The rumen microbiota is strongly associated with host health, nutrient absorption, and adaptability. However, the composition, functioning and adaptability of rumen microbiota in Tibetan sheep (TS) ...across different phenological periods are unclear. In this study we used sequencing of the V4-V5 region of 16S rRNA, qPCR technology and metagenomics to investigate the adaption of rumen microbiota to forage in different stages of phenology. In a grassy period, due to the high nutritional quality of the forage, TS can produce high concentrations of NH
3
-N and short fatty acids by increasing the content of key bacteria in the rumen, such as Bacteroidetes,
Prevotella
,
Succiniclasticum
,
Treponema
,
Butyrivibrio fibrisolvens
,
Fibrobacter succinogenes
,
Prevotella ruminicola
,
Ruminococcus albus
, and
Ruminococcus flavefaciens
to aid in growth. In the withering period, there was a positive correlation between microorganisms which indicated the closely cooperation between microorganisms, and metagenomic analysis showed that the high genes (GHs and CBMs) and subtribe (GH8, GH12, GH45, GH6, GH9, GH5, GH10, GH3, GH52, GH11, GH57, CBM1, CBM4, CBM6, CBM16, CBM37, CBM13, CBM35, CBM42, CBM32, and CBM62) that encode cellulolytic enzymes were significantly increased when the host faced low quantity and quality of forage. Genes involved in metabolic pathways, fatty acid biosynthesis and biosynthesis of antibiotics were significantly enriched, which indicated that rumen microbiota could improve plant biomass deconstruction and energy maintenance in the face of nutritional deficiencies. In the regreen period, both the composition and function of rumen microbiota had obvious disadvantages, therefore, to improve the competitiveness of microorganisms, we suggest TS should be supplemented with high-protein feed. This study is of great significance for exploring the high altitude adaptability of TS.
In modern breeding systems, cows are subjected to many stress factors. Animals fed with a high-grain diet may have a decreased rumen pH, which would lead to subacute ruminal acidosis syndrome. The ...aim of this study was to investigate the evolution of microbial community composition in cows undergoing a dietary stress challenge. Twelve cows were subjected to a challenge period consisted in a rapid change of ration, from a normal (45.4:54.6 forage: concentrate) to a high-grain content diet (24.8:75.2 forage: concentrate) to induce sub-acute ruminal acidosis. Individual rumen fluid content samples were collected before (T0), and during the challenge (T3, T14, T28). DNA from rumen contents was extracted, purified, and sequenced to evaluate Bacterial populations and sequencing was performed on Illumina MiSeq. The effect of animal conditions on rumen microbial community was quantified through a linear mixed model. The acidogenic diet created 2 main clusters: ruminal hypomotility (RH) and milk fat depression (MFD). The microbial composition did not differ in T0 between the 2 groups, while during the challenge Ruminococcus spp., Treponema spp., Methanobrevibacter spp., and Methanosphaera spp. concentrations increased in RH cows; Succinivibrio spp. and Butyrivibrio spp. concentrations increased in MFD cows. Prevotella spp. and Ruminococcus spp., were negatively correlated, while Christenellaceae family were positively correlated with both Methanobrevibacter spp. and Methanosphaera spp. Moreover, the same diet affected differently cows' microbiota composition, underlying the impact of the host effect. Other studies are necessary to deepen the relationship between microbiota composition and host.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Many strategies for mitigating enteric methane (CH4) emissions in ruminants have focused on suppressing the activity of rumen methanogens, but this often leads to excess dihydrogen (H2) accumulation ...in the rumen, which is subsequently expelled and represents a potential energy loss. We hypothesized that phloroglucinol could act as a H2 acceptor when rumen methanogenesis is inhibited and be potentially transformed into beneficial compounds for the animal. Eight adult goats were randomly assigned to a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments: two levels of Asparagopsis taxiformis as CH4 inhibitor 0 vs. 5g/kg on a dry matter (DM) basis; AT- and AT+, respectively and two levels of phloroglucinol as alternative H2 acceptor (0 vs. 20g/kg DM, PG- and PG+, respectively). Therefore, four dietary treatments were considered: i) basal diet (AT-PG-); ii) A. taxiformis alone (AT+PG-); iii) phloroglucinol alone (AT-PG+); and iv) the combination of A. taxiformis and phloroglucinol (AT+PG+). Animals were fed a maintenance diet with a 70:30 forage-to-concentrate ratio. After 10 d of adaptation to the diet, enteric gas emissions were measured in respiration chambers during 3 d prior to rumen content sampling on d 14. Dietary supplementation with A. taxiformis decreased CH4 production (-33.9%) and increased H2 emissions (+3465%), along with greater rumen propionate concentration. In contrast, phloroglucinol supplementation alone did not impact CH4 emissions or the rumen concentration of the main microbial groups but substantially increased acetate molar proportion (+10.2%) which could act as an alternative H2 acceptor. Moreover, when A. taxiformis was combined with phloroglucinol, it resulted in a decrease in H2 emissions (-68.1%). However, this decrease in H2 emissions was not fully explained by the increase in the acetate as phloroglucinol led to an increase in acetate both when methanogenesis was inhibited and when it was not. These findings suggest that the rumen fermentation of phloroglucinol may capture some of the additional H2 arising from the inhibition of methanogenesis by A. taxiformis through pathways other than acetate formation. Moreover, H2 emissions were not eliminated and most of the decrease occurred during the post-prandial stage, suggesting that the efficiency of H2 redirection could be further improved.
•Asparagopsis taxiformis acts as a CH4 inhibitor resulting in an excess rumen H2 production•Acetate production from phloroglucinol degradation can act as H2 acceptor•These effects are particularly evident during postprandial periods•The combined mitigation strategy could favour rumen fermentation efficiency
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
is an ecologically important rumen bacterium that metabolizes lactate and relieves rumen acidosis (RA) induced by a high-grain-diet. Understanding the regulatory mechanisms of the lactate metabolism ...of this species in RA conditions might contribute to developing dietary strategies to alleviate RA.
was co-cultured with four lactate producers (
,
,
, and
) and a series of substrate starch doses (1, 3, and 9 g/L) were used to induce one normal and two RA models (subacute rumen acidosis, SARA and acute rumen acidosis, ARA) under batch conditions. The associations between bacterial competition and the shift of organic acids' (OA) accumulation patterns in both statics and dynamics manners were investigated in RA models. Furthermore, we examined the effects of substrate lactate concentration and pH on
lactate degradation pattern and genes related to the lactate utilizing pathways in the continuous culture.
The positive growth of
and
caused OA accumulation in the SARA model to shift from lactate to butyrate and resulted in pH recovery. Furthermore, both the quantities of substrate lactate and pH had remarkable effects on
lactate utilization due to the transcriptional regulation of metabolic genes, and the lactate utilization in
was more sensitive to pH changes than to the substrate lactate level. In addition, compared with associations based on statics data, associations discovered from dynamics data showed greater significance and gave additional explanations regarding the relationships between bacterial competition and OA accumulation.
Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is ...scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows.
We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera:
, and
(RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (
> 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (
< 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (
< 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database.
The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.
Increasing the nitrogen-utilization efficiency (NUE) of dairy cows by breeding selection would offer advantages from nutritional, environmental, and economic perspectives. Because data collection of ...NUE phenotypes is not feasible in large cow cohorts, the cow individual milk urea concentration (MU) has been suggested as an indicator trait. Considering the symbiotic interplay between dairy cows and their rumen microbiome, individual MU was thought to be influenced by host genetics and by the rumen microbiome, the latter in turn being partly attributed to host genetics. To enhance our knowledge of MU as an indicator trait for NUE, we aimed to identify differential abundant rumen microbial genera between Holstein cows with divergent genomic breeding values for MU (GBVMU; GBVHMU vs. GBVLMU, where H and L indicate high and low MU phenotypes, respectively). The microbial genera identified were further investigated for their correlations with MU and 7 additional NUE-associated traits in urine, milk, and feces in 358 lactating Holsteins. Statistical analysis of microbial 16S rRNA amplicon sequencing data revealed significantly higher abundances of the ureolytic genus Succinivibrionaceae UCG-002 in GBVLMU cows, whereas GBVHMU animals hosted higher abundances of Clostridia unclassified and Desulfovibrio. The entire discriminating ruminal signature of 24 microbial taxa included a further 3 genera of the Lachnospiraceae family that revealed significant correlations to MU values and were therefore proposed as considerable players in the GBVMU–microbiome–MU axis. The significant correlations of Prevotellaceae UCG-003, Anaerovibrio, Blautia, and Butyrivibrio abundances with MU measurements, milk nitrogen, and N content in feces suggested their contribution to genetically determined N-utilization in Holstein cows. The microbial genera identified might be considered for future breeding programs to enhance NUE in dairy herds.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
•Carcass, meat traits, and rumen bacteria were analysed between two sheep breeds.•Dorper × Chinese Mongolian crossbred sheep had a faster growth rate.•Dorper × Chinese Mongolian crossbred sheep had ...better carcass traits.•Metabolites and rumen bacteria differed between two sheep breeds.•The study benefits breeding strategies of improving carcass and meat traits.
Mutton is one of the most widely consumed meats globally. The Chinese Mongolian sheep (MS) breed is an indigenous breed of sheep characterised by high-quality meat and strong adaptability. Dorper × Chinese Mongolian crossbred sheep (DS) is an improved breed with a rapid growth rate and high mutton yield found in parts of China. The rumen microbiota is known to play a key role in shaping host nutrition and health. However, the carcass traits and meat nutritional qualities of DS and MS remain poorly defined, as does how rumen microbes affect these characteristics. The objective of this study was to compare carcass profiles, rumen bacterial communities, and meat nutritional qualities between MS and DS and clarify the associations between rumen microbiota and meat nutritional composition. We found that DS had a faster growth rate and better carcass traits than MS, including BW, carcass weight, meat weight, and loin-eye area. We further found that metabolite and rumen bacterial community composition differed between the two sheep breeds. First, compared with MS, DS had lower contents of some sweet amino acids, monounsaturated fatty acids, n-3 polyunsaturated fatty acids, and beneficial metabolites. Secondly, MS and DS had distinct rumen bacterial compositions, and these differential bacteria were related to carcass traits as well as to contents of meat amino acids, free fatty acids, and other metabolites. Taken together, our data showed that DS had better carcass characteristics but lower meat nutritional quality, parameters that were associated with differences in rumen bacterial community composition. These findings may benefit future breeding strategies aimed at improving sheep carcass performance and meat quality worldwide.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Zearalenone (ZEN) and fumonisins (FUM) jeopardize fertility and health in cattle; yet, their toxigenic effects on rumen health and microbiota, both being crucial for animal health, are not clarified. ...This study determined the effects of a short-term exposure to ZEN or FUM on the rumen ecosystem, and further evaluated acute implications on health parameters. Six cows were fed a basal diet with 40% grain (dry matter basis) and exposed to either 5 mg of ZEN or 20 mg of FUM daily for two consecutive days each, separated by a 7-days washout period. The exposure to ZEN or FUM led to a reduction of Lachnospiraceae and Prevotellaceae in the rumen. Similarly, ZEN lowered the ruminal pH and total short-chain fatty acid concentration, despite increased rumination activity of the cows. Fumonisins increased the number of observed features and significantly impacted β-diversity structure and metagenome predicted function. At the systemic level, FUM exposure suggested an immediate hepatotoxic effect, as evidenced by increased liver enzyme concentrations, which were accompanied by altered heart and respiratory rates. Similarly, ZEN increased the body temperature up to a mild fever. Concluding, short-term exposure to ZEN and FUM can harm the rumen ecosystem and acutely impair systemic health.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Lignocellulosic biomass is an abundant resource with untapped potential for biofuel, enzymes, and chemical production. Its complex recalcitrant structure obstructs its bioconversion into biofuels and ...other value-added products. For improving its bioconversion efficiency, it is important to deconstruct its complex structure. In natural systems like rumen, diverse microbial communities carry out hydrolysis, acidogenesis, acetogenesis, and methanogenesis of lignocellulosic biomass through physical penetration, synergistic and enzymatic actions enhancing lignocellulose degradation activity. This review article aims to discuss comprehensively the rumen microbial ecosystem, their interactions, enzyme production, and applications for efficient bioconversion of lignocellulosic waste to biofuels. Furthermore, meta ‘omics’ approaches to elucidate the structure and functions of rumen microorganisms, fermentation mechanisms, microbe-microbe interactions, and host-microbe interactions have been discussed thoroughly. Additionally, feed additives' role in improving ruminal fermentation efficiency and reducing environmental nitrogen losses has been discussed. Finally, the current status of rumen microbiota applications and future perspectives for the development of rumen mimic bioreactors for efficient bioconversion of lignocellulosic wastes to biofuels and chemicals have been highlighted.
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•Application of rumen microbiota for enhanced biomass conversion is assessed.•Biomimicry of rumen digestion aids in designing anaerobic bioreactors.•Synergism between rumen microbes and enzymes efficiently convert biomass to biofuel.•Omics gives valuable insights of microbial community structure and functions.•Prospects on the development of an efficient anaerobic digestion system are proposed.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Limited lignocellulose degradation is the primary obstacle to feed digestion efficiency in ruminant animals. Low-quality forage with high levels of fibrous components can favor the proliferation of ...fibrolytic bacteria, but whether this can result a profound microbial shift after dietary intervention remains unclear. In this study, we monitored the microbial communities in the rumens of five ruminally cannulated Hu sheep through dietary transition from alfalfa hay (AH, pre-CS) to corn stover (CS, post-CS) and then back to AH (post-AH), with each treatment lasting for 14 days. The CS intervention significantly increased the relative abundance of microorganisms involved in lignocellulose degradation, including
and
. When the diet was switched back to AH, the microbial community did not completely return to a pre-CS treatment state. In the post-AH microbial community, the relative abundances of
and
were persistently high, and were similar to those in the post-CS community. Meanwhile, the diversity of the microbial community increased after dietary transition from AH to CS and remained significantly higher after transition from CS to AH compared to those under the original AH diet. Enzyme activity measurement verified significant increase of carboxymethyl cellulase (CMCase) and xylanase catalytic activities in the rumen. Microbial functional predictions using Tax4Fun revealed that this microbial persistence may enhance the carbohydrate metabolism pathway in the rumen. In summary, persistence of
and
can be enhanced through a low-quality forage intervention at least for 2 weeks, which may enlighten the reprogram of microbial population in the rumen in the future.
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