Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows

Feeding a Saccharomyces cerevisiae fermentation product during a gut barrier challenge in lactating Holstein cows impacts the ruminal microbiota and metabolome

Through its influence on the gut microbiota, the feeding of Saccharomyces cerevisiae fermentation products (SCFP) has been a successful strategy to enhance the health of dairy cows during periods of physiological stresses. Although production and metabolic outcomes from feeding SCFP are well-known, its combined impacts on the ruminal microbiota and metabolome during gut barrier challenges remain unclear. To address this gap in knowledge, multiparous Holstein cows (97.1 ± 7.6 DIM [SD]; n = 8/group) fed a control diet (CON) or CON plus 19 g/d SCFP for 9 wk were subjected to a feed restriction (FR) challenge for 5 d, during which they were fed 40% of their ad libitum intake from the 7 d before FR. The DNA extracted from ruminal fluid was subjected to PacBio full-length 16S rRNA gene sequencing, real-time PCR of 12 major ruminal bacteria, and metabolomics analysis of up to 189 metabolites via GC/MS. High-quality amplicon sequence analyses were performed with the TADA (Targeted Amplicon Diversity Analysis), MicrobiomeAnalyst, PICRUSt2, and STAMP software packages, and metabolomics data were analyzed via MetaboAnalyst 5.0. Ruminal fluid metabolites from the SCFP group exhibited a greater α-diversity Chao 1 (P = 0.03) and Shannon indices (P = 0.05), and the partial least squares discriminant analysis clearly discriminated metabolite profiles between dietary groups. The abundance of CPla_4_termite_group, Candidatus Saccharimonas, Oribacterium, and Pirellula genus in cows fed SCFP was greater. In the SCFP group, concentrations of ethanolamine, 2-amino-4,6-dihydroxypyrimidine, glyoxylic acid, serine, threonine, cytosine, stearic acid, and pyrrole-2-carboxylic acid were greater in ruminal fluid. Both Fretibacterium and Succinivibrio abundances were positively correlated with metabolites across various biological processes: gamma-aminobutyric acid, galactose, butane-2,3-diol, fructose, 5-amino pentanoic acid, β-aminoisobutyric acid, ornithine, malonic acid, 3-hydroxy-3-methylbutyric acid, hexanoic acid, heptanoic acid, cadaverine, glycolic acid, β-alanine, 2-hydroxybutyric acid, methyl alanine, and alanine. In the SCFP group, compared with CON, the mean proportion of 14 predicted pathways based on metabolomics data was greater, whereas 10 predicted pathways were lower. Integrating metabolites and upregulated predicted enzymes (NADP+-dependent glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, serine: glyoxylate aminotransferase, and d-glycerate 3-kinase) indicated that the pentose phosphate pathway and photorespiration pathway were most upregulated by SCFP. Overall, SCFP during FR led to alterations in ruminal microbiota composition and key metabolic pathways. Among those, we identified a shift from the tricarboxylic acid cycle to the glyoxylate cycle, and nitrogenous base production was enhanced.

The effect of Phyllanthus emblica (Amla) fruit supplementation on the rumen microbiota and its correlation with rumen fermentation in dairy cows

Introduction

Medicinal plants, rich in phytochemicals like phenolic acids, flavonoids, and tannins, offer potential benefits in enhancing productivity, quality, and animal health. Amla fruit (Phyllanthus emblica) is one such plant with promising attributes. This study aimed to investigate the impact of fresh Amla fruit (FAF) supplementation on ruminal microbial composition and its correlation with rumen fermentation in lactating dairy cows.

Methods

The study employed a repeated crossover design involving eight ruminally cannulated mid-lactation Holstein dairy cows. Animals received varying levels of fresh Amla fruit supplementation (0, 200, 400, and 600 g/d).

Results

When 400 g/d of FAF was added to the diet, there was a significant increase in the relative abundance of Firmicutes (p = 0.02). However, at 200 g/d, the relative abundance of ruminal Bacteroidota was higher than the 0 and 400 g/d FAF supplementation (p < 0.01). LEfSe analysis identified distinct taxa, such as Clostridia vadinBB60 in the 200 g/d group, Oscillospiraceae in the 400 g/d group, and Elusimicrobium in the 600 g/d group. Notably, the random forest species abundance statistics identified Oscillospiraceae V9D2013 as a biomarker related to milk yield. Oscillospiraceae, Bacilli RF39, norank_f Prevotellaceae, and Bifidobacterium were positively correlated with ruminal total VFA and molar proportion of propionate, while Rikenellaceae RC9 gut group and Clostridia vadinBB60 were negatively correlated.

Discussion

FAF supplementation affects the abundance of beneficial microbes in a dose-dependent manner, which can improve milk yield, efficiency, rumen health, desirable fatty acids, and animal health.

Effects of diets for three growing stages by rumen inocula donors on in vitro rumen fermentation and microbiome

Hanwoo and Jeju Black cattle (Jeju Black) are native breeds of Korean cattle. Jeju Black cattle are recognized as natural monuments and are known to exhibit slower growth rates compared to Hanwoo. While several studies have analyzed the genetic characteristics of these cattle, there has been limited research on the differences in their microbiome. In this study, rumen fluid was obtained from three Hanwoo steers and three Jeju Black steers, and three different diets (total mixed rations [TMRs] for growing, early fattening, and late fattening periods) were used as substrates for in vitro fermentation. The in vitro incubation was conducted for 3 h and 24 h following a 2 × 3 factorial arrangement. After both incubation periods, fermentation characteristics were analyzed, and ruminal microbiome analysis was performed using 16S rRNA gene sequencing, employing both QIIME2 and PICRUSt2. The results revealed significant differences in the ruminal microbiota due to the inoculum effect. At the phylum level, Patescibacteria and Synergistota were found to be enriched in the Jeju Black inoculum-treated group. Additionally, using different inocula also affected the relative abundance of major taxa, including Ruminococcus, Pseudoramibacter, Ruminococcaceae CAG-352, and the [Eubacterium] ruminantium group. These microbial differences induced by the inoculum may have originated from varying levels of domestication between the two subspecies of donor animals, which mainly influenced the fermentation and microbiome features in the early incubation stages, although this was only partially offset afterward. Furthermore, predicted commission numbers of microbial enzymes, some of which are involved in the biosynthesis of secondary metabolites, fatty acids, and alpha amylase, differed based on the inoculum effect. However, these differences may account for only a small proportion of the overall metabolic pathway. Conversely, diets were found to affect protein biosynthesis and its related metabolism, which showed differential abundance in the growing diet and were potentially linked to the growth-promoting effects in beef cattle during the growing period. In conclusion, this study demonstrated that using different inocula significantly affected in vitro fermentation characteristics and microbiome features, mainly in the early stages of incubation, with some effects persisting up to 24 h of incubation.

Differences in the intestinal microbiota and association of host metabolism with hair coat status in cattle

Introduction

The hair coat status of cattle serves as an easily observed indicator of economic value in livestock production; however, the underlying mechanism remains largely unknown. Therefore, the objective of the current study was to determine differences in the intestinal microbiota and metabolome of cattle based on a division of with either slick and shining (SHC) or rough and dull (MHC) hair coat in Simmental cows.

Methods

Eight SHC and eight MHC late-pregnancy Simmental cows (with similar parities, body weights, and body conditions) were selected based on their hair coat status, and blood samples (plasma) from coccygeal venipuncture and fecal samples from the rectum were collected. The intestinal microbiota (in the fecal samples) was characterized by employing 16S rRNA gene sequencing targeting the V3-V4 hypervariable region on the Illumina MiSeq PE300 platform, and plasma samples were subjected to LC-MS/MS-based metabolomics with Progenesis QI 2.3. Plasma macromolecular metabolites were examined for differences in the metabolism of lipids, proteins, mineral elements, and hormones.

Results

Notable differences between the SHC and MHC groups related to host hair coat status were observed in the host metabolome and intestinal microbiota (P < 0.05). The host metabolome was enriched in histidine metabolism, cysteine and methionine metabolism, and purine metabolism in the SHC group, and the intestinal microbiota were also enriched in histidine metabolism (P < 0.05). In the MHC group, the symbiotic relationship transitioned from cooperation to competition in the MHC group, and an uncoupling effect was present in the microbe-metabolite association of intestine microbiota-host interactions. The hubs mediating the relationships between intestinal microbiota and plasma metabolites were the intestinal bacterial genus g__norank_f__Eubacterium_coprostanoligenes_group, plasma inosine, triiodothyronine, and phosphorus, which could be used to differentiate cows' hair coat status (P < 0.05).

Conclusion

Overall, the present study identified the relationships between the features of the intestinal microbiota and host hair coat status, thereby providing evidence and a new direction (intestine microbiota-host interplay) for future studies aimed at understanding the hair coat status of cattle.

Differences in serum metabolome profile explain individual variation in growth performance of young goats

High growth rates and body weight are important traits of young dairy goats that can shorten generation intervals, improve animal performance, and increase economic benefits. In the present study, ninety-nine, 6-month-old, female goats were fed with the same diet and kept under the same management condition. The ten goats with highest average daily gain (ADG, HADG, 135.27 ± 4.59 g/d) and ten goats with lowest ADG (LADG, 87.74 ± 3.13 g/d) were selected to identify the key serum metabolites associated with ADG, and to investigate the relationships of serum metabolome profiles with digestive tract microbiota. The results showed that a total of 125 serum metabolites were significantly different between HADG and LADG. Of these, 43 serum metabolites were significantly higher levels in HADG, including D-ornithine, l-glutamine, L-histidine, carnosine, LysoPC (16:1(9Z)/0:0), DCTP and hydroxylysine, while, 82 serum metabolites were significantly higher levels in LADG, including P-salicylic acid and deoxycholic acid 3-glucuronide. Pathway analysis indicated that these different metabolites were mainly involved in amino acid and lipid metabolism. Furthermore, Spearman's rank correlation analysis revealed that these differential serum metabolites were correlated with ADG and ADG-related bacteria. Notably, serum hydroxylysine and L-histidine could be used as biomarkers for distinguishing HADG and LADG goats, with an accuracy of >92.0%. SIGNIFICANCE: Our study confirms that individual microbiota and metabolic differences contribute to the variations of growth rate in young goats. Some serum metabolites may be useful in improving the growth performance of young goats, which provides directions for developing further nutritional regulation in the goat industry to achieve healthy feeding and efficiency enhancement.

Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats

BACKGROUND

The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period.

RESULTS

Based on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats' growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats' growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%).

CONCLUSIONS

This study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants. Video Abstract.

Effect of grape pomace supplement on growth performance, gastrointestinal microbiota, and methane production in Tan lambs

Grape pomace (GP), a by-product in wine production, is nutritious and can be used as a feed ingredient for ruminants; however, its role in shaping sheep gastrointestinal tract (GIT) microbiota is unclear. We conducted a controlled trial using a randomized block design with 10 Tan lambs fed a control diet (CD) and 10 Tan lambs fed a pelleted diet containing 8% GP (dry matter basis) for 46 days. Rumen, jejunum, cecum, and colon bacterial and archaeal composition were identified by 16S rRNA gene sequencing. Dry matter intake (DMI) was greater (p < 0.05) in the GP than CD group; however, there was no difference in average daily gain (ADG, p < 0.05) and feed conversion ratio (FCR, p < 0.05) between the two groups. The GP group had a greater abundance of Prevotella 1 and Prevotella 7 in the rumen; of Sharpe, Ruminococcaceae 2, and [Ruminococcus] gauvreauii group in the jejunum; of Ruminococcaceae UCG-014 and Romboutsia in the cecum, and Prevotella UCG-001 in the colon; but lesser Rikenellaceae RC9 gut group in the rumen and cecum, and Ruminococcaceae UCG-005 and Ruminococcaceae UCG-010 in the colon than the CD group. The pathways of carbohydrate metabolism, such as L-rhamnose degradation in the rumen, starch and glycogen degradation in the jejunum, galactose degradation in the cecum, and mixed acid fermentation and mannan degradation in the colon were up-graded; whereas, the pathways of tricarboxylic acid (TCA) cycle VIII, and pyruvate fermentation to acetone in the rumen and colon were down-graded with GP. The archaeal incomplete reductive TCA cycle was enriched in the rumen, jejunum, and colon; whereas, the methanogenesis from H2 and CO2, the cofactors of methanogenesis, including coenzyme M, coenzyme B, and factor 420 biosynthesis were decreased in the colon. The study concluded that a diet including GP at 8% DM did not affect ADG or FCR in Tan lambs. However, there were some potential benefits, such as enhancing propionate production by microbiota and pathways in the GIT, promoting B-vitamin production in the rumen, facilitating starch degradation and amino acid biosynthesis in the jejunum, and reducing methanogenesis in the colon.

In vitro ruminal fermentation and cow-to-mouse fecal transplantations verify the inter-relationship of microbiome and metabolome biomarkers: potential to promote health in dairy cows

Introduction

There are differences in the gut microbiome and metabolome when the host undergoes different physical or pathological conditions. However, the inter-relationship of microbiome and metabolome biomarkers to potentially promote the health of dairy cows needs to be studied. Further, the development of next-generation probiotics for dairy cattle health promotion has not been demonstrated.

Objective

In the present study, we identified the microbiome and metabolome biomarkers associated with healthy cows.

Methods

We analyzed the relationships of the ruminal microorganism profile and metabolites between healthy and mastitis lactating dairy cows. The roles of bacterial biomarker were further verified by in vitro fermentation and cow-to-mouse fecal microbiota transplantation (FMT).

Results

Two species, Ruminococcus flavefaciens and Bifidobacterium longum subsp. longum, and six rumen metabolites were positively correlated with healthy cows by Spearman's correlation analysis. Through in vitro ruminal fermentation, inoculating R. flavefaciens and B. longum subsp. longum showed the upregulation of the levels of putrescine, xanthurenic acid, and pyridoxal in the mastitis ruminal fluid, which confirmed the inter-relationships between these microbiota and metabolites associated with healthy cows. Further, we verified the role of R. flavefaciens and B. longum subsp. longum in promoting health by FMT. The administration of R. flavefaciens and B. longum subsp. longum reduced the death rate and recovered the bodyweight loss of germ-free mice caused by FMT mastitis feces.

Discussion

We provided evidence that the bacterial biomarkers alter downstream metabolites. This could indirectly indicate that the two bacterial biomarkers have the potential to be used as next-generation probiotics for dairy cattle, although it needs more evidence to support our hypothesis. Two species, R. flavefaciens and B. longum subsp. longum, with three metabolites, putrescine, xanthurenic acid, and pyridoxal, identified in the ruminal fluid, may point to a new health-promoting and disease-preventing approach for dairy cattle.

Shaoyao-Gancao-Tang regulates the T-helper-type 1/T-helper-type 2 ratio in the lung and gut and alters gut microbiota in rats with ovalbumin-induced asthma

ETHNOPHARMACOLOGICAL RELEVANCE

Shaoyao-Gancao Tang (SGT) is a traditional Chinese medicine formulation. It has been used to treat kinds of pain and to alleviate asthma in clinic. However, the mechanism of action is not known.

AIM OF THE STUDY

To investigate the anti-asthma effect of SGT involving modulation of the T-helper type 1 (Th1) Th1/Th2 ratio in the gut-lung axis and alteration of the gut microbiota (GM) in rats with ovalbumin (OVA)-induced asthma.

MATERIALS AND METHODS

The main constituents of SGT were analyzed by high-performance liquid chromatography (HPLC). A model of asthma was established in rats by OVA-induced allergen challenge. Rats suffering from asthma (RSAs) were treated with SGT (2.5, 5.0 and 10.0 g/kg), dexamethasone (1 mg/kg) or physiologic saline for 4 weeks. The level of immunoglobulin (Ig)E in bronchoalveolar lavage fluid (BALF) and serum was determined by enzyme-linked immunosorbent assay. Histology of lung and colon tissues was investigated using staining (hematoxylin and eosin and periodic acid-Schiff). The Th1/Th2 ratio and levels of cytokines (interferon (IFN)-γ and interleukin (IL)-4) in the lung and colon were detected by immunohistochemistry. The GM in fresh feces was analyzed by 16 S rRNA gene sequencing.

RESULTS

Twelve main constituents (gallic acid, albiflorin, paeoniflorin, liquiritin apioside, liquiritin, benzoic acid, isoliquiritin apioside, isoliquiritin, liquiritigenin, glycyrrhizic acid, isoliquiritigenin and glycyrrhetinic acid) of SGT were simultaneously determined by HPLC. SGT treatment (5.0 and 10.0 g/kg) was found to reduce the IgE level (a vital marker of hyper-responsiveness) in BALF and serum, improve typical morphological changes (inflammatory-cell infiltration and goblet cell metaplasia) in the lung and colon, alleviate airway remodeling (including bronchiostenosis and basement membrane-thickening) in the lung, significantly decrease the IL-4 level and increase the IFN-γ level in the lung and colon, which led to restoration of the IFN-γ/IL-4 ratio. The dysbiosis and dysfunction of GM in RSAs were modulated by SGT. The abundance of bacteria of the genera Ethanoligenens and Harryflintia was increased in RSAs and was decreased upon SGT treatment. The abundance of Family_XIII_AD3011_group was decreased in RSAs and increased upon SGT treatment. Moreover, SGT therapy increased the abundance of bacteria of the genera Ruminococcaceae_UCG-005 and Candidatus_Sacchrimonas, and decreased that of Ruminococcus_2 and Alistipes.

CONCLUSIONS

SGT ameliorated rats with OVA-induced asthma via regulation of the Th1/Th2 ratio in the lung and gut, and modulated the GM.

Effects of Thymbra capitata essential oil on in vitro fermentation end-products and ruminal bacterial communities

An in vitro trial was carried out to investigate the effects of natural Thymbra capitata essential oil (NEO) and its main compounds [including carvacrol, p-cymene, γ-terpinene given alone or in a synthetic combination (SEO)] on ruminal fermentation and the bacterial community using batch cultures inoculated with ruminal digesta and incubating two different basal diets [high-forage (F) and high-concentrate (C) diet]. After 24 h of incubation, primary fermentation end-products [gas, methane, volatile fatty acids (VFAs) and ammonia] and rumen microbial diversity were determined. NEO reduced the total VFA concentration (P < 0.05) only in the C diet. In contrast, SEO and carvacrol decreased the total VFA concentration (P < 0.05) only in the F diet. Methane production was not affected (P > 0.05) by any of the experimental treatments or diets evaluated. Microbial diversity analysis showed only a moderate effect of carvacrol and SEO on 13 genera, including, mainly, Atopobium and Blautia (involved in subacute ruminal acidosis) or Candidatus Saccharimonas (related to laminitis). In conclusion, T. capitata EO has a limited potential to attain nutritional or environmental benefits, but further research should be carried out to clarify its effects on animal health and microbial food safety.

Rumen microbial-driven metabolite from grazing lambs potentially regulates body fatty acid metabolism by lipid-related genes in liver

BACKGROUND

Lipid metabolism differs significantly between grazing and stall-feeding lambs, affecting the quality of livestock products. As two critical organs of lipid metabolism, the differences between feeding patterns on rumen and liver metabolism remain unclear. In this study, 16S rRNA, metagenomics, transcriptomics, and untargeted metabolomics were utilized to investigate the key rumen microorganisms and metabolites, as well as liver genes and metabolites associated with fatty acid metabolism under indoor feeding (F) and grazing (G).

RESULTS

Compared with grazing, indoor feeding increased ruminal propionate content. Using metagenome sequencing in combination with 16S rRNA amplicon sequencing, the results showed that the abundance of propionate-producing Succiniclasticum and hydrogenating bacteria Tenericutes was enriched in the F group. For rumen metabolism, grazing caused up-regulation of EPA, DHA and oleic acid and down-regulation of decanoic acid, as well as, screening for 2-ketobutyric acid as a vital differential metabolite, which was enriched in the propionate metabolism pathway. In the liver, indoor feeding increased 3-hydroxypropanoate and citric acid content, causing changes in propionate metabolism and citrate cycle, while decreasing the ETA content. Then, the liver transcriptome revealed that 11 lipid-related genes were differentially expressed in the two feeding patterns. Correlation analysis showed that the expression of CYP4A6, FADS1, FADS2, ALDH6A1 and CYP2C23 was significantly associated with the propionate metabolism process, suggesting that propionate metabolism may be an important factor mediating the hepatic lipid metabolism. Besides, the unsaturated fatty acids in muscle, rumen and liver also had a close correlation.

CONCLUSIONS

Overall, our data demonstrated that rumen microbial-driven metabolite from grazing lambs potentially regulates multiple hepatic lipid-related genes, ultimately affecting body fatty acid metabolism.

Chordicoccus furentiruminis, gen. nov., sp. nov., a novel succinic acid producing bacterium isolated from a steer on a high grain diet

This study presents MP1D12^T (=NRRL B-67553^T=NCTC 14480^T), an isolate from the ruminal content of an Angus steer fed a high grain diet. Phenotypic and genotypic traits of the isolate were explored. MP1D12^T was found to be a strictly anaerobic, catalase-negative, oxidase-negative, coccoid bacterium that frequently grows in chains. Analysis of metabolic products as a result of carbohydrate fermentation showed succinic acid as the major organic acid produced with lactic acid and acetic acid as minor products. Phylogenetic analysis of MP1D12^T based on 16S rRNA nucleotide sequence and amino acid sequences from the whole genome presents a divergent lineage from other members in the family Lachnospiraceae. 16S rRNA sequence comparison, whole genome average nucleotide identity digital DNA-DNA hybridization and average amino acid identity results suggest that MP1D12^T represents a novel species in a novel genus within the family Lachnospiraceae. We propose the creation of the genus Chordicoccus in which MP1D12^T represents the type strain for the novel species Chordicoccus furentiruminis.

Integrating data from spontaneous and induced trans-10 shift of ruminal biohydrogenation reveals discriminant bacterial community changes at the OTU level

Introduction

Microbial digestion is of key importance for ruminants, and disturbances can affect efficiency and quality of products for human consumers. Ruminal biohydrogenation of dietary unsaturated fatty acids leads to a wide variety of specific fatty acids. Some dietary conditions can affect the pathways of this transformation, leading to trans-10 fatty acids rather than the more usual trans-11 fatty acids, this change resulting in milk fat depression in dairy cows.

Materials and methods

We combined data from an induced and spontaneous trans-10 shift of ruminal biohydrogenation, providing new insight on bacterial changes at different taxonomic levels. A trans-10 shift was induced using dietary addition of concentrate and/or unsaturated fat, and the spontaneous milk fat depression was observed in a commercial dairy herd.

Results and discussion

Most changes of microbial community related to bacteria that are not known to be involved in the biohydrogenation process, suggesting that the trans-10 shift may represent the biochemical marker of a wide change of bacterial community. At OTU level, sparse discriminant analysis revealed strong associations between this change of biohydrogenation pathway and some taxa, especially three taxa belonging to [Eubacterium] coprostanoligenes group, Muribaculaceae and Lachnospiraceae NK3A20 group, that could both be microbial markers of this disturbance and candidates for studies relative to their ability to produce trans-10 fatty acids.

Dynamics of rumen microbiome in sika deer (Cervus nippon yakushimae) from unique subtropical ecosystem in Yakushima Island, Japan

Yaku sika deer (Cervus nippon yakushimae) are endemic to Yakushima Island, whose landscape covered with primary evergreen forest is recognized as a World Heritage Site. In this study, the rumen bacterial microbiota (RBM) of wild Yaku sika was characterized using high throughput sequencing of bacterial 16S rRNA genes combined with targeted cultivation and functional analyses. Comparative analyses of RBM datasets from other ruminant animals revealed distinct community structure among domesticated and wild ruminants. Wild Yaku sika RBM exhibited higher species richness than other sika deer (i.e. wild Ezo sika and domesticated sika deer), likely reflecting their dietary variations associated with unique ecosystem in the island. The Yaku sika RBM of high deer population density samples exhibited higher diversity and contained higher proportion of Firmicutes than those of lower density samples. Moreover, the highest abundance of tannase gene were observed in individuals from the highest population density area, consistent with the previous observation that Yaku sika in the high density areas expanded their feed to include tannin-rich unpalatable plants. This study indicated that RBM of unique wild Yaku sika contribute to the flexibility of dietary shift and thus maintaining nutritional status of Yaku sika under high density conditions.

Fermented soybean meal modified the rumen microbiome to enhance the yield of milk components in Holstein cows

The study was conducted to evaluate the rumen microbiota as well as the milk composition and milk component yields of Holstein cows supplemented with fermented soybean meal (FSBM). Eighteen Holstein cows in their 2nd parity with 54.38 ± 11.12 SD days in milking (DIM) were divided into two dietary groups (CON and TRT) of nine cows per group. The cows in the TRT group received 300 g of FSBM per cow per day in addition to the conventional diet, while each cow in the CON group was supplemented with 350 g of soybean meal (SBM) in their diet daily throughout the 28-day feeding trial. Rumen bacterial composition was detected via 16S rRNA sequencing, and the functional profiles of bacterial communities were predicted. Milk composition, milk yield, as well as rumen fermentation parameters, and serum biochemistry were also recorded. The inclusion of FSBM into the diets of Holstein cows increased the milk urea nitrogen (MUN), milk protein yield, fat corrected milk (FCM), and milk fat yield while the milk somatic cell count (SCC) was decreased. In the rumen, the relative abundances of Fibrobacterota, and Spirochaetota phyla were increased in the TRT group, while the percentage of Proteobacteria was lower. In addition, the supplementation of FSBM to Holstein cows increased the acetate percentage, rumen pH, and acetate to propionate ratio, while the proportion of propionate and propionate % was observed to decrease in the TRT group. The KEGG pathway and functional prediction revealed an upregulation in the functional genes associated with the biosynthesis of amino acids in the TRT group. This enrichment in functional genes resulted in an improved synthesis of several essential amino acids including lysine, methionine, and branch chain amino acids (BCAA) which might be responsible for the increased milk protein yield. Future studies should employ shotgun metagenomics, transcriptomics, and metabolomics technology to investigate the effects of FSBM on other rumen microbiomes and milk protein synthesis in the mammary gland in Holstein cows. KEY POINTS: • The supplementation of fermented soybean meal (FSBM) to Holstein cows modified the proportion of rumen bacteria. • Predicted metabolic pathways and functional genes of rumen bacteria revealed an enrichment in pathway and genes associated with biosynthesis of amino acids in the group fed FSBM. • The cows supplemented with FSBM record an improved rumen fermentation. • Cows supplemented with FSBM recorded an increased yield of milk protein and milk fat.

Carbon‑sulfur coupling in a seasonally hypoxic, high-sulfate reservoir in SW China: Evidence from stable CS isotopes and sulfate-reducing bacteria

Anthropogenic input of sulfate (SO₄^2-) in reservoirs may enhance bacterial sulfate reduction (BSR) under seasonally hypoxic conditions in the water column. However, factors that control BSR and its coupling to organic carbon (OC) mineralization in seasonally hypoxic reservoirs remain unclear. The present study elucidates the coupling processes by analyzing the concentrations and isotopic composition of dissolved inorganic carbon (DIC) and sulfur (SO₄^2-, sulfide) species, and the microbial community in water of the Aha reservoir, SW China, which has high SO₄^2- concentration due to the inputs from acid mine drainage about twenty years ago. The water column at two sites in July and October revealed significant thermal stratification. In the hypoxic bottom water, the δ¹³C-DIC decreased while the δ³⁴S-SO₄^2- increased, implying organic carbon mineralization due to BSR. The magnitude of S isotope fractionation (Δ³⁴S, obtained from δ³⁴S_sulfate-δ³⁴S_sulfide) during the process of BSR fell in the range of 3.4‰ to 27.0‰ in July and 21.6‰ to 31.8‰ in October, suggesting a change in the community of sulfate-reducing bacteria (SRB). The relatively low water column stability in October compared to that in July weakened the difference of water chemistry and ultimately affected the SRB diversity. The production of DIC (ΔDIC) scaled a strong positive relationship with the Δ³⁴S in July (p < 0.01), indicating that high OC availability favored the survival of incomplete oxidizers of SRB. However, in October, Δ¹³C-DIC was correlated with the Δ³⁴S in the bottom hypoxic water (p < 0.01), implying that newly degraded OC depleted in ¹³C could favor the dominance of complete oxidizers of SRB which caused greater S isotope fractionation. Moreover, the sulfide supplied by BSR might stimulate the reductive dissolution of Fe and Mn oxides (Fe(O)OH and MnO₂). The present study helps to understand the coupling of C and S in seasonally hypoxic reservoirs characterized by high SO₄^2- concentration.

Differential Responses of Digesta- and Mucosa-Associated Jejunal Microbiota of Hu Sheep to Pelleted and Non-Pelleted High-Grain Diets

In the present study, we utilized 16S rRNA sequencing to uncover the impacts of non-pelleted (HG) or high-grain pelleted (HP) diets on the microbial structure and potential functions of digesta- and mucosa-associated microbiota in the jejunum of Hu sheep. Here, we randomly assigned 15 healthy male Hu sheep into three groups and fed the control diets (CON), HG, and HP diets, respectively. The experiment period was 60 days. The HP diets had the same nutritional ingredients as the HG diets but in pelleted form. At the finish of the experiment, the jejunal digesta and mucosa were gathered for microbial sequencing. The results of PCoA and PERMANOVA showed that different dietary treatments had significant impact (p < 0.05) on digesta- and mucosa-associated microbiota in the jejunum of Hu sheep. For specific differences, HG diets significantly increased (p < 0.05) the abundance of some acid-producing bacteria in both jejunal digesta (Bifidobacterium, OTU151, and OTU16) and mucosa (Rikenellaceae RC9 gut group, and Bifidobacterium) of Hu sheep compared with the CON diets. Besides the similar effects of the HG diets (increased the acid-producing bacteria such as Olsenella, Pseudoramibacter, and Shuttleworthia), our results also showed that the HP diets significantly decreased (p < 0.05) the abundance of some pro-inflammatory bacteria in the jejunal digesta (Mogibacterium, and Marvinbryantia) and mucosa (Chitinophaga, and Candidatus Saccharimonas) of Hu sheep compared with the HG diets. Collectively, these findings contributed to enriching the knowledge about the effects of HG diets on the structure and function of intestinal microbiota in ruminants.

Alterations in rumen microbiota via oral fiber administration during early life in dairy cows

Bacterial colonization in the rumen of pre-weaned ruminants is important for their growth and post-weaning productivity. This study evaluated the effects of oral fiber administration during the pre-weaning period on the development of rumen microbiota from pre-weaning to the first lactation period. Twenty female calves were assigned to control and treatment groups (n = 10 each). Animals in both groups were reared using a standard feeding program throughout the experiment, except for oral fiber administration (50–100 g/day/animal) from 3 days of age until weaning for the treatment group. Rumen content was collected during the pre-weaning period, growing period, and after parturition. Amplicon sequencing of the 16S rRNA gene revealed that oral fiber administration facilitated the early establishment of mature rumen microbiota, including a relatively higher abundance of Prevotella, Shuttleworthia, Mitsuokella, and Selenomonas. The difference in the rumen microbial composition between the dietary groups was observed even 21 days after parturition, with a significantly higher average milk yield in the first 30 days of lactation. Therefore, oral fiber administration to calves during the pre-weaning period altered rumen microbiota, and its effect might be long-lasting until the first parturition.

Metagenomic and Metabolomic Insights Into the Mechanism Underlying the Disparity in Milk Yield of Holstein Cows

This study was conducted to investigate the metabolic mechanism underlying the disparity in the milk yield of Holstein cows. Eighteen lactating Holstein cows in their second parity and 56 (±14.81 SD) days in milking (DIM) were selected from 94 cows. Based on the milk yield of the cows, they were divided into two groups of nine cows each, the high milk yield group (HP) (44.57 ± 2.11 kg/day) and the low milk yield group (LP) (26.71 ± 0.70 kg/day). The experimental cows were fed the same diet and kept under the same management system for more than 60 days. Rumen metagenomics revealed that two Archaea genera, one Bacteria genus, eight Eukaryota genera, and two Virus genera differ between the HP and LP groups. The analysis of metabolites in the rumen fluid, milk, and serum showed that several metabolites differed between the HP and LP groups. Correlation analysis between the predominant microbiota and milk yield-associated metabolites (MP-metabolites) revealed that four Bacteria and two Eukaryota genera have a positive relationship with MP-metabolites. Pathway enrichment analysis of the differential metabolites revealed that five pathways were enriched in all the samples (two pathways in the milk, two pathways in the serum, and one pathway in the rumen fluid). Further investigation revealed that the low milk yield observed in the LP group might be due to an upregulation in dopamine levels in the rumen fluid and milk, which could inhibit the release of prolactin or suppress the action of oxytocin in the udder resulting in reduced milk yield. On the other hand, the high milk yield in the HP group is attributed to an upregulation in citrulline, and N-acetylornithine, which could be used as substrates for energy metabolism in the citric acid cycle and ultimately gluconeogenesis.

Ruminal bacterial community is associated with the variations of total milk solid content in Holstein lactating cows

Total milk solid (TMS) content directly reflects the quality of milk. Rumen bacteria ferment dietary components, the process of which generates the precursors for the synthesis of milk solid, therefore, the variation in rumen bacterial community could be associated with milk solid in dairy cows. In this study, 45 healthy mid-lactation Holstein dairy cows with the similar body weight, lactation stage, and milk yield were initially used for the selection of 10 cows with high TMS (HS) and 10 cows with low TMS (LS). All those animals were under the same feeding management, and the individual milk yield was recorded for 14 consecutive days before milk and rumen fluid were sampled. Rumen fluid was used to determine bacterial community by 16S rRNA gene sequencing technique. The HS cows had significantly greater feed intake and milk TMS, fat, protein content than LS cows (P < 0.05). Among the volatile fatty acids (VFA), propionic acid and valeric acid concentrations were significantly greater in HS cows than those in LS cows (P < 0.05). There was no significant difference in the concentrations of acetate, butyrate, isobutyrate, valerate, and the total VFA (P > 0.05), nor was the acetate-to-propionate ratio, pH value, ammonia nitrogen and microbial crude protein concentrations (P > 0.05). Significant differences in the relative abundances of some bacterial genera were found between HS and LS cows. Spearman’s rank correlation analysis revealed that TMS content was correlated positively with the abundances of Ruminococcaceae UCG-014, Ruminococcaceae NK4A214 group, Prevotellaceae UCG-001, Butyrivibrio 2, Prevotellaceae UCG-003, Candidatus Saccharimonas, Ruminococcus 2, Lachnospiraceae XPB1014 group, probable genus 10, Eubacterium ventriosum group, but negatively correlated with Pyramidobacte. In addition, Ruminococcaceae UCG-014, Ruminococcus 2, Ruminococcaceae UCG001, probable genus 10 and Eubacterium ventriosum group might boost the total VFA production in the rumen. In conclusion, the dry matter intake of dairy cows and some special bacteria in rumen were significantly associated with TMS content, which suggests the potential function of rumen bacteria contributing to TMS content in dairy cows.

Exploring the relationship between bacterial genera and lipid metabolism in bovine rumen

The rumen is characterised by a complex microbial ecosystem, which is particularly active in lipid metabolism. Several studies demonstrated a role of diet and breed on bacterial community profile, with the effect on metabolic pathways. Despite the knowledge achieved on metabolism and the bacterial profile, little is known about the relationship between individual bacteria and metabolic pathways. Therefore, a multivariate approach was used to search for possible relationships between bacteria and products of several pathways. The correlation between rumen bacterial community composition and rumen lipid metabolism was assessed in 40 beef steers (20 Maremmana and 20 Aubrac) reared with the same system and fed the same diet. A canonical discriminant analysis combined with a canonical correlation analysis (CCA) was performed to explore this correlation. The variables showing a Pearson correlation higher than 0.6 as absolute value and significant were retained for CCA considering the relationship of bacterial composition with several metabolic pathways. The results indicated that some bacterial genera could have significant impacts on the presence of several fatty acids. However, the relationship between genera and fatty acid changes according to the breed, demonstrating that the metabolic pathways change according to the host genetic background, related to breed evolution, although there is also an intra-breed genetic background which should not be ignored. In Maremmana, Succiniclasticum and Rikenellaceae_RC9_gut_group showed a high positive correlation with dimethylacetals (DMAs) DMA_C13:0, DMA_C14:0, DMA_C14:0iso, DMA_C15:0, DMA_C15:0iso, and DMA_C18:0. Prevotellaceae_UCG-003 correlates with C18:3c9c12c15 and C18:1t11, while Fibrobacter and Succiniclasticum correlate with C18:2c9t11 and Lachnospiraceae_NK3A20_group correlates with C18:1c12. Prevotellaceae_UCG-003, Ruminococcaceae_UCG-010, and Oribacterium showed a positive correlation with C13:0iso, and C17:0. Conversely, in Aubrac, Treponema_2 and Rikenellaceae_RC9_gut_group correlated with DMA_C14:0iso, DMA_C16:0iso, DMA_C17:0iso, while Ruminococcaceae_UCG-010, Christensenellaceae_R-7_group and Ruminococcaceae_NK4A214_group correlated with DMA_C18:1t11, DMA_C14:0, DMA_C18:1c12. Acetitomaculum correlated with C18:2c9c12, C18:1c12, C18:1c13, C18:1t12 and Lachnospiraceae_NK3A20_group with C18:1t6-8 and C18:1t9. Saccharofermentas, Ruminococcaceae_UCG-010 and Rikenellaceae_RC9_gut_group correlated with C18:2c9t11 while, Prevotellaceae_UCG-001 and Ruminococcus_1 correlated with C14:0iso, C15:0, C15:0iso, C17:0. Saccharofermentans, Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, and Ruminococcaceae_UCG-010 correlated with C13:1c12 and C16:0iso. These results lead to hypothesise a possible association between several metabolic pathways and one or a few bacterial genera. If these associations are confirmed by further investigations that verify the causality of a bacterial genus with a particular metabolic process, it will be possible to deepen the knowledge on the activity of the rumen population in lipid metabolism. This approach appears to be a promising tool for uncovering the correlation between bacterial genera and products of rumen lipid metabolism.

Application of MinION Amplicon Sequencing to Buccal Swab Samples for Improving Resolution and Throughput of Rumen Microbiota Analysis

The Illumina MiSeq platform has been widely used as a standard method for studying the rumen microbiota. However, the low resolution of taxonomic identification is the only disadvantage of MiSeq amplicon sequencing, as it targets a part of the 16S rRNA gene. In the present study, we performed three experiments to establish a high-resolution and high-throughput rumen microbial profiling approach using a combination of MinION platform and buccal swab sample, which is a proxy for rumen contents. In experiment 1, rumen contents and buccal swab samples were collected simultaneously from cannulated cattle (n = 6) and used for microbiota analysis using three different analytical workflows: amplicon sequencing of the V3–V4 region of the 16S rRNA gene using MiSeq and amplicon sequencing of near full-length 16S rRNA gene using MinION or PacBio Sequel II. All reads derived from the MinION and PacBio platforms were classified at the species-level. In experiment 2, rumen fluid samples were collected from beef cattle (n = 28) and used for 16S rRNA gene amplicon sequencing using the MinION platform to evaluate this sequencing platform for rumen microbiota analysis. We confirmed that the MinION platform allowed species-level taxa assignment for the predominant bacterial groups, which were previously identified at the family- and genus-level using the MiSeq platform. In experiment 3, buccal swab samples were collected from beef cattle (n = 30) and used for 16S rRNA gene amplicon sequencing using the MinION platform to validate the applicability of a combination of the MinION platform and buccal swab samples for rumen microbiota analysis. The distribution of predominant bacterial taxa in the buccal swab samples was similar to that in the rumen samples observed in experiment 2. Based on these results, we concluded that the combination of the MinION platform and buccal swab samples may be potentially applied for rumen microbial analysis in large-scale studies.

Comparison of raw cow milk microbiota in two milking systems: a field study

This study investigated the effect of different milking systems on the milk composition and microbial community of raw milk in a commercial dairy farm. Raw milk samples from conventional milking system (CMS) and automatic milking system (AMS) were collected and the microbiota on each was assessed by 16S rRNA gene sequencing. Results showed that the acetone (P = 0.031) and β-hydroxybutyrate (P≤0.001) levels in the raw milk of the AMS group were increased compared with the CMS group. Principal component analysis, unweighted and weighted principal coordinates analysis, and heat map of microbial community composition in the raw milk showed a clear separation between two groups. AMS increased the abundance of the genera Acinetobacter (FDR = 0.004) and Staphylococcus (FDR = 0.004) in the raw milk compared with the CMS group. In contrast, the abundance of the genera Pseudomonas (FDR = 0.028), Lactococcus (FDR = 0.015), Sphingobacterium (FDR = 0.004), Brevundimonas (FDR = 0.005), and Chryseobacterium (FDR = 0.042) in the raw milk was reduced in the AMS group compared with the CMS group. The abundance of the genera Acinetobacter and Staphylococcus in the raw milk was positively correlated with the β-hydroxybutyrate, acetone, free fatty acid, citric acid, and urea nitrogen levels. Furthermore, the abundance of the genus Acinetobacter in the raw milk was negatively correlated with the somatic cell counts. The study demonstrates that the introduction of AMS in the dairy farm can regulate microbiota composition in the raw milk and this modification may exert an effect on reducing the somatic cell counts in the raw milk.

Characterization of the Bacterial Community of Rumen in Dairy Cows with Laminitis

Laminitis is the inflammation of the lamella, and it has caused great economic loss to the dairy industry and attracted wide attention around the world. In recent years, microbiota are considered to play a significant role in various diseases processes. Therefore, our study aimed to explore the characteristics of ruminal microbiota in laminitis cows. The serum of bovines with or without laminitis was collected to detect concentrations of lipopolysaccharide (LPS), lactic acid, and histamine, and ruminal fluid was collected for 16S rDNA sequence analysis. The results showed a significant increase in LPS and lactic acid levels in the laminitis group compared to the control group cows. In addition, a higher abundance of Candidatus Saccharimonas, Saccharofermentans, Erysipelotrichaceae UCG-009 genus, Acetobacter pasteurianus, Clostridium papyrosolvens, Ruminococcaceae bacterium AE2021, Porphyromonas crevioricanis, Pseudomonas boreopolis, Pseudomonas psychrotolerans, Rothia nasimurium, and Rothia pickettii was detected in the rumen fluid of laminitis bovines. In conclusion, this article confirms that there are differences in rumen microbiota between healthy and laminitis bovines. The elevated abundance of bacteria that enrich acid-enhancing metabolites, as well as increase the concentration of lactic acid and LPS, could be harmful factors to bovines and increase the risk of laminitis.

Effect of Whole or Ground Flaxseed Supplementation on Fatty Acid Profile, Fermentation, and Bacterial Composition in Rumen of Dairy Cows

Flaxseed is rich in α-linolenic acid (ALA) and can increase omega-3 polyunsaturated fatty acid in the milk of dairy cows. However, the response of rumen fermentation to different forms of flaxseed supplementation is unknown. This study aimed to investigate the effect of different forms of flaxseed on the fatty acid profile, fermentation, and composition of bacteria in the rumen of dairy cows. In total, 30 Holstein dairy cows were selected and randomly assigned into three groups (10/group). Cows were fed a basal diet (control check; CK) or basal diets supplemented with either 1,500 g per day whole flaxseed (WF) or 1,500 g per day ground flaxseed (GF). The WF group had the highest ALA content in rumen fluid, whereas no difference was found between the CK and GF groups. However, the molar proportion of acetate increased in the WF and GF groups and was the highest in the GF group, and a similar trend was shown by propionate, isobutyrate, butyrate, isovalerate, and valerate (CK < WF < GF). The abundance of Ruminococcaceae_NK4A214_group, Christensenellaceae_R-7_group, and Eubacterium_coprostanoligenes_group also showed the same trend (CK < WF < GF). Different forms of flaxseed release ALA by different mechanisms in the rumen, and the molar proportions of volatile fatty acids and the bacterial composition were potentially influenced mainly by the amount of ALA released into the rumen.

Microbiome and Metabolic Changes of Milk in Response to Dietary Supplementation With Bamboo Leaf Extract in Dairy Cows

Bamboo leaf extracts, with high content of flavonoids and diverse biological activities, are used in animal husbandry. Increasing evidence has suggested an association between the bovine physiology and the udder microbiome, yet whether the microbiota and the metabolites of milk affect the mammary gland health or the milk quality remains unknown. In this study, we provide a potential mechanism for the effects of bamboo leaf extracts on milk microbiota and metabolites of dairy cows. Twelve multiparous lactating Chinese Holstein dairy cows were randomly separated into two groups: basal diet as the control group (CON, n = 6) and a diet supplemented with 30 g/d bamboo leaf extract per head as antioxidants of bamboo leaf (AOB) group (AOB, n = 6) for 7 weeks (2-week adaptation, 5-week treatment). Milk samples were collected at the end of the trial (week 7) for microbiome and associated metabolic analysis by 16S ribosomal RNA (rRNA) gene sequencing and liquid chromatography-mass spectrometry (LC-MS). The results showed that the milk protein was increased (p < 0.0001) and somatic cell count (SCC) showed a tendency to decrease (p = 0.09) with AOB supplementation. The relative abundance of Firmicutes was significantly decreased (p = 0.04) while a higher relative abundance of Probacteria (p = 0.01) was seen in the group receiving AOB compared to the CON group. The AOB group had a significantly lower relative abundance of Corynebacterium_1 (p = 0.01), Aerococcus (p = 0.01), and Staphylococcus (p = 0.02). There were 64 different types of metabolites significantly upregulated, namely, glycerophospholipids and fatty acyls, and 15 significantly downregulated metabolites, such as moracetin, sphinganine, and lactulose in the AOB group. Metabolic pathway analysis of the different metabolites revealed that the sphingolipid signaling pathway was significantly enriched, together with glycerophospholipid metabolism, sphingolipid metabolism, and necroptosis in response to AOB supplementation. Several typical metabolites were highly correlated with specific ruminal bacteria, demonstrating a functional correlation between the milk microbiome and the associated metabolites. These insights into the complex mechanism and corresponding biological responses highlight the potential function of AOB, warranting further investigation into the regulatory role of specific pathways in the metabolism.

Microbial Dynamics and In Vitro Degradation of Plant Secondary Metabolites in Hanwoo Steer Rumen Fluids

Plant secondary metabolite (PSM) degradations and feed breakdown into small particles may occur primarily in the rumen. It is possible to predict the rate and extent of feed disappearance in the rumen during incubation by different in vitro techniques, which differ based on the PSM structures, including phenolics, and flavonoids. However, PSM degradation and conversion efficiency in the rumen remains unclear. This study's objective was to evaluate the in vitro degradation of a group of PSMs in the rumen fluid, collected from Hanwoo steer samples. PSMs including rutin, vitexin, myricetin, p-coumaric acid, ferulic acid, caffeic acid, quercetin, luteolin, propyl gallate, and kaempferol were used in their pure forms at 1mg/250 mL in a rumen fluid buffer system. The mixture of selected PSMs and buffer was incubated at 39 °C for 12-72 h, and samples were collected every 12 h and analyzed by a high-performance liquid chromatography-diode array detector (HPLC-DAD) to determine the biotransformation of the polyphenolics. The results revealed that the luteolin, ferulic acid, caffeic acid, coumaric acid, rutin, myricetin, vitexin, kaempferol, and quercetin were decreased after 12 h of incubation in the rumen fluid (p ≤ 0.05) and were more than 70% decreased at 72 h. In contrast, the propyl gallate concentrations were not significantly changed after 24 h of incubation in rumen fluid compared to other metabolites. Finally, microbial dynamics study showed that the Firmicutes, Bacterodetes, Actinobacteria, and Syngergistetes were the dominant phyla found in rumen fluids. The data suggest that most polyphenolic compounds may degrade or reform new complex structures in the rumen.

Compositional analysis of ruminal bacteria from ewes selected for somatic cell score and milk persistency

Ruminants are dependent on their rumen microbiota to obtain energy from plants. The composition of the microbiome was well-known to be associated with health status, and production traits, but published results are difficult to reproduce due to large sources of variation. The objectives of this study were to evaluate the associations of ruminal microbiota and its association with genetic lines selected by somatic cell score (SCS) or milk persistency (PERS), as well as milk production, somatic cell score, fat and protein contents, and fatty acids and proteins of milk, using the principles of compositional data. A large sample of 700 Lacaune dairy ewes from INRAE La Fage feeding the same diet and belonging to two divergent genetic lines selected for SCS or PERS was used. The ruminal bacterial metagenome was sequenced using the 16S rRNA gene, resulting in 2,059 operational taxonomic units affiliated with 112 genera. The abundance data were centred log-transformed after the replacement of zeros with the geometric Bayesian method. Discriminant analysis of the SCS showed differences between SCS+ and SCS- ewes, while for PERS no difference was obtained. Milk traits as fat content, protein content, saturated fatty acids and caseins of milk were negatively associated with Prevotella (R = [-0.08;-0.16]), Suttonella (R = [-0.09;-0.16]) and Ruminococcus (R = [-0.08;-0.16]), and positively associated with Lachnospiraceae (R = [0.09;0.16]) and Christensenellaceae (R = [0.09;0.16]). Our findings provide an understanding of the application of compositional data to microbiome analysis, and the potential association of Prevotella, Suttonella, Ruminococcaceae and Lachnospiraceae with milk production traits such as milk fatty acids and proteins in dairy sheep.

Long-Term Effects of Dietary Supplementation with Olive Oil and Hydrogenated Vegetable Oil on the Rumen Microbiome of Dairy Cows

Dietary lipids increase energy density in dairy cow diets and in some cases can increase beneficial fatty acids (FA) in milk and dairy products. However, the degree of FA saturation may affect the rumen microbiome. The objective of this study was to determine the long-term effects of feeding saturated (hydrogenated vegetable oil; HVO) or unsaturated (olive oil; OO) fatty acid (FA) sources on the rumen microbiome of dairy cows. For 63 days, 15 mid-lactating cows were fed with either a basal diet (no fat supplement), or the basal diet supplemented with 3% dry matter (DM), either HVO or OO. Rumen contents were collected on days 21, 42 and 63 for 16S rRNA gene sequencing using the Illumina MiSeq platform. The results reveal dominance of the phyla Firmicutes (71.5%) and Bacteroidetes (26.2%), and their respective prevalent genera Succiniclasticum (19.4%) and Prevotella (16.6%). Succiniclasticum increased with both treatments at all time points. Prevotella was reduced on day 42 in both diets. Bacterial diversity alpha or beta were not affected by diets. Predicted bacterial functions by CowPI showed changes in energy and protein metabolism. Overall, 3% DM of lipid supplementation over 63 days can be used in dairy cow diets without major impacts on global bacterial community structure.

Dietary Supplementation of Yeast Culture Into Pelleted Total Mixed Rations Improves the Growth Performance of Fattening Lambs

There is a growing interest in the use of yeast (Saccharomyces cerevisiae) culture (YC) for the enhancement of growth performance and general animal health. Grain-based pelleted total mixed rations (TMR) are emerging in intensive sheep farming systems, but it is uncertain if the process of pelleting results in YC becoming ineffective. This study aimed to examine the effects of YC supplemented to pelleted TMR at two proportions of corn in the diet on animal performance, feed digestion, blood parameters, rumen fermentation, and microbial community in fattening lambs. A 2 × 2 factorial design was adopted with two experimental factors and two levels in each factor, resulting in four treatments: (1) low proportion of corn in the diet (LC; 350 g corn/kg diet) without YC, (2) LC with YC (5 g/kg diet), (3) high proportion of corn in the diet (HC; 600 g corn/kg diet) without YC, and (4) HC with YC. Fifty-six 3-month-old male F2 hybrids of thin-tailed sheep and Northeast fine-wool sheep with a liveweight of 19.9 ± 2.7 kg were randomly assigned to the four treatment groups with an equal number of animals in each group. The results showed that live yeast cells could not survive during pelleting, and thus, any biological effects of the YC were the result of feeding dead yeast and the metabolites of yeast fermentation rather than live yeast cells. The supplementation of YC resulted in 31.1 g/day more average daily gain regardless of the proportion of corn in the diet with unchanged feed intake during the 56-day growth measurement period. The digestibility of neutral detergent fibre and acid detergent fibre was increased, but the digestibility of dry matter, organic matter, and crude protein was not affected by YC. The supplementation of YC altered the rumen bacterial population and species, but the most abundant phyla Bacteroidetes, Firmicutes, and Proteobacteria remained unchanged. This study indicates that YC products can be supplemented to pelleted TMR for improved lamb growth performance, although live yeast cells are inactive after pelleting. The improved performance could be attributed to improved fibre digestibility.

Influence of industry standard feeding frequencies on behavioral patterns and rumen and fecal bacterial communities in Holstein and Jersey cows

This study aimed to evaluate the effects of feeding frequency on behavioral patterns and on diurnal fermentation and bacteriome profiles of the rumen and feces in Holstein and Jersey cows. Ten Holstein and 10 Jersey cows were offered a TMR (53:47 forage-to-concentrate ratio dry matter basis) for ad libitum consumption and were randomly allocated within breed to one of the following feeding frequencies: (1) TMR delivered 1×/d (at 0600 h) or (2) TMR delivered 2×/d (at 0600 and 1800 h). The experiment lasted for 28 d with the first 14 d for cow adaptation to the Calan gates and the next 14 d for data collection. On d 23 and 24, an observer manually recorded the time budget (time spent lying, eating, drinking, standing, and milking), rumination activity, and number of visits to the feeding gate from each animal. On d 28, 5 concomitant collections of rumen and fecal samples were performed at intervals of 6 h via esophageal tubing and fecal grab, respectively. The bacteriome composition from these samples was determined through sequencing of the V4 region of the 16S rRNA gene. Feeding frequency did not affect behavioral patterns; however, Holstein cows spend more time lying (15.4 vs. 13.5 ± 0.8 h) and ruminating (401 vs. 331 ± 17.5 min) than Jersey cows. Fermentation profiles were similar by feeding frequency in both breeds. While no major diurnal fluctuations were observed in the fecal bacterial community from both breeds, diurnal fluctuations were identified in the rumen bacterial community from Holstein cows which appeared to follow pH responses. Overall, the bacterial community composition was not differentiated by industry standard feeding frequencies but was differentiated by breed and sample type.

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks

BACKGROUND

Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level.

RESULTS

The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks.

CONCLUSIONS

Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.

A Cross-Sectional Study of Dairy Cattle Metagenomes Reveals Increased Antimicrobial Resistance in Animals Farmed in a Heavy Metal Contaminated Environment

The use of heavy metals in economic and social development can create an accumulation of toxic waste in the environment. High concentrations of heavy metals can damage human and animal health, lead to the development of antibiotic resistance, and possibly change in bovine microbiota. It is important to investigate the influence of heavy metals in food systems to determine potential harmful effects environmental heavy metal contamination on human health. Because of a mining dam rupture, 43 million cubic meters of iron ore waste flowed into the Doce river basin surrounding Mariana City, Brazil, in 2015. Following this environmental disaster, we investigated the consequences of long-term exposure to contaminated drinking water on the microbiome and resistome of dairy cattle. We identified bacterial antimicrobial resistance (AMR) genes in the feces, rumen fluid, and nasopharynx of 16 dairy cattle 4 years after the environmental disaster. Cattle had been continuously exposed to heavy metal contaminated water until sample collection (A) and compared them to analogous samples from 16 dairy cattle in an unaffected farm, 356 km away (B). The microbiome and resistome of farm A and farm B differed in many aspects. The distribution of genes present in the cattle's nasopharynx, rumen, and feces conferring AMR was highly heterogeneous, and most genes were present in only a few samples. The relative abundance and prevalence (presence/absence) of AMR genes were higher in farm A than in farm B. Samples from farm A had a higher prevalence (presence) of genes conferring resistance to multiple drugs, metals, biocides, and multi-compound resistance. Fecal samples had a higher relative abundance of AMR genes, followed by rumen fluid samples, and the nasopharynx had the lowest relative abundance of AMR genes detected. Metagenome functional annotation suggested that selective pressures of heavy metal exposure potentially skewed pathway diversity toward fewer, more specialized functions. This is the first study that evaluates the consequences of a Brazilian environmental accident with mining ore dam failure in the microbiome of dairy cows. Our findings suggest that the long-term persistence of heavy metals in the environment may result in differences in the microbiota and enrichment of antimicrobial-resistant bacteria. Our results also suggest that AMR genes are most readily detected in fecal samples compared to rumen and nasopharyngeal samples which had relatively lower bacterial read counts. Since heavy metal contamination has an effect on the animal microbiome, environmental management is warranted to protect the food system from hazardous consequences.

A longitudinal study reveals the alterations of the Microtus fortis colonic microbiota during the natural resistance to Schistosoma japonicum infection

The gut microbiota has been demonstrated to associate with protection against helminth infection and mediate via microbial effects on the host humoral immunity. As a non-permissive host of Schistosoma japonicum, the Microtus fortis provides an ideal animal model to be investigated, because of its natural self-healing capability. Although researches on the systemic immunological responses have revealed that the host immune system contributes a lot to the resistance, the role of gut microbiome remains unclear. In this study, we exposed the M. fortis to the S.japonicum infection, carried out a longitudinal research (uninfected control, infected for 7 days, 14 days, 21 days, and 31 days) on their colonic microbiota based on the 16S rRNA gene amplicon sequencing. The bacterial composition disclosed a disturbance-recovery alteration followed by the resistance to S. japonicum. The alpha diversity of colon microbiota was reduced after the infection, but it gradually recovered along with self-healing process. Further LEfSe analysis revealed that phyla shifted from Firmicutes to Bacteroidetes, which were mainly driven by an increase of Ruminococcaceae and a depletion of Muribaculaceae in the family level along the Control-Infection-Recovery (CIR) process. We identified a temporary blooming of Lactobacillaceae and Lactobacillus in the mid infection stage (D14). As a recognized probiotics repository, we speculate the increased abundance of Lactobacillaceae in M. fortis colonic microbiota might relate to the natural resistance to the schistosome. Besides, potential microbial functions were also significantly changed in the resistance process. These results demonstrate the remarkable alterations of reed vole colonic microbiota in both community structure and potential functions along with the resistance to S. japonicum infection. The identified microbial biomarkers might offer new ways for drug development to conquer human schistosomiasis.

Endophyte-Infected Tall Fescue Affects Rumen Microbiota in Grazing Ewes at Gestation and Lactation

Tall fescue (Schedonorus arundinaceus) is a cool-season perennial grass that is widely used as a forage for many livestock species including sheep. An endophyte (Neotyphodium coenophialum) in tall fescue produces ergot alkaloids that enhance plant survival but produce toxicosis in animals. The objective of this study was to investigate the rumen microbiota from gestation and lactation in ewes grazing tall fescue pastures with high (HA) or moderate (MA) levels of endophyte infection, and their relationship with serum parameters. Data were collected at the beginning of the study (d1), the week before initiation of lambing (d51), and at the end of the trial (d115). The rumen microbiota was evaluated using 16S rRNA gene sequencing. Ewes grazing HA had greater serum non-esterified fatty acid (NEFA) (P = 0.024) levels compared with ewes in MA pasture at d115. Both the number of observed OTUs and Shannon diversity index tended (P = 0.08, P = 0.06) to be greater for HA than for MA on d115. At the genus level, Prevotella relative abundance increased with time in both MA and HA (on d1, d51, and d115: 15.17, 25.59, and 24.78% in MA; 14.17, 18.10, and 19.41% in HA). Taxa unclassified at the genus level including (unclassified) Lachnospiraceae, Coriobacteriaceae, and Veillonellaceae exhibited higher abundances in HA at d51 (3.72, 2.07, and 11.22%) compared with MA (2.06, 1.28, and 7.42%). The predictor microbiota for HA and MA were identified by a random forest classification model. The HA predictors included bacteria associated with unclassified Coriobacteriaceae and Ruminococcaceae. Other OTUs classified as Prevotella and Clostridiales could be microbial predictors for MA. The OTUs classified as Prevotella and Lachnospiraceae were negatively correlated with serum concentration of prolactin. Negative correlations with NEFA were observed in the microbiota such as species affiliated to unclassified Clostridiales and Prevotella. OTUs classified as Bacteroidetes and Coriobacteriaceae exhibited a positive correlation with NEFA. Our study confirmed that the rumen microbiota populations were affected by high levels of toxins in endophyte-infected tall fescue and were associated with host hormone and energy metabolism.

Brisket Disease Is Associated with Lower Volatile Fatty Acid Production and Altered Rumen Microbiome in Holstein Heifers

Simple Summary

Development of the dairy industry in the high-altitude plateau environment through incorporation of Holstein cows is complicated by the risk of brisket disease. While the physiological effects of brisket disease are well-studied, its effects on rumen function and microbial community composition are not. There are clear shifts in volatile fatty acids production and rumen microbial community composition in Holstein heifers suffering from brisket disease. Observed shifts reveal key genera associated with healthy and disease states and suggest that bovine brisket disease is associated with impaired rumen functioning. This work supports further understanding of the roles of key rumen taxa in bovine brisket disease, with particular focus on candidate rumen biomarkers in healthy animals that may be able to reduce economic losses for farmers.

Abstract

Brisket disease is heritable but is also associated with non-genetic risk factors and effects of the disease on the rumen microbiome are unknown. Ten Holstein heifers were exposed to the plateau environment for three months and divided into two groups according to the index of brisket disease, the mean pulmonary arterial pressure (mPAP): brisket disease group (BD, n = 5, mPAP > 63 mmHg) and healthy heifer group (HH, n = 5, mPAP < 41 mmHg). Rumen fluid was collected for analysis of the concentrations of volatile fatty acids (VFAs). Extracted DNA from rumen contents was analyzed using Illumina MiSeq 16S rRNA sequencing technology. The concentration of total VFA and alpha-diversity metrics were significantly lower in BD group (p < 0.05). Ruminococcus and Treponema were significantly decreased in BD heifers (p < 0.05). Correlation analysis indicated that 10 genera were related to the mPAP (p < 0.05). Genera of Anaerofustis, Campylobacter, and Catonella were negatively correlated with total VFA and acetic acid (R < −0.7, p < 0.05), while genera of Blautia, YRC22, Ruminococcus, and Treponema were positively related to total VFA and acetic acid (R > 0.7; p < 0.05). Our findings may be a useful biomarker in future brisket disease work.

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

The dynamics of the community structure and composition of the dairy cow fecal bacterial communities during early lactation is unclear, therefore this study was conducted to characterize the fecal bacterial communities in dairy cows during early lactation using 16S rRNA gene sequencing. Feces were sampled from 20 healthy fresh Holstein dairy cows on day 1 (Fresh1d group) and day 14 (Fresh14d group) after calving. After calving, cows were fed the same fresh diet. The dominant phyla Firmicutes and Proteobacteria were decreased (P ≤ 0.01) with lactating progress and phyla Bacteroidetes were increased (P = 0.008) with lactating progress and dietary transition. At family level, the predominant families were Ruminococcaceae (35.23%), Lachnospiraceae (11.46%), Rikenellaceae (10.44%) and Prevotellaceae (6.89%). A total of 14 genera were different between fecal samples from Fresh1d and Fresh14d, included the predominant genera, such as Ruminococcaceae_UCG-005 (P = 0.008), Rikenellaceae_RC9_gut_group (P = 0.043) and Christensenellaceae_R-7_group (P = 0.008). All fecal bacterial communities shared members of the genera Ruminococcaceae_UCG-005, Bacteroides and Rikenellaceae_RC9_gut_group. These findings help to improve our understanding of the composition and structure of the fecal microbial community in fresh cows and may provide insight into bacterial adaptation time and dietary in lactating cows.

Effects of Bacillus amyloliquefaciens and Bacillus pumilus on Rumen and Intestine Morphology and Microbiota in Weanling Jintang Black Goat

The importance of Bacillus as feed additives in animals' production is well recognized. Bacillus amyloliquefaciens and Bacillus pumilus are involved in promoting animal growth performance and immunological indicators. However, their precise roles in the modulation of microbiota and immune response in goat rumen and intestines have not been investigated. The aim of the current work was to evaluate the impacts of Bacillus amyloliquefaciens fsznc-06 and Bacillus pumilus fsznc-09 in the development of rumen and small intestinal and microbial communities in rumen and caecum of weanling Jintang black goats. Morphological alterations of rumen and small intestine (duodenum, jejunum, and ileum) were evaluated by histochemical staining, and ruminal contents and cecal feces were analyzed by 16S rRNA sequencing in an Illumina NovaSeq platform. Morphological analysis showed that feeding weanling goats with Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09 enhanced ruminal papilla and small intestinal villus growth. In addition, 16S rRNA sequencing analysis indicated that microbial richness and diversity (Shannon, Simpson, Chao1, and ACE) and the relative richness of multiple or potential beneficial bacteria were higher in weaned black goats fed on Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09, but that of multiple or potentially pathogenic bacteria were lower, as compared with the control group. Tax4Fun analysis predicting the functional profiling of microbial communities showed that microbial communities in rumen or caecum were highly influential on metabolism and organism systems after feeding weanling goats with Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09. It was suggested that Bacillus amyloliquefaciens fsznc-06 and Bacillus pumilus fsznc-09 might be an auspicious antibiotic alternative to improve black goat growth and health by changing rumen and gut microbiota positively.

A Mixed Phytogenic Modulates the Rumen Bacteria Composition and Milk Fatty Acid Profile of Water Buffaloes

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

Microbiome and metabolic changes in milk in response to artemisinin supplementation in dairy cows

This study aimed to explore the effects of artemisinin (ART) on the milk microbiome and metabolites of dairy cow. A total of 12 mid-lactation Holstein dairy cows with similar parity, days in milk were randomly divided into 2 groups receiving either a total mixed ration (TMR) as the control group or this TMR and 120 g/d/head ART as the ART group. The milk samples were collected weekly to determine the contents, and end-of-trial (week 8) milk samples were used to identify microbial species and metabolite profiles by 16S rRNA sequencing and LC–MS analyses, respectively. We observed that the milk fat content significantly increased by ART treatment (P < 0.05). The bacterial community richness was significantly lower in the ART group (P < 0.05), while the diversity showed no difference (P > 0.05). Compared with its abundance in the control (CON) group, Firmicutes was significantly decreased, whereas Proteobacteria was significantly increased. Furthermore, in the ART group, the relative abundances of the genera Aerococcus, Staphylococcus, Corynebacterium_1 and Facklamia were significantly lower (P < 0.01). Metabolomics analysis revealed that ART significantly increasing the concentrations of glycerophospholipids, glycerolipids and flavonoids compared with those in the CON group. An enrichment analysis of the different metabolites showed that ART mainly affected glycerophospholipid metabolism and the pantothenate and CoA biosynthesis pathways. These findings revealed that ART supplementation could affect the milk microbiota and metabolites, that glycerophospholipids and glycerolipids could be potential biomarkers in the milk response to ART feed in dairy cows, and that ART changes substances in milk by maintaining lipid metabolism in the mammary gland.

Effect of gaseous hydrogen sulphide on growth performance and cecal microbial diversity of weaning pigs

The purpose of this study was to examine the effect of gaseous hydrogen sulphide on growth performance and cecal microbial diversity in weaning pigs. A total of 24 weaning pigs (Landrace × Yorkshire × Duroc; average body weight = 8.55 ± 0.68 kg；weaning at 28 days) were selected and randomly divided into four groups (six replicates in each group). The piglets were exposed to hydrogen sulphide (0, 5, 10 and 15 mg/m³) during the experiment period, which lasted 28 days in four controlled environmental chambers. The results showed that exposure to hydrogen sulphide reduced the average daily gain (ADG), average daily feed intake (ADFI), and increased the diarrhoea rate of piglets. Hydrogen sulphide could increase the abundance and diversity of intestinal microbiota. The abundance of Firmicutes and Proteobacteria increased and Bacteroides decreased in the treatment groups. Five biomarkers, such as Eubacterium_1coprostanoligenes, Clostridiales, Phascolarctobacterium, Acidaminococcaceae and Ruminococcaceae_UCG_002 were selected by Lefse analysis. Our results reveal that hydrogen sulphide damaged the growth performance and destroyed the microbial bacteria balance of weaning pigs. The concentrations of hydrogen sulphide should fall below 5 mg/m³.

Microbiota in Dung and Milk Differ Between Organic and Conventional Dairy Farms

Organic farming is increasingly promoted as a means to reduce the environmental impact of artificial fertilizers, pesticides, herbicides, and antibiotics in conventional dairy systems. These factors potentially affect the microbial communities of the production stages (soil, silage, dung, and milk) of the entire farm cycle. However, understanding whether the microbiota representative of different production stages reflects different agricultural practices - such as conventional versus organic farming - is unknown. Furthermore, the translocation of the microbial community across production stages is scarcely studied. We sequenced the microbial communities of soil, silage, dung, and milk samples from organic and conventional dairy farms in the Netherlands. We found that community structure of soil fungi and bacteria significantly differed among soil types, but not between organic versus conventional farming systems. The microbial communities of silage also did not differ among conventional and organic systems. Nevertheless, the dung microbiota of cows and the fungal communities in the milk were significantly structured by agricultural practice. We conclude that, while the production stages of dairy farms seem to be disconnected in terms of microbial transfer, certain practices specific for each agricultural system, such as the content of diet and the use of antibiotics, are potential drivers of shifts in the cow's microbiota, including the milk produced. This may reflect differences in farm animal health and quality of dairy products depending on farming practices.

Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition

Alfalfa (Medicago sativa L.) silage (AS) is an important feedstuff in ruminant nutrition. However, its high non-protein nitrogen content often leads to poor ruminal nitrogen retention. Various pre-ensiling treatments differing with respect to dry matter concentrations, wilting intensities and sucrose addition have been previously shown to improve the quality and true protein preservation of AS, and have substantial effects on in vitro ruminal fermentation of the resulting silages. However, it is unknown how these pre-ensiling treatments affect the ruminal microbiota composition, and whether alterations in the microbiota explain previously observed differences in ruminal fermentation. Therefore, during AS incubation in a rumen simulation system, liquid and solid phases were sampled 2 and 7 days after first incubating AS, representing an early (ET) and late (LT) time point, respectively. Subsequently, DNA was extracted and qPCR (bacteria, archaea, and anaerobic fungi) and prokaryotic 16S rRNA gene amplicon sequence analyses were performed. At the ET, high dry matter concentration and sucrose addition increased concentrations of archaea in the liquid phase (P = 0.001) and anaerobic fungi in the solid phase (P < 0.001). At the LT, only sucrose addition increased archaeal concentration in the liquid phase (P = 0.014) and anaerobic fungal concentration in the solid phase (P < 0.001). Bacterial concentrations were not affected by pre-ensiling treatments. The prokaryotic phylogenetic diversity index decreased in the liquid phase from ET to LT (P = 0.034), whereas the solid phase was not affected (P = 0.060). This is suggestive of a general adaption of the microbiota to the soluble metabolites released from the incubated AS, particularly regarding the sucrose-treated AS. Redundancy analysis of the sequence data at the genus level indicated that sucrose addition (P = 0.001), time point (P = 0.001), and their interaction (P = 0.001) affected microbial community composition in both phases. In summary, of the pre-ensiling treatments tested sucrose addition had the largest effect on the microbiota, and together with sampling time point affected microbiota composition in both phases of the rumen simulation system. Thus, microbiota composition analysis helped to understand the ruminal fermentation patterns, but could not fully explain them.

Gut Microbiome of Chinese Forest Musk Deer Examined across Gender and Age

Animal gut microbiota begins to colonize after birth and is functionally indispensable for maintaining the health of the host. It has been reported that gender and age influence the composition of the intestinal microbiome. However, the effects of gender and age on the intestinal microorganism of forest musk deer (FMD) remain unclear. The aim of this study was to establish the relationship between the structure and composition of fecal microbiota of male and female forest musk deer with age. Here, Illumina Miseq 300PE sequencing platform targeting 16S rRNA V3–V4 hypervariable region applied to define the fecal microbiota of male and female FMD with two age groups, juvenile (age 1–2 years) and adult (age 4–10 years). Alpha diversity index did not show significant difference in bacterial diversity between the males and females or among age groups. The intestinal microbiota of FMD was dominated by three phyla, the Firmicutes, Proteobacteria and Bacteroidetes regardless of gender and different ages. Higher proportions of Proteobacteria were found in adult male and juvenile female individuals. The composition of Bacteroidetes was stable with the gender and age of FMD. Interestingly, the relative abundance of genera Clostridiales and Bacteroidales were higher in the juvenile FMD. Conversely, proportions of Pseudomonas and Lachnospiraceae were abundant in the adult FMD. Higher proportions of Ruminococcaceae, Dore, and 5-7N15 were found in the juvenile male groups. They may reflect the different immune resistance of male and female individuals at different stages of development. This study explored the fecal microbiota composition of forest musk deer in relation to gender and age, which may provide an effective strategy for developing intestinal microecological preparations and potential musk deer breeding.

Perilla frutescens Leaf Alters the Rumen Microbial Community of Lactating Dairy Cows

Perilla frutescens (L.) Britt., an annual herbaceous plant, has antibacterial, anti-inflammation, and antioxidant properties. To understand the effects of P. frutescens leaf on the ruminal microbial ecology of cattle, Illumina MiSeq 16S rRNA sequencing technology was used. Fourteen cows were used in a randomized complete block design trial. Two diets were fed to these cattle: a control diet (CON); and CON supplemented with 300 g/d P. frutescens leaf (PFL) per cow. Ruminal fluid was sampled at the end of the experiment for microbial DNA extraction. Overall, our findings revealed that supplementation with PFL could increase ruminal fluid pH value. The ruminal bacterial community of cattle was dominated by Bacteroidetes, Firmicutes, and Proteobacteria. The addition of PFL had a positive effect on Firmicutes, Actinobacteria, and Spirochaetes, but had no effect on Bacteroidetes and Proteobacteria compared with the CON. The supplementation with PFL significantly increased the abundance of Marvinbryantia, Acetitomaculum, Ruminococcus gauvreauii, Eubacterium coprostanoligenes, Selenomonas_1, Pseudoscardovia, norank_f__Muribaculaceae, and Sharpea, and decreased the abundance of Treponema_2 compared to CON. Eubacterium coprostanoligenes, and norank_f__Muribaculaceae were positively correlated with ruminal pH value. It was found that norank_f__Muribaculaceae and Acetitomaculum were positively correlated with milk yield, indicating that these different genera are PFL associated bacteria. This study suggests that PFL supplementation could increase the ruminal pH value and induce shifts in the ruminal bacterial composition.

Microbiome and Metabolome Analyses of Milk From Dairy Cows With Subclinical Streptococcus agalactiae Mastitis-Potential Biomarkers

The microbial ecosystem in the udders of dairy cows directly influences the flavor and quality of milk. However, to our knowledge, no published research has analyzed the complex relationship between the udder microbiome and its associated metabolism in animals with subclinical mastitis. We identified the bacterial species and measured relative population numbers in the milk of cows with subclinical Streptococcus agalactiae mastitis (GBS) and compared this information to that from the milk of healthy cows. Metabolite profiles were determined to investigate correlations between the milk microbiota and metabolic factors in healthy vs. GBS dairy cows. Six milk samples from GBS cows and six from healthy cows were subjected to 16S rRNA gene sequencing to identify the microbial species using a MiSeq high-throughput sequencing apparatus. The metabolites present in the milk were identified by gas chromatography time-of-flight mass spectrometry. Both principal component analysis and orthogonal partial least squares discriminant analysis indicated that the metabolites were well-separated from each other in the milk samples from the two groups. GBS dramatically altered microbial diversity, and the GBS group had significantly fewer Proteobacteria, Actinobacteria, and Acidobacteria than the CON group, with greater relative abundance of Firmicutes (p < 0.01). Several bacterial genera, such as Streptococcus, were significantly more abundant in milk from the GBS group than in milk from the CON group, and there was a tendency for greater abundance of Turicibacter (p = 0.07) and Enterococcus spp. (p = 0.07) in the GBS group. The levels of five milk metabolites were significantly higher in the GBS group than in the CON group: phenylpyruvic acid, the homogentisic acid: 4-hydroxyphenylpyruvic acid ratio, the xanthine: guanine ratio, uridine and glycerol. Metabolic pathway analysis of the different metabolites revealed that the following were enriched in both groups: galactose metabolism; pentose and glucuronate interconversion; starch and sucrose metabolism; alanine, aspartate and glutamate metabolism; arginine biosynthesis; citrate cycle (TCA cycle); D-glutamine and D-glutamate metabolism; and the neomycin, kanamycin, and gentamicin biosynthesis pathways. Several typical metabolites were highly correlated with specific ruminal bacteria, such as Streptococcaceae, Lachnospiraceae, Lactobacillaceae and Corynebacteriaceae, demonstrating the functional correlations between the milk microbiome and associated metabolites. These findings revealed that the milk microbiota and metabolite profiles were significantly different between the two groups of cows, raising the question of whether the microbiota associated with the bovine mammary gland could be related to mammary gland health. There was also a relationship between milk quality and the presence of spoilage bacteria. Other bacterial taxa should be investigated, as related information may provide insights into how perturbations in milk metabolomics profiles relate to differences in milk synthesis between healthy cows and those with subclinical mastitis.

Temporal Dynamics in Rumen Bacterial Community Composition of Finishing Steers during an Adaptation Period of Three Months

The objective of this study was to explore whether collecting rumen samples of finishing steers at monthly intervals differed, and whether this difference or similarity varied with diets. For these purposes, 12 Chinese Holstein steers were equally divided into two groups. The dietary treatments were either standard energy and standard protein (C) or low energy and low protein (L). Rumen samples were obtained on day 30, day 60 and day 90 from both dietary treatments and were analyzed by using 16S rRNA gene sequencing. The results showed that monthly intervals had no effect on the richness and evenness of the rumen bacterial community in the two diets. However, taxonomic difference analysis (relative abundance >0.5%) revealed that the relative abundance of three phyla (Proteobacteria, Fibrobacteres and Cyanobacteria) and six genera (Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, Fibrobacter, Eubacterium_coprostanoligenes_group, Ruminococcaceae_UCG-010 and Ruminobacter) were significantly different between monthly sampling intervals, and the difference was prominent between sampling in the first month and the subsequent two months. Moreover, the differences in abundances of phyla and genera between monthly sampling intervals were affected by diets. Analysis of similarity (ANOSIM) showed no significant differences between monthly sampling intervals in the C diet. However, ANOSIM results revealed that significant differences between the first month and second month and between the first month and third month were present in the L diet. These results indicated that temporal dynamics in rumen bacterial community composition did occur even after an adaptation period of three months. This study tracked the changes in rumen bacterial populations of finishing cattle after a shift in diet with the passage of time. This study may provide insight into bacterial adaptation time to dietary transition in finishing steers.

Metabolomics reveals potential biomarkers in the rumen fluid of dairy cows with different levels of milk production

Objective

In the present study, an liquid chromatography/mass spectrometry (LC/MS) metabolomics approach was performed to investigate potential biomarkers of milk production in high- and low-milk-yield dairy cows and to establish correlations among rumen fluid metabolites.

Methods

Sixteen lactating dairy cows with similar parity and days in milk were divided into high-yield (HY) and low-yield (LY) groups based on milk yield. On day 21, rumen fluid metabolites were quantified applying LC/MS.

Results

The principal component analysis and orthogonal correction partial least squares discriminant analysis showed significantly separated clusters of the ruminal metabolite profiles of HY and LY groups. Compared with HY group, a total of 24 ruminal metabolites were significantly greater in LY group, such as 3-hydroxyanthranilic acid, carboxylic acids, carboxylic acid derivatives (L-isoleucine, L-valine, L-tyrosine, etc.), diazines (uracil, thymine, cytosine), and palmitic acid, while the concentrations of 30 metabolites were dramatically decreased in LY group compared to HY group, included gentisic acid, caprylic acid, and myristic acid. The metabolite enrichment analysis indicated that protein digestion and absorption, ABC transporters and unsaturated fatty acid biosynthesis were significantly different between the two groups. Correlation analysis between the ruminal microbiome and metabolites revealed that certain typical metabolites were exceedingly associated with definite ruminal bacteria; Firmicutes, Actinobacteria, and Synergistetes phyla were highly correlated with most metabolites.

Conclusion

These findings revealed that the ruminal metabolite profiles were significantly different between HY and LY groups, and these results may provide novel insights to evaluate biomarkers for a better feed digestion and may reveal the potential mechanism underlying the difference in milk yield in dairy cows.

Illumina MiSeq sequencing reveals the effects of grape seed procyanidin on rumen archaeal communities in vitro

Objective

The present study explored the effects of grape seed procyanidin extract (GSPE) on rumen fermentation, methane production and archaeal communities in vitro.

Methods

A completely randomized experiment was conducted with in vitro incubation in a control group (CON, no GSPE addition; n = 9) and the treatment group (GSPE, 1 mg/bottle GSPE, 2 g/kg dry matter; n = 9). The methane and volatile fatty acid concentrations were determined using gas chromatography. To explore methane inhibition after fermentation and the response of the ruminal microbiota to GSPE, archaeal 16S rRNA genes were sequenced by MiSeq high-throughput sequencing.

Results

The results showed that supplementation with GSPE could significantly inhibit gas production and methane production. In addition, GSPE treatment significantly increased the proportion of propionate, while the acetate/propionate ratio was significantly decreased. At the genus level, the relative abundance of Methanomassiliicoccus was significantly increased, while the relative abundance of Methanobrevibacter decreased significantly in the GSPE group.

Conclusion

In conclusion, GSPE is a plant extract that can reduce methane production by affecting the structures of archaeal communities, which was achieved by a substitution of Methanobrevibacter with Methanomassiliicoccus.