Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions

Aerobic or anaerobic? Microbial degradation of per- and polyfluoroalkyl substances: A review

The widespread utilization of per- and polyfluoroalkyl substances (PFASs) as "forever chemicals" is posing significant environmental risks and adverse effects on human health. Microbial degradation (e.g., bacteria and fungi) has been identified as a cost-effective and environmentally friendly method for PFAS degradation. However, its degradation efficiency, biotransformation pathway, and microbial mechanism vary significantly under aerobic and anaerobic conditions. This review provides a comprehensive overview of the similarities and differences in PFAS microbial degradation by bacteria and fungi under different oxygen conditions. Initially, the efficiencies and metabolites of PFAS microbial degradation were compared under aerobic and anaerobic conditions, including perfluorinated and polyfluorinated compounds. Additionally, the microbial mechanisms of PFAS microbial degradation were obtained by summarizing key degrading microbes and enzymes. Finally, the comparisons between aerobic and anaerobic conditions in PFAS microbial degradation were provided, addressing the main challenges and proposing future research directions focused on seeking combined biodegradation techniques, exploring novel microbial species capable of degrading PFAS, and confirming complete biodegradation pathways. The understanding of PFAS microbial degradation in aerobic and anaerobic environments is crucial for providing potential solutions and future research efforts in dealing with these "forever chemicals".

Metagenomics-Metabolomics Exploration of Three-Way-Crossbreeding Effects on Rumen to Provide Basis for Crossbreeding Improvement of Sheep Microbiome and Metabolome of Sheep

The objective of this experiment was to explore the effects of three-way hybridization on rumen microbes and metabolites in sheep using rumen metagenomics and metabolomics. Healthy Hu and CAH (Charolais × Australian White × Hu) male lambs of similar birth weight and age were selected for short-term fattening after intensive weaning to collect rumen fluid for sequencing. Rumen metagenomics diversity showed that Hu and CAH sheep were significantly segregated at the species, KEGG-enzyme, and CAZy-family levels. Moreover, the CAH significantly increased the ACE and Chao1 indices. Further, correlation analysis of the abundance of the top 80 revealed that the microorganisms were interrelated at the species, KEGG-enzyme, and CAZy-family levels. Overall, the microbiome significantly affected metabolites of the top five pathways, with the strongest correlation found with succinic acid. Meanwhile, species-level microbial markers significantly affected rumen differential metabolites. In addition, rumen microbial markers in Hu sheep were overall positively correlated with down-regulated metabolites and negatively correlated with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs were overall negatively correlated with down-regulated metabolites and positively correlated with up-regulated metabolites. These results suggest that three-way crossbreeding significantly affects rumen microbial community and metabolite composition, and that significant interactions exist between rumen microbes and metabolites.

Development of a defined medium for the heterotrophic cultivation of Metallosphaera sedula

The heterotrophic cultivation of extremophilic archaea still heavily relies on complex media. However, complex media are associated with unknown composition, high batch-to-batch variability, potential inhibiting and interfering components, as well as regulatory challenges, hampering advancements of extremophilic archaea in genetic engineering and bioprocessing. For Metallosphaera sedula, a widely studied organism for biomining and bioremediation and a potential production host for archaeal ether lipids, efforts to find defined cultivation conditions have still been unsuccessful. This study describes the development of a novel chemically defined growth medium for M. sedula. Initial experiments with commonly used complex casein-derived media sources deciphered Casamino Acids as the most suitable foundation for further development. The imitation of the amino acid composition of Casamino Acids in basal Brock medium delivered the first chemically defined medium. We could further simplify the medium to 5 amino acids based on the respective specific substrate uptake rates. This first defined cultivation medium for M. sedula allows advanced genetic engineering and more controlled bioprocess development approaches for this highly interesting archaeon.

Defluorination of monofluorinated alkane by Rhodococcus sp. NJF-7 isolated from soil

Microbial degradation of fluorinated compounds raised significant attention because of their widespread distribution and potential environmental impacts. Here, we report a bacterial isolate, Rhodococcus sp. NJF-7 capable of defluorinating monofluorinated medium-chain length alkanes. This isolate consumed 2.29 ± 0.13 mmol L- 1 of 1-fluorodecane (FD) during a 52 h incubation period, resulting in a significant release of inorganic fluoride amounting to 2.16 ± 0.03 mmol L- 1. The defluorination process was strongly affected by the initial FD concentration and pH conditions, with lower pH increasing fluoride toxicity to bacterial cells and inhibiting enzymatic defluorination activity. Stoichiometric conversion of FD to fluoride was observed at neutral pH with resting cells, while defluorination was significantly lower at reduced pH (6.5). The discovery of the metabolites decanoic acid and methyl decanoate suggests that the initial attack by monooxygenases may be responsible for the biological defluorination of FD. The findings here provide new insights into microbial defluorination processes, specifically aiding in understanding the environmental fate of organic semi-fluorinated alkane chemicals.

Relationship between Rumen Microbial Differences and Phenotype Traits among Hu Sheep and Crossbred Offspring Sheep

This experiment was conducted to investigate the effect of three-way hybrid sheep and Hu sheep on serum indicators, rumen fermentation, rumen enzyme activity, and microorganisms in sheep. Healthy and similar birth weights from three groups (Hu, n = 11; Charolais × Australian White × Hu, CAH, n = 11; Charolais × Dorper × Hu, CDH, n = 11) were selected to be fed by the ewes until 45 days of age. Subsequently, they were weaned intensively and underwent short-term fattening for 3 months along with selected male lambs fed intensively. During this period, they were fed and watered ad libitum. Blood and rumen fluid were collected and analyzed for serum indicators and rumen fluid microorganisms, enzyme activity, and VFA, respectively, at the end of the fattening period. Compared with Hu lamb, the offspring of the three-way hybrid lamb showed significant improvements in body weight, serum lactate dehydrogenase, and creatinine content. However, there was no significant effect on serum immunity and antioxidant indices. In addition, the rumen fluid volatile fatty acid (VFA) molar concentration and microcrystalline cellulose and lipase content were significantly lower in the three-way hybrid lamb compared to Hu lamb, but β-glucosidase, amylase, pepsin, and VFA molar ratio were not significantly affected. Subsequently, 16S rRNA sequencing diversity analysis revealed that three-way hybrid lamb significantly increased rumen microbial ACE and Chao1 indices compared to Hu lamb. Meanwhile, the abundance of Verrucomicrobiota and Synergistota significantly increased at the phylum level. Correlation analysis showed that Prevotella had the highest proportion, while Rikenellaceae_RC9_gut_group correlated most closely with others genus. The microbial communities isovaleric acid molar concentration and proportion were strongly correlated. In addition, there were significant differences in correlations between microbial communities and isobutyric acid, butyric acid and valeric acid content, and their molar proportion, but they were not significantly correlated with digestive enzymes. From the functional enrichment analysis, it was found that hybrid progeny were mainly enriched in the pyruvate metabolism, microbial metabolism in diverse environments, carbon metabolism, and quorum sensing pathways. In contrast, the Hu sheep were primarily enriched in the cysteine and methionine, amino sugar and nucleotide sugar, and biosynthesis of secondary metabolite pathways. These results suggest that hybridization can play a role in regulating organismal metabolism and improve animal production performance by influencing the structure and characteristics of microbial communities.

Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum Synergistota

OBJECTIVE

Monofluoroacetate (MFA) is a potent toxin that blocks ATP production via the Krebs cycle and causes acute toxicity in ruminants consuming MFA-containing plants. The rumen bacterium, Cloacibacillus porcorum strain MFA1 belongs to the phylum Synergistota and can produce fluoride and acetate from MFA as the end-products of dehalorespiration. The aim of this study was to identify the genomic basis for the metabolism of MFA by this bacterium.

METHODS

A draft genome sequence for C. porcorum strain MFA1 was assembled and quantitative transcriptomic analysis was performed thus highlighting a candidate operon encoding four proteins that are responsible for the carbon-fluorine bond cleavage. Comparative genome analysis of this operon was undertaken with three other species of closely related Synergistota bacteria.

RESULTS

Two of the genes in this operon are related to the substrate-binding components of the glycine reductase protein B (GrdB) complex. Glycine shares a similar structure to MFA suggesting a role for these proteins in binding MFA. The remaining two genes in the operon, an antiporter family protein and an oxidoreductase belonging to the radical S-adenosyl methionine superfamily, are hypothesised to transport and activate the GrdB-like protein respectively. Similar operons were identified in a small number of other Synergistota bacteria including type strains of Cloacibacillus porcorum, C. evryensis, and Pyramidobacter piscolens, suggesting lateral transfer of the operon as these genera belong to separate families. We confirmed that all three species can degrade MFA, however, substrate degradation in P. piscolens was notably reduced compared to Cloacibacillus isolates possibly reflecting the loss of the oxidoreductase and antiporter in the P. piscolens operon.

CONCLUSION

Identification of this unusual anaerobic fluoroacetate metabolism extends the known substrates for dehalorespiration and indicates the potential for substrate plasticity in amino acid-reducing enzymes to include xenobiotics.

Magnetite Alters the Metabolic Interaction between Methanogens and Sulfate-Reducing Bacteria

It is known that the presence of sulfate decreases the methane yield in the anaerobic digestion systems. Sulfate-reducing bacteria can convert sulfate to hydrogen sulfide competing with methanogens for substrates such as H2 and acetate. The present work aims to elucidate the microbial interactions in biogas production and assess the effectiveness of electron-conductive materials in restoring methane production after exposure to high sulfate concentrations. The addition of magnetite led to a higher methane content in the biogas and a sharp decrease in the level of hydrogen sulfide, indicating its beneficial effects. Furthermore, the rate of volatile fatty acid consumption increased, especially for butyrate, propionate, and acetate. Genome-centric metagenomics was performed to explore the main microbial interactions. The interaction between methanogens and sulfate-reducing bacteria was found to be both competitive and cooperative, depending on the methanogenic class. Microbial species assigned to the Methanosarcina genus increased in relative abundance after magnetite addition together with the butyrate oxidizing syntrophic partners, in particular belonging to the Syntrophomonas genus. Additionally, Ruminococcus sp. DTU98 and other species assigned to the Chloroflexi phylum were positively correlated to the presence of sulfate-reducing bacteria, suggesting DIET-based interactions. In conclusion, this study provides new insights into the application of magnetite to enhance the anaerobic digestion performance by removing hydrogen sulfide, fostering DIET-based syntrophic microbial interactions, and unraveling the intricate interplay of competitive and cooperative interactions between methanogens and sulfate-reducing bacteria, influenced by the specific methanogenic group.

A review of microbial degradation of per- and polyfluoroalkyl substances (PFAS): Biotransformation routes and enzymes

Since the 1950s, copious amounts of per- and polyfluoroalkyl substances (PFAS) (dubbed "forever chemicals") have been dumped into the environment, causing heavy contamination of soil, surface water, and groundwater sources. Humans, animals, and the environment are frequently exposed to PFAS through food, water, consumer products, as well as waste streams from PFAS-manufacturing industries. PFAS are a large group of synthetic organic fluorinated compounds with widely diverse chemical structures that are extremely resistant to microbial degradation. Their persistence, toxicity to life on earth, bioaccumulation tendencies, and adverse health and ecological effects have earned them a "top priority pollutant" designation by regulatory bodies. Despite that a number of physicochemical methods exist for PFAS treatment, they suffer from major drawbacks regarding high costs, use of high energy and incomplete mineralization (destruction of the CF bond). Consequently, microbial degradation and enzymatic treatment of PFAS are highly sought after as they offer a complete, cheaper, sustainable, and environmentally friendly alternative. In this critical review, we provide an overview of the classification, properties, and interaction of PFAS within the environment relevant to microbial degradation. We discuss latest developments in the biodegradation of PFAS by microbes, transformation routes, transformation products and degradative enzymes. Finally, we highlight the existing challenges, limitations, and prospects of bioremediation approaches in treating PFAS and proffer possible solutions and future research directions.

Anaerobic co-digestion of three commercial bio-plastic bags with food waste: Effects on methane production and microbial community structure

The emergence of bioplastic bags as a replacement for traditional petroleum-based plastic bags is promising for their simultaneous anaerobic digestion with food waste. In this study, the degradation of three bioplastic bags is evaluated during anaerobic co-digestion with food waste under mesophilic/thermophilic conditions, and the results indicated PBAT/PLA/starch > PLA > PBAT for methane production rate. The PBAT/PLA/starch mixture produced 23.4 ml/g of methane at 55 °C, and the cumulative methane production increased by 28.4 % compared to the control. In addition, the lag time before methane production was reduced by one to four days when anaerobic co-digestion was performed under thermophilic conditions, and the conversion of the bioplastics improved by 9.11-11.2 %. Microscopy further showed obvious physical degradation of the PBAT/PLA/starch material. The FTIR analysis showed that the characteristic peaks of the material at 3320, 2957, and 934 cm^-1 decreased significantly after anaerobic fermentation. The biodegradability of the polymer decreased with an increase in the content of the crystalline area in the structure. The addition of a comonomer reduced the crystallinity of the polymer. In addition, the biodegradability was increased by adjusting the hydrolysis reaction and microbial activity of the polymer surface. An analysis of the structural features of the microbial communities revealed that Archaea exhibited different biodiversity at distinct temperatures. In particular, under thermophilic conditions, the relative abundance of Methanothermobacter was 56.0 %, and it plays an important role in the anaerobic degradation of PBAT/PLA/starch materials, while bacterial communities showed smaller differences. Overall, the bioplastic was able to be co-digested anaerobically with food waste to produce renewable energy. This study provides a plan for the practical application of biodegradable plastic bag collection for the combined treatment of food waste in anaerobic digesters. It provides a theoretical basis for modifications of bioplastic and domestication of anaerobic microorganisms.

Microbial Defluorination of Unsaturated Per- and Polyfluorinated Carboxylic Acids under Anaerobic and Aerobic Conditions: A Structure Specificity Study

The recently discovered microbial reductive defluorination of two C₆ branched and unsaturated fluorinated carboxylic acids (FCAs) provided valuable insights into the environmental fate of per- and polyfluoroalkyl substances (PFASs) and potential bioremediation strategies. However, a systematic investigation is needed to further demonstrate the role of C═C double bonds in the biodegradability of unsaturated PFASs. Here, we examined the structure-biodegradability relationships of 13 FCAs, including nine commercially available unsaturated FCAs and four structurally similar saturated ones, in an anaerobic defluorinating enrichment and an activated sludge community. The anaerobic and aerobic transformation/defluorination pathways were elucidated. The results showed that under anaerobic conditions, the α,β-unsaturation is crucial for FCA biotransformation via reductive defluorination and/or hydrogenation pathways. With sp² C-F bonds being substituted by C-H bonds, the reductive defluorination became less favorable than hydrogenation. Moreover, for the first time, we reported enhanced degradability and defluorination capability of specific unsaturated FCA structures with trifluoromethyl (-CF₃) branches at the α/β-carbon. Such FCA structures can undergo anaerobic abiotic defluorination in the presence of reducing agents and significant aerobic microbial defluorination. Given the diverse applications and emerging concerns of fluorochemicals, this work not only advances the fundamental understanding of the fate of unsaturated PFASs in natural and engineered environments but also may provide insights into the design of readily degradable fluorinated alternatives to existing PFAS compounds.

Characterization and survey in cattle of a rumen Pyrimadobacter sp. which degrades the plant toxin fluoroacetate

Among the natural halogenic compounds, the plant toxin fluoroacetate (FA) causes livestock fatalities in southern hemisphere countries. Here, we report on the isolation of a rumen bacterium, strain C12-8 that degrades FA under anaerobic conditions. 16S rRNA gene sequence analysis showed this bacterium belonged to the Pyramidobacter genus within the Synergistetes phylum and was 98% similar to Pyramidobacter piscolens W5455 isolated from the human oral cavity. Transmission electron microscopy showed the cell envelope to be unusual, with only one membrane and no obvious external wall. Growth and FA degradation were enhanced by peptide-rich protein hydrolysates but not carbohydrates. End products of metabolism were mainly acetate, propionate/isovalerate and isobutyrate. Strain C12-8 preferentially used peptide-bound amino acids rather than free amino acids. Glycine, serine, threonine, leucine, histidine and isoleucine were utilized as free and peptide-bound amino acids, but there was minimal utilization of alanine, proline, methionine, aspartic acid, lysine and arginine in either form. A survey of several cattle properties in northern Australia showed that strain C12-8 and other FA degrading bacteria affiliated with Cloacibacillus porcorum strain MFA1 were endemic to cattle in the northern beef herd and may help to reduce toxicity.

Microbial Cleavage of C-F Bonds in Two C6 Per- and Polyfluorinated Compounds via Reductive Defluorination

The C-F bond is one of the strongest single bonds in nature. Although microbial reductive dehalogenation is well known for the other organohalides, no microbial reductive defluorination has been documented for perfluorinated compounds except for a single, nonreproducible study on trifluoroacetate. Here, we report on C-F bond cleavage in two C₆ per- and polyfluorinated compounds via reductive defluorination by an organohalide-respiring microbial community. The reductive defluorination was demonstrated by the release of F^- and the formation of the corresponding product when lactate was the electron donor, and the fluorinated compound was the sole electron acceptor. The major dechlorinating species in the seed culture, Dehalococcoides, were not responsible for the defluorination as no growth of Dehalococcoides or active expression of Dehalococcoides-reductive dehalogenases was observed. It suggests that minor phylogenetic groups in the community might be responsible for the reductive defluorination. These findings expand our fundamental knowledge of microbial reductive dehalogenation and warrant further studies on the enrichment, identification, and isolation of responsible microorganisms and enzymes. Given the wide use and emerging concerns of fluorinated organics (e.g., per- and polyfluoroalkyl substances), particularly the perfluorinated ones, the discovery of microbial defluorination under common anaerobic conditions may provide valuable insights into the environmental fate and potential bioremediation strategies of these notorious contaminants.

Methylene blue and monosodium glutamate improve neurologic signs after fluoroacetate poisoning

Fluoroacetate (FA) is a tasteless, odorless, water-soluble metabolic poison with severe toxicological effects. Characterized in the mid-1900s, it has been used as a rodenticide but is comparably lethal to all mammals. Many countries have restricted its use, and modern-day accidental human exposures are rare, but recently, concerns have been raised about its application as a chemical weapon with no known antidote. A combined treatment of methylene blue (MB), an antioxidant, and monosodium glutamate (MSG), a precursor of the citric acid cycle substrate alpha-ketoglutarate, has been recommended as an effective countermeasure; however, no peer-reviewed articles documenting the efficacy of this therapy have been published. Using a rodent model, we assessed the effects of MB and MSG on the neurologic, cardiac, and pulmonary systems. Transcriptomic analysis was used to elucidate inflammatory pathway activation and guide bioassays, which revealed the advantages and disadvantages of these candidate countermeasures. Results show that MB and MSG can reduce neurologic signs observed in rats exposed to sodium FA and improve some effects of intoxication. However, while this strategy resolved some signs of intoxication, ultimately it was unable to significantly reduce lethality.

Effects and mechanisms of calcium peroxide on purification of severely eutrophic water

In consideration of severe eutrophication of scenic water caused by pollutants released from sediments in summer, calcium peroxide (CaO₂) was adopted as the slow release peroxide to improve the water quality in a field experiment of 600 m². The effect of CaO₂ on the overlying water, interstitial water, sediment, and sediment microorganisms of scenic water was studied. Results for two months indicated that the dissolved oxygen (DO) concentration of the overlying water in the test zone was 3.78 times that in the control zone; the oxidation-reduction potential (ORP) in the overlying water and sediment increased significantly (p = 0.002 and p = 0). Meanwhile, CaO₂ could effectively inhibit the release of nitrogen (N) and phosphorus (P) from the sediment and could obviously reduce the concentrations of N and P in the overlying water by enhancing the microbiological action. Moreover, the average concentrations of total nitrogen and total phosphorus in the overlying water of the test zone were 46.27% and 50.51% of those in control zone, respectively, and the concentrations of N and P in the interstitial water decreased during the entire experiment. In addition, CaO₂ decreased the relative abundance of anaerobic bacteria in the sediment, whereas it increased that of aerobic bacteria and promoted the appearance of the functional bacteria, such as Nitrospirae and Thermodesulfoba. In conclusion, CaO₂ can improve the DO and ORP in the eutrophic water effectively and change the microbial community in the sediment to a certain extent, thereby controlling the pollutants released from the sediment and reducing the N and P concentrations in the overlying water. Thus, CaO₂ can effectively realize the purification and restoration of the severely eutrophic scenic water.

3-NOP vs. Halogenated Compound: Methane Production, Ruminal Fermentation and Microbial Community Response in Forage Fed Cattle

The aim of this study was to investigate the effects of 3-nitrooxypropanol (3-NOP) and chloroform on methane (CH₄) and H₂ production, ruminal metabolites and microbial community structure in cattle fed a tropical forage diet. Eight rumen-fistulated steers were fed a roughage hay diet (Rhodes grass; Chloris gayana) for 31 days (control period). Four animals received the antimethanogenic compound chloroform (1.6 g chloroform-cyclodextrin/100 kg live weight (LW)) while the other four received 3-NOP (2.5 g 3-NOP/animal/day) for 21 days. Methane decrease compared with control period was similar for both treatments (30-38%) with no differences for expelled H₂ between controls and treatments. Daily weight gain (DWG) was significantly increased when animals were treated with 3-NOP compared with chloroform and control. Regarding the ruminal fermentation parameters increases in ammonia, acetate and branched chain fatty acids were observed with both compounds compared with the controls. Also, methylamines, alcohols and dimethyl sulfone (DMSO₂) concentrations were significantly increased with the treatments compared with control, being greater with 3-NOP. The rumen microbial analyses revealed a similar profile for both treatments, with a shift in operational taxonomic units (OTUs) assigned to the Prevotellaceae and Campylobacteraceae family. Moreover, major archaeal OTUs associated with Methanobrevibacter and Methanosphaera were significantly affected to varying extents based on the inhibitory treatments compared to the control. The abundance of the Methanobrevibacter spp. was decreased by 3-NOP and chloroform, while the Methanomassiliicoccaceae family was inhibited only by 3-NOP. The results suggest that despite the specific mode of action of 3-NOP on methanogens, inhibition of methanogenesis by both compounds resulted in similar responses in metabolism and microbial community structure in the rumen. We hypothesized that these changes were driven by the redirection of metabolic hydrogen ([H]) by both treatments. Therefore results from previous publications using chloroform as an inhibitor of methanogenesis may be useful in predicting ruminal microbiota and fermentation responses to 3-NOP.

Antibiotic pretreatment minimizes dietary effects on reconstructure of rumen fluid and mucosal microbiota in goats

We used 16S rRNA gene sequencing to examine the posteffects of antibiotic treatment on the structure and metabolism of rumen microbiota. Twelve goats were randomly assigned into two groups, with one group receiving intramuscular streptomycin injection at 40 mg/kg bodyweight daily for 10 days. At 4 weeks after treatment with antibiotic, three goats were randomly selected from each group and switched to a 35% concentrate diet. The remaining six goats continued with the 10% concentrate diet. At 4 weeks after dietary shift, ruminal fluid and epithelium were collected to analyze the microbiota composition and short‐chain fatty acid (SCFA) concentrations of the rumen. We found that antibiotic administration led to increases in the diversity and richness of recovered mucosal microbiota and to decreases in those of recovered fluid microbiota. When dietary modulation was performed after antibiotic intake, both communities showed little difference in structure from premodulated states. Additionally, antibiotic pretreatment reduced the basal lines of individual SCFAs but did not affect the increased percentages of SCFAs. Overall, our results indicate that antibiotic administration affects the structure of both rumen fluid and mucosal microbiota and reduces the functional redundancy of rumen microbiota.

Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats

BACKGROUND

Diet-derived short-chain fatty acids (SCFAs) in the rumen have broad effects on the health and growth of ruminants. The microbe-G-protein-coupled receptor (GPR) and microbe-histone deacetylase (HDAC) axes might be the major pathway mediating these effects. Here, an integrated approach of transcriptome sequencing and 16S rRNA gene sequencing was applied to investigate the synergetic responses of rumen epithelium and rumen microbiota to the increased intake of dietary non-fiber carbohydrate (NFC) from 15 to 30% in the goat model. In addition to the analysis of the microbial composition and identification of the genes and signaling pathways related to the differentially expressed GPRs and HDACs, the combined data including the expression of HDACs and GPRs, the relative abundance of the bacteria, and the molar proportions of the individual SCFAs were used to identify the significant co-variation of the SCFAs, clades, and transcripts.

RESULTS

The major bacterial clades promoted by the 30% NFC diet were related to lactate metabolism and cellulose degradation in the rumen. The predominant functions of the GPR and HDAC regulation network, under the 30% NFC diet, were related to the maintenance of epithelium integrity and the promotion of animal growth. In addition, the molar proportion of butyrate was inversely correlated with the expression of HDAC1, and the relative abundance of the bacteria belonging to Clostridum_IV was positively correlated with the expression of GPR1.

CONCLUSIONS

This study revealed that the effects of rumen microbiota-derived SCFA on epithelium growth and metabolism were mediated by the GPR and HDAC regulation network. An understanding of these mechanisms and their relationships to dietary components provides better insights into the modulation of ruminal fermentation and metabolism in the promotion of livestock production.

Biofilm compartmentalisation of the rumen microbiome: modification of fermentation and degradation of dietary toxins

Many deleterious chemicals in plant materials ingested by ruminants produce clinical effects, varying from losses of production efficiency through to death. Many of the effects are insidious, often going unrecognised by animal managers. When secondary plant compounds enter the rumen, they may undergo modification by rumen microbes, which often removes the deleterious compounds, but in specific instances, the deleterious effect may be enhanced. Improved understanding of rumen ecology, particularly concerning the biofilm mode of microbial fermentation, has led to major advances in our understanding of fermentation. In the present review, the potential impact of the physical structuring of the rumen microbiome is discussed in relation to how several economically important secondary plant compounds and other toxins are metabolised by the rumen microbiome and how their toxic effects may be remedied by providing inert particles with a large surface area to weight ratio in the diet. These particles provide additional surfaces for attachment of rumen microorganisms that help alleviate toxicity problems associated with deleterious compounds, including fluoroacetate, mimosine, mycotoxins, cyanoglycosides and hydrogen cyanide. The review first summarises the basic science of biofilm formation and describes the properties of biofilms and their roles in the rumen. It then addresses how biofilms on inert solids and fermentable particulates may assist in detoxification of potentially toxic compounds. A hypothesis that explains how nitrate poisoning may occur as a result of compartmentalisation of nitrate and nitrite reduction in the rumen is included.

Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and Fermentation Response in the Rumen of Cattle

Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with hay:concentrate diet. A shift in rumen fermentation toward propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those fed only roughage hay. Metabolomic analyses revealed an increase in the concentration of amino acids, organic, and nucleic acids in the fluid phase for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under chloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionate in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa, and fungi, which suggests that fiber degradation was not impaired. The observed 30% decrease in methanogenesis did not adversely affect rumen metabolism and the rumen microbiota was able to adapt and redirect [H] into other microbial end-products for both diets. However, it is also required dietary supplements or microbial treatments to capture the additional H2 expelled by the animal to further improve rumen digestive efficiency.