in biological changes, as well as changes in rumen metabolites and metabolic pathways depending on the breed of cow. In addition, significant changes in rumen bacterial taxa and functional gene abundance were observed. Overall, the findings of this study improve our understanding of heat-vulnerable ruminal bacteria and related genes.The microbial community within the rumen can be changed and shaped by heat stress. Accumulating data have suggested that different breeds of dairy cows have differential heat stress resistance; however, the underlying mechanism by which nonanimal factors contribute to heat stress are yet to be understood. This study is designed to determine changes in the rumen microbiome of Holstein and Jersey cows to normal and heat stress conditions. Under heat stress conditions, Holstein cows had a significantly higher respiration rate than Jersey cows. Heat stress increased the rectal temperature of Holstein but not Jersey cows. In the Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, Jersey cows had a significantly higher proportion of genes associated with energy metabolism in the normal condition than that with other treatments. Linear discriminant analysis effect size (LEfSe) results identified six taxa as distinguishing taxa between normal and heat stress conditions in Holstein cows; in Jersey cows, 29 such taxa were identified. Changes in the rumen bacterial taxa were more sensitive to heat stress in Jersey cows than in Holstein cows, suggesting that the rumen mechanism is different in both breeds in adapting to heat stress. Collectively, distinct changes in rumen bacterial taxa and functional gene abundance in Jersey cows may be associated with better adaptation ability to heat stress.

Tannin-Rich Plants as Natural Manipulators of Rumen Fermentation in the Livestock Industry

Condensed tannins (CTs) are plant anti-herbivore compounds with antimicrobial activity that can be used in ruminant diets as ruminal microbiome manipulators. However, not all CTs from fodder legumes are bioactive due to their wide structural diversity. The aim of our study was to investigate the effect of 10 CT-containing plants (Flemingia macrophylla, Leucaena leucocephala, Stylosanthes guianensis, Gliricidia sepium, Cratylia argentea, Cajanus cajan, Desmodium ovalifolium, Macrotiloma axilare, D. paniculatum, and Lespedeza procumbens) on in vitro fermentation kinetics of Nelore beef cattle. Polyethylene glycol (PEG), a specific CT-binding agent, was added to neutralize condensed tannin. Tifton and alfalfa hay were used as controls lacking CT. The experimental layout included a randomized complete block with factorial design and four blocks. The data were subjected to analysis of variance followed by Duncan’s test to determine differences (p < 0.05) among treatment means. The addition of PEG in browse incubations resulted in increased gas production, fermentation rate, short-chain fatty acid (SCFA) and N-NH3 release. Within our study, Lespedeza procumbens, Desmodium paniculatum, Leucaena leucocephala, Desmodium ovalifolium, and Flemingia macrophylla showed superior bioactivity compared to other species evaluated, suggesting a natural alternative for replacing ionophores to modify ruminal fermentation. Condensed tannins from L. pocumbens, D. paniculatum, L. leucocephala, D. ovalifolium, and F. macrophylla have the potential to modify rumen fermentation in beef cattle.

Differential dynamics of the Jersey ruminal microbiome and immune response in the heat stress environment

Abstract The rumen microbiome and immune cell play important roles in metabolism and immune responses of dairy cows. Accumulation data suggesting that different species of dairy cow have differential heat stress resistance, however underlying mechanism by which non-host factors contribute heat stress responses. Thus, our study was designed to understand the changes of rumen microbiome and immune cell function to heat stress response in Holstein and Jersey cows. Respiration rate and rectal temperature were measured and rumen fluid and blood were collected for microbiome analysis and immune cell analysis under normal or heat-stressed environment from eight Holstein and Jersey cows. The rumen bacteria diversity and microbial gene enrichment was analyzed by using the Illumina HiSeq™ 4000 platform. The blood of dairy cows was collected for peripheral blood mononuclear cells (PBMCs) isolation and PBMCs were analyzed by RNA sequencing (Marcrogen, Korea) under the same environmental condition. Holstein had significantly higher respiration rate compared to that of Jersey in heat stress environment. We also find that gene transcription patterns associated with functional activities in PBMCs are differ between Holstein and Jersey. Distinct and more prominent changes of rumen bacteria taxa and functional gene abundance in Jersey cows may be associated with better adaption ability to heat stress. These data suggest that different species of dairy cows had different metabolic and immunological system to adapt heat stress responses.

Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine.

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

Tannin supplementation modulates the composition and function of ruminal microbiome in lambs infected with gastrointestinal nematodes.

This study was carried out to evaluate the effects of tannin supplementation on ruminal microbiota of sixteen lambs infected and non-infected with Haemonchus contortus and Trichostrongylus colubriformis. Animals were fed with hay, concentrate and supplemented with Acacia mearnsii (A. mearnsii). The animals were divided into four treatments: two control groups without infection, either receiving A. mearnsii (C+) or not (C-), and two infected groups, one with A. mearnsii (I+) and another without A. mearnsii (I-). Ruminal short-chain fatty acids (SCFA) and metagenome sequencing of ruminal microbiota were used to evaluate the effect of tannin and infection on ruminal microbiome. For SCFA, differences were observed only with A. mearnsii. Total SCFA and acetate molar percentage were decreased in C+ and I+ (P<0.05). Butyrate, valerate and isovalerate were higher in lambs that received A. mearnsii in the diet (P<0.05). The infection changed the microbiome structure and decreased the abundance of butyrate-producing microorganisms. In addition, A. mearnsii supplementation also affected the structure the microbial community, increasing the diversity and abundance of the butyrate-producing and probiotics bacteria, amino acid metabolic pathways, purine, pyrimidine and sphingolipid metabolism. Together, our findings indicate that A. mearnsii supplementation modulates important groups related to nitrogen, amino acid, purine and pyrimidine metabolism, in rumen microbiome, affected by gastrointestinal nematodes infection in lambs.

Residual feed intake divergence during the preweaning period is associated with unique hindgut microbiome and metabolome profiles in neonatal Holstein heifer calves

BackgroundRecent studies underscored that divergence in residual feed intake (RFI) in mature beef and dairy cattle is associated with changes in ruminal microbiome and metabolome profiles which may contribute, at least in part, to better feed efficiency. Because the rumen in neonatal calves during the preweaning period is underdeveloped until close to weaning, they rely on hindgut microbial fermentation to breakdown undigested diet components. This leads to production of key metabolites such as volatile fatty acids (VFA), amino acids, and vitamins that could potentially be absorbed in the hind-gut and help drive growth and development. Whether RFI divergence in neonatal calves is associated with changes in hindgut microbial communities and metabolites is largely unknown. Therefore, the objective of the current study was to determine differences in hindgut microbiome and metabolome in neonatal Holstein heifer calves retrospectively-grouped based on feed efficiency as most-efficient (M-eff) or least-efficient (L-eff) calves using RFI divergence during the preweaning period.MethodsTwenty-six Holstein heifer calves received 3.8 L of first-milking colostrum from their respective dams within 6 h after birth. Calves were housed in individual outdoor hutches bedded with straw, fed twice daily with a milk replacer, and had ad libitum access to a starter grain mix from birth to weaning at 42 d of age. Calves were classified into M-eff [n = 13; RFI coefficient = − 5.72 ± 0.94 kg DMI (milk replacer + starter grain)/d] and L-eff [n = 13; RFI coefficient = 5.61 ± 0.94 kg DMI (milk replacer + starter grain)/d] based on a linear regression model including the combined starter grain mix and milk replacer DMI, average daily gain (ADG), and metabolic body weight (MBW). A deep sterile rectal swab exposed only to the rectum was collected immediately at birth before colostrum feeding (i.e., d 0), and fecal samples at d 14, 28, and 42 (prior to weaning) for microbiome and untargeted metabolome analyses using 16S rRNA gene sequencing and LC-MS. Microbiome data were analyzed with the QIIME 2 platform and metabolome data with the MetaboAnalyst 4.0 pipeline.ResultsNo differences (P > 0.05) in body measurements including body weight (BW), body length (BL), hip height (HH), hip width (HW), and wither height (WH) were detected between M-eff and L-eff calves at birth and during preweaning. Although milk replacer intake did not differ between groups, compared with L-eff, M-eff heifers had lower starter intake (P < 0.01) between d 18 to 42 of age, whereas no differences (P > 0.05) for ADG, cumulative BWG, or body measurements were observed between RFI groups during the preweaning period. Microbiome and metabolome profiles through the first 42 d of age indicated greater hindgut capacity for the production of energy-generating substrates (butyrate and propionate) and essential nutrients (vitamins and amino acids) in heifers with greater estimated feed efficiency.ConclusionDespite consuming approximately 54.6% less solid feed (cumulative intake, 10.90 vs. 19.98 ± 1.66 kg) from birth to weaning, the microbiome-metabolome changes in the hindgut of most-efficient heifers might have helped them maintain the same level of growth as the least-efficient heifers.

High fibre selection by roe deer (Capreolus capreolus): evidence of ruminal microbiome adaption to seasonal and geographical differences in nutrient composition

Context. The European roe deer owes its ability to digest fibre to its microbiome. This is made up of many different species at different levels of abundance and with different differentiations. In Europe, the roe deer is often classified as a so-called ‘concentrate selector’. This term has often been interpreted by different researchers to mean a selector of either protein- or energy-rich food. According to various studies, this selection behaviour is due to the low abundance of fibre-degrading microorganisms. Aims. The aim of the present study was to determine the concentration of crude nutrients in the rumen of roe deer, with the focus on the fibre fractions, and to show changes among seasons and between habitats. Furthermore, the aim was to find out how far the composition of the ruminal microbiota adapts to these changes. Methods. From 2011 to 2014, we collected the rumens of 245 roe deer in two Bavarian habitat types, a forest and an agricultural habitat. The crude nutrient contents and the size of the total microbiome and the proportions of individual genera were determined in the rumen content. Key results. The average annual concentration of crude fibre in the ingested food is 26–30% and this rises to 38% in certain months. The forest roe deer had the highest proportions of crude fibre in their food and the concentrations of other nutrients were also highly dependent on the season and habitat. Furthermore, the animals also have far less protein in their rumen content than often assumed. The total number of microorganisms in the rumens of the forest deer is significantly higher than in animals living in the agricultural area. The number of microorganisms was highest in the forest roe deer in winter, and in the roe deer from the agricultural area in summer. Clear connections can also be seen between individual groups of microorganisms and particular crude nutrients. The high crude-fibre concentration leads to a high number of fibre-degrading microorganisms, such as, for example, anaerobic fungi or the Ruminococcus flavefaciens. Conclusions. The results showed a high adaptability of the animals to a fibre-rich diet. The microbiome adapts very well to the respective nutrient availabilities. This, in turn, is what allows the roe deer to adapt so readily to diverse habitats and environmental conditions. Implications. Due to the generally high concentrations of fibre, combined with the high numbers of fibre-degraders in the rumen, we suggest that, from now on, we should talk of a roe deer as being a ‘selector’ or ‘browser’ rather than a ‘concentrate selector’.