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Frontiers in Microbiology 2020The present study aimed to investigate the effects of organic acids (OA) as alternatives for antibiotic growth promoters (AGP) on growth performance, intestinal...
The present study aimed to investigate the effects of organic acids (OA) as alternatives for antibiotic growth promoters (AGP) on growth performance, intestinal structure, as well as intestinal microbial composition and short-chain fatty acids (SCFAs) profiles in broilers. A total of 336 newly hatched male Arbor Acres broiler chicks were randomly allocated into 3 dietary treatments including the basal diet [negative control (NC)], the basal diet supplemented with 5 mg/kg flavomycin, and the basal diet supplemented with OA feed additives. Each treatment had eight replicates with 14 birds each. The results showed that AGP and OA promoted growth during day 22-42 compared with the NC group ( < 0.05). OA significantly increased the jejunal goblet cell density and ileal villus height on day 42 compared with the NC group ( < 0.05). Meanwhile, OA up-regulated the mRNA expression of jejunal barrier genes (Claudin-3 and ZO-1) relative to the NC group ( < 0.05). Significant changes of microbiota induced by the OA were also found on day 42 ( < 0.05). Several SCFAs-producing bacteria like Ruminococcaceae, Christensenellaceae, and Peptococcaceae affiliated to the order Clostridiales were identified as biomarkers of the OA group. Higher concentrations of SCFAs including formic acid and butyric acid were observed in the cecum of OA group ( < 0.05). Simultaneously, the abundance of family Ruminococcaceae showed highly positive correlations with the body weight and mRNA level of ZO-1 on day 42 ( < 0.05). However, AGP supplementation had the higher mRNA expression of Claudin-2, lower goblet cell density of jejunum, and decreased Firmicutes to Bacteroidetes ratio, suggesting that AGP might have a negative impact on intestinal immune and microbiota homeostasis. In conclusion, the OA improved growth performance, intestinal morphology and barrier function in broilers, which might be attributed to the changes of intestinal microbiota, particularly the enrichment of SCFAs-producing bacteria, providing a more homeostatic and healthy intestinal microecology.
PubMed: 33519778
DOI: 10.3389/fmicb.2020.618144 -
Scientific Reports Mar 2018In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture....
In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
Topics: Anaerobiosis; Benzene; Biodegradation, Environmental; Biofilms; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Metabolic Networks and Pathways; Microbial Consortia; Nitrates; Oxidation-Reduction; Oxygen; Peptococcaceae; Transcriptome
PubMed: 29540736
DOI: 10.1038/s41598-018-22617-x -
PloS One 2014A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem...
A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities.
Topics: Bacteroidetes; Biodiversity; Geologic Sediments; Gram-Positive Bacteria; Proteobacteria; RNA, Ribosomal, 16S; Soil Microbiology
PubMed: 25101630
DOI: 10.1371/journal.pone.0104134 -
Nature Chemical Biology Jan 2018Cobamides such as vitamin B are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In...
Cobamides such as vitamin B are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In organohalide respiration, a vital biological process for the global cycling of natural and anthropogenic organohalogens, cobamides are the requisite prosthetic groups for carbon-halogen bond-cleaving reductive dehalogenases. This study reports the biosynthesis of a new cobamide with unsubstituted purine as the lower base and assigns unsubstituted purine a biological function by demonstrating that Coα-purinyl-cobamide (purinyl-Cba) is the native prosthetic group in catalytically active tetrachloroethene reductive dehalogenases of Desulfitobacterium hafniense. Cobamides featuring different lower bases are not functionally equivalent, and purinyl-Cba elicits different physiological responses in corrinoid-auxotrophic, organohalide-respiring bacteria. Given that cobamide-dependent enzymes catalyze key steps in essential metabolic pathways, the discovery of a novel cobamide structure and the realization that lower bases can effectively modulate enzyme activities generate opportunities to manipulate functionalities of microbiomes.
Topics: Biosynthetic Pathways; Cobamides; Desulfitobacterium; Oxidoreductases; Protein Conformation; Purines; Trichloroethylene
PubMed: 29106396
DOI: 10.1038/nchembio.2512 -
Genome Announcements Aug 2015We report the draft genome of the Peptococcaceae strain CEB3 that originated from an acidic (pH 2.5) stream draining an abandoned copper mine. Strain CEB3 is one of the...
We report the draft genome of the Peptococcaceae strain CEB3 that originated from an acidic (pH 2.5) stream draining an abandoned copper mine. Strain CEB3 is one of the very few reported acidophilic sulfate-reducing isolates. The 5.04-Mb draft genome harbors 5,069 predicted protein-encoding and 66 RNA genes.
PubMed: 26251503
DOI: 10.1128/genomeA.00886-15 -
Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition.Applied Microbiology and Biotechnology Jun 2017Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of...
Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions. Benzene was degraded at a rate of 0.15 μmol/mg protein/day and a first-order rate constant of 3.04/day which was fourfold higher than rates reported previously. Bacteria belonging to the Peptococcaceae were found to play an important role in this anaerobic benzene-degrading biofilm culture, but also members of the Anaerolineaceae were predicted to be involved in benzene degradation or benzene metabolite degradation based on Illumina MiSeq analysis of 16S ribosomal RNA genes. Biomass retention in the reactor using a filtration finger resulted in reduction of benzene degradation capacity. Detection of the benzene carboxylase encoding gene, abcA, and benzoic acid in the culture vessel indicated that benzene degradation proceeds through an initial carboxylation step.
Topics: Anaerobiosis; Bacteria; Benzene; Benzoic Acid; Biodegradation, Environmental; Biofilms; Culture Media; Denitrification; Microbial Consortia; Nitrates; Peptococcaceae; RNA, Ribosomal, 16S
PubMed: 28321487
DOI: 10.1007/s00253-017-8214-8 -
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor.The ISME Journal Aug 2015Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms,...
Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4.
Topics: Acetogenins; Bacteria; Biodegradation, Environmental; Bioreactors; Butyrates; Energy Metabolism; Euryarchaeota; Fermentation; Gene Expression Profiling; Metagenomics; Methane; Peptococcaceae; Phthalic Acids; Phylogeny; Propionates
PubMed: 25615435
DOI: 10.1038/ismej.2014.256 -
Nature Communications Oct 2020Nickel-iron composites are efficient in catalyzing oxygen evolution. Here, we develop a microorganism corrosion approach to construct nickel-iron hydroxides. The...
Nickel-iron composites are efficient in catalyzing oxygen evolution. Here, we develop a microorganism corrosion approach to construct nickel-iron hydroxides. The anaerobic sulfate-reducing bacteria, using sulfate as the electron acceptor, play a significant role in the formation of iron sulfide decorated nickel-iron hydroxides, which exhibit excellent electrocatalytic performance for oxygen evolution. Experimental and theoretical investigations suggest that the synergistic effect between oxyhydroxides and sulfide species accounts for the high activity. This microorganism corrosion strategy not only provides efficient candidate electrocatalysts but also bridges traditional corrosion engineering and emerging electrochemical energy technologies.
Topics: Corrosion; Density Functional Theory; Desulfotomaculum; Electrochemistry; Electrodes; Hydroxides; Nickel; Oxygen; Spectrum Analysis, Raman; X-Ray Absorption Spectroscopy
PubMed: 33033245
DOI: 10.1038/s41467-020-18891-x -
Microbial Biotechnology Mar 2019Cobamides (Cbas) are essential cofactors of reductive dehalogenases (RDases) in organohalide-respiring bacteria (OHRB). Changes in the Cba structure can influence RDase...
Cobamides (Cbas) are essential cofactors of reductive dehalogenases (RDases) in organohalide-respiring bacteria (OHRB). Changes in the Cba structure can influence RDase function. Here, we report on the cofactor versatility or selectivity of Desulfitobacterium RDases produced either in the native organism or heterologously. The susceptibility of Desulfitobacterium hafniense strain DCB-2 to guided Cba biosynthesis (i.e. incorporation of exogenous Cba lower ligand base precursors) was analysed. Exogenous benzimidazoles, azabenzimidazoles and 4,5-dimethylimidazole were incorporated by the organism into Cbas. When the type of Cba changed, no effect on the turnover rate of the 3-chloro-4-hydroxy-phenylacetate-converting enzyme RdhA6 and the 3,5-dichlorophenol-dehalogenating enzyme RdhA3 was observed. The impact of the amendment of Cba lower ligand precursors on RDase function was also investigated in Shimwellia blattae, the Cba producer used for the heterologous production of Desulfitobacterium RDases. The recombinant tetrachloroethene RDase (PceA ) appeared to be non-selective towards different Cbas. However, the functional production of the 1,2-dichloroethane-dihaloeliminating enzyme (DcaA) of Desulfitobacterium dichloroeliminans was completely prevented in cells producing 5,6-dimethylbenzimidazolyl-Cba, but substantially enhanced in cells that incorporated 5-methoxybenzimidazole into the Cba cofactor. The results of the study indicate the utilization of a range of different Cbas by Desulfitobacterium RDases with selected representatives apparently preferring distinct Cbas.
Topics: Cobamides; Coenzymes; Desulfitobacterium; Enterobacteriaceae; Hydrolases; Vitamin B Complex
PubMed: 30549216
DOI: 10.1111/1751-7915.13339 -
Frontiers in Microbiology 2018A sulfidogenic bioreactor, operated at low pH (4-5), was set up and used to remove transition metals (copper, nickel, cobalt, and zinc) from a synthetic mine water,...
A sulfidogenic bioreactor, operated at low pH (4-5), was set up and used to remove transition metals (copper, nickel, cobalt, and zinc) from a synthetic mine water, based on the chemistry of a moderately acidic (pH 5) drainage stream at an operating copper mine in Brazil. The module was constructed as an upflow biofilm reactor, with microorganisms immobilized on porous glass beads, and was operated continuously for 462 days, during which time the 2 L bioreactor processed >2,000 L of synthetic mine water. The initial treatment involved removing copper (the most abundant metal present) off-line in a stream of HS-containing gas generated by the bioreactor, which caused the synthetic mine water pH to fall to 2.1. The copper-free water was then amended with glycerol (the principal electron donor), yeast extract and basal salts, and pumped directly into the bioreactor where the other three transition metals were precipitated (also as sulfides), concurrent with increased solution pH. Although some acetate was generated, most of the glycerol fed to the bioreactor was oxidized to carbon dioxide, and was coupled to the reduction of sulfate to hydrogen sulfide. No archaea or eukaryotes were detected in the bioreactor microbial community, which was dominated by acidophilic sulfate-reducing ( strain CEB3 and ); facultatively anaerobic non-sulfidogens ( and strain AR3) were also found in small relative abundance. This work demonstrated how a single low pH sulfidogenic bioreactor can be used to remediate a metal-rich mine water, and to facilitate the recovery (and therefore recycling) of target metals. The system was robust, and was operated empirically by means of pH control. Comparison of costs of the main consumables (glycerol and yeast extract) and the values of the metals recovered showed a major excess of the latter, supporting the view that sulfidogenic biotechnology can have significant economic as well as environmental advantages over current approaches used to remediate mine waters which produce secondary toxic wastes and fail to recover valuable metals.
PubMed: 30214439
DOI: 10.3389/fmicb.2018.02051