Journal articles on the topic 'Methanobacteriaceae'
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Tagawa, T., K. Syutsubo, Y. Sekiguchil, A. Ohashi, and H. Harada. "Quantification of methanogen cell density in anaerobic granular sludge consortia by fluorescence in-situ hybridization." Water Science and Technology 42, no. 3-4 (August 1, 2000): 77–82. http://dx.doi.org/10.2166/wst.2000.0361.
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Whole cell fluorescence in-situ hybridization (FISH) with 16S rRNA targeted oligonucleotides was applied to reveal the microbial ecological structure of UASB-grown granular sludge. The FISH analysis indicated that the members of the domain Archaea accounted for 28 to 53% of the total cells in various granular sludge sources, while Methanosaeta and Methanobacteriaceae cells accounted for 13 to 38%, and 4 to 27%, respectively. Methanosaeta cell density and Methanobacteriaceae cell density were strongly correlated, respectively, with acetate-utilizing methane production activity and with hydrogen-utilizing methane production activity.
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Kotsyurbenko, O. R., M. W. Friedrich, M. V. Simankova, A. N. Nozhevnikova, P. N. Golyshin, K. N. Timmis, and R. Conrad. "Shift from Acetoclastic to H2-Dependent Methanogenesis in a West Siberian Peat Bog at Low pH Values and Isolation of an Acidophilic Methanobacterium Strain." Applied and Environmental Microbiology 73, no. 7 (February 2, 2007): 2344–48. http://dx.doi.org/10.1128/aem.02413-06.
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ABSTRACT Methane production and archaeal community composition were studied in samples from an acidic peat bog incubated at different temperatures and pH values. H2-dependent methanogenesis increased strongly at the lowest pH, 3.8, and Methanobacteriaceae became important except for Methanomicrobiaceae and Methanosarcinaceae. An acidophilic and psychrotolerant Methanobacterium sp. was isolated using H2-plus-CO2-supplemented medium at pH 4.5.
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Depkat-Jakob, Peter S., Sindy Hunger, Kristin Schulz, George G. Brown, Siu M. Tsai, and Harold L. Drake. "Emission of Methane by Eudrilus eugeniae and Other Earthworms from Brazil." Applied and Environmental Microbiology 78, no. 8 (February 17, 2012): 3014–19. http://dx.doi.org/10.1128/aem.07949-11.
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ABSTRACTEarthworms emit denitrification-derived nitrous oxide and fermentation-derived molecular hydrogen. The present study demonstrated that the earthwormEudrilus eugeniae, obtained in Brazil, emitted methane. Other worms displayed a lesser or no capacity to emit methane. Gene and transcript analyses ofmcrA(encoding the alpha subunit of methyl-CoM reductase) in gut contents ofE. eugeniaesuggested thatMethanosarcinaceae,Methanobacteriaceae, andMethanomicrobiaceaemight be associated with this emission.
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Xing, Peng, Huabing Li, Qing Liu, and Jiuwen Zheng. "Composition of the archaeal community involved in methane production during the decomposition of Microcystis blooms in the laboratory." Canadian Journal of Microbiology 58, no. 10 (October 2012): 1153–58. http://dx.doi.org/10.1139/w2012-097.
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We investigated the microbial processes involved in methane (CH4) production from Microcystis bloom scums at different temperatures. A Microcystis slurry was collected from Lake Taihu and incubated in airtight bottles at 15, 25, and 35 °C. The production of CH4 was monitored, and the emission rate was calculated. The dynamics of the methanogenic community were analyzed by terminal restriction fragment length polymorphism analysis of archaeal 16S rRNA genes. Phylogenetic information for the methanogens was obtained by cloning and sequencing selected samples. Significant CH4 emission from the Microcystis scums was delayed by approximately 12 days by the natural oxygen depletion process, and CH4 production was enhanced at higher temperatures. Phylogenetic analysis indicated that the archaeal community was composed of Methanomicrobiales, Methanobacteriaceae, and a novel cluster of Archaea. An apparent succession of the methanogenic community was demonstrated, with a predominance of Methanobacteriaceae at higher temperatures. Higher temperatures enhanced the methanogenic transformation of the Microcystis biomass and the phylogenetic dominance of hydrogenotrophic methanogens, suggesting that H2 and CO2 might be the primary substrates for CH4 production during Microcystis decomposition without the participation of lake sediment. This work provides insight into the microbial components involved in Microcystis biomass fermentation in controlled systems.
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Steinberg, Lisa M., and John M. Regan. "mcrA-Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities." Applied and Environmental Microbiology 75, no. 13 (May 15, 2009): 4435–42. http://dx.doi.org/10.1128/aem.02858-08.
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ABSTRACT Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase α-subunit (mcrA) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total mcrA and mcrA levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4°C or 20°C. Only members of the Methanosaetaceae, Methanosarcina, Methanobacteriaceae, and Methanocorpusculaceae and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus Methanosarcina, whereas the sample from the pig manure digester contained detectable levels of only members of the Methanobacteriaceae. The acidic peat samples were dominated by both Methanosarcina spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members.
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Hunger, Sindy, Oliver Schmidt, Maik Hilgarth, Marcus A. Horn, Steffen Kolb, Ralf Conrad, and Harold L. Drake. "Competing Formate- and Carbon Dioxide-Utilizing Prokaryotes in an Anoxic Methane-Emitting Fen Soil." Applied and Environmental Microbiology 77, no. 11 (April 8, 2011): 3773–85. http://dx.doi.org/10.1128/aem.00282-11.
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ABSTRACTMethanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. Formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen Schlöppnerbrunnen. Formate dissimilation also yields CO2as a potential secondary substrate. The objective of this study was to resolve potential differences between anaerobic formate- and CO2-utilizing prokaryotes of this fen by stable isotope probing. Anoxic soil microcosms were pulsed daily with low concentrations of [13C]formate or13CO2(i.e., [13C]bicarbonate). Taxa were evaluated by assessment of 16S rRNA genes,mcrA(encoding the alpha-subunit of methyl-coenzyme M reductase), andfhs(encoding formyltetrahydrofolate synthetase). Methanogens, acetogens, and formate-hydrogen lyase-containing taxa appeared to compete for formate. Genes affiliated withMethanocellaceae,Methanobacteriaceae,Acetobacteraceae, andRhodospirillaceaewere13C enriched (i.e., labeled) in [13C]formate treatments, whereas genes affiliated withMethanosarcinaceae,Conexibacteraceae, andSolirubrobacteraceaewere labeled in13CO2treatments. [13C]acetate was enriched in [13C]formate treatments, but labeling of known acetogenic taxa was not detected. However, several phylotypes were affiliated with acetogen-containing taxa (e.g.,Sporomusa).Methanosaetaceae-affiliated methanogens appeared to participate in the consumption of acetate. Twelve and 58 family-level archaeal and bacterial 16S rRNA phylotypes, respectively, were detected, approximately half of which had no isolated representatives.Crenarchaeotaconstituted half of the detected archaeal 16S rRNA phylotypes. The results highlight the unresolved microbial diversity of the fen Schlöppnerbrunnen, suggest that differing taxa competed for the same substrate, and indicate thatMethanocellaceae,Methanobacteriaceae,Methanosarcinaceae, andMethanosaetaceaewere linked to the production of methane, but they do not clearly resolve the taxa responsible for the apparent conversion of formate to acetate.
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Nakamura, Kohei, Takeshi Terada, Yuji Sekiguchi, Naoya Shinzato, Xian-Ying Meng, Miho Enoki, and Yoichi Kamagata. "Application of Pseudomurein Endoisopeptidase to Fluorescence In Situ Hybridization of Methanogens within the Family Methanobacteriaceae." Applied and Environmental Microbiology 72, no. 11 (September 1, 2006): 6907–13. http://dx.doi.org/10.1128/aem.01499-06.
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ABSTRACT In situ detection of methanogens within the family Methanobacteriaceae is sometimes known to be unsuccessful due to the difficulty in permeability of oligonucleotide probes. Pseudomurein endoisopeptidase (Pei), a lytic enzyme that specifically acts on their cell walls, was applied prior to 16S rRNA-targeting fluorescence in situ hybridization (FISH). For this purpose, pure cultured methanogens within this family, Methanobacterium bryantii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, and Methanothermobacter thermautotrophicus together with a Methanothermobacter thermautotrophicus-containing syntrophic acetate-oxidizing coculture, endosymbiotic Methanobrevibacter methanogens within an anaerobic ciliate, and an upflow anaerobic sludge blanket (UASB) granule were examined. Even without the Pei treatment, Methanobacterium bryantii and Methanothermobacter thermautotrophicus cells are relatively well hybridized with oligonucleotide probes. However, almost none of the cells of Methanobrevibacter ruminantium, Methanosphaera stadtmanae, cocultured Methanothermobacter thermautotrophicus, and the endosymbiotic methanogens and the cells within UASB granule were hybridized. Pei treatment was able to increase the probe hybridization ratio in every specimen, particularly in the specimen that had shown little hybridization. Interestingly, the hybridizing signal intensity of Methanothermobacter thermautotrophicus cells in coculture with an acetate-oxidizing H2-producing syntroph was significantly improved by Pei pretreatment, whereas the probe was well hybridized with the cells of pure culture of the same strain. We found that the difference is attributed to the differences in cell wall thicknesses between the two culture conditions. These results indicate that Pei treatment is effective for FISH analysis of methanogens that show impermeability to the probe.
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MORII, Hiroyuki, Masateru NISHIHARA, and Yosuke KOGA. "Composition of polar lipids of Methanobrevibacter arboriphilicus and structure determination of the signature phosphoglycolipid of Methanobacteriaceae." Agricultural and Biological Chemistry 52, no. 12 (1988): 3149–56. http://dx.doi.org/10.1271/bbb1961.52.3149.
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Ruaud, Albane, Niklas Pfister, Ruth E. Ley, and Nicholas D. Youngblut. "Interpreting tree ensemble machine learning models with endoR." PLOS Computational Biology 18, no. 12 (December 14, 2022): e1010714. http://dx.doi.org/10.1371/journal.pcbi.1010714.
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Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.
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Horn, Marcus A., Carola Matthies, Kirsten Küsel, Andreas Schramm, and Harold L. Drake. "Hydrogenotrophic Methanogenesis by Moderately Acid-Tolerant Methanogens of a Methane-Emitting Acidic Peat." Applied and Environmental Microbiology 69, no. 1 (January 2003): 74–83. http://dx.doi.org/10.1128/aem.69.1.74-83.2003.
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ABSTRACT The emission of methane (1.3 mmol of CH4 m−2 day−1), precursors of methanogenesis, and the methanogenic microorganisms of acidic bog peat (pH 4.4) from a moderately reduced forest site were investigated by in situ measurements, microcosm incubations, and cultivation methods, respectively. Bog peat produced CH4 (0.4 to 1.7 μmol g [dry wt] of soil−1 day−1) under anoxic conditions. At in situ pH, supplemental H2-CO2, ethanol, and 1-propanol all increased CH4 production rates while formate, acetate, propionate, and butyrate inhibited the production of CH4; methanol had no effect. H2-dependent acetogenesis occurred in H2-CO2-supplemented bog peat only after extended incubation periods. Nonsupplemented bog peat initially produced small amounts of H2 that were subsequently consumed. The accumulation of H2 was stimulated by ethanol and 1-propanol or by inhibiting methanogenesis with bromoethanesulfonate, and the consumption of ethanol was inhibited by large amounts of H2; these results collectively indicated that ethanol- or 1-propanol-utilizing bacteria were trophically associated with H2-utilizing methanogens. A total of 109 anaerobes and 107 hydrogenotrophic methanogens per g (dry weight) of bog peat were enumerated by cultivation techniques. A stable methanogenic enrichment was obtained with an acidic, H2-CO2-supplemented, fatty acid-enriched defined medium. CH4 production rates by the enrichment were similar at pH 4.5 and 6.5, and acetate inhibited methanogenesis at pH 4.5 but not at pH 6.5. A total of 27 different archaeal 16S rRNA gene sequences indicative of Methanobacteriaceae, Methanomicrobiales, and Methanosarcinaceae were retrieved from the highest CH4-positive serial dilutions of bog peat and methanogenic enrichments. A total of 10 bacterial 16S rRNA gene sequences were also retrieved from the same dilutions and enrichments and were indicative of bacteria that might be responsible for the production of H2 that could be used by hydrogenotrophic methanogens. These results indicated that in this acidic bog peat, (i) H2 is an important substrate for acid-tolerant methanogens, (ii) interspecies hydrogen transfer is involved in the degradation of organic carbon, (iii) the accumulation of protonated volatile fatty acids inhibits methanogenesis, and (iv) methanogenesis might be due to the activities of methanogens that are phylogenetic members of the Methanobacteriaceae, Methanomicrobiales, and Methanosarcinaceae.
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Granada, Camille E., Camila Hasan, Munique Marder, Odorico Konrad, Luciano K. Vargas, Luciane M. P. Passaglia, Adriana Giongo, et al. "Biogas from slaughterhouse wastewater anaerobic digestion is driven by the archaeal family Methanobacteriaceae and bacterial families Porphyromonadaceae and Tissierellaceae." Renewable Energy 118 (April 2018): 840–46. http://dx.doi.org/10.1016/j.renene.2017.11.077.
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Brazelton, William J., Christopher N. Thornton, Alex Hyer, Katrina I. Twing, August A. Longino, Susan Q. Lang, Marvin D. Lilley, Gretchen L. Früh-Green, and Matthew O. Schrenk. "Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy." PeerJ 5 (January 26, 2017): e2945. http://dx.doi.org/10.7717/peerj.2945.
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The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.
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Zhang, T., S. Z. Ke, Y. Liu, and H. P. Fang. "Microbial characteristics of a methanogenic phenol-degrading sludge." Water Science and Technology 52, no. 1-2 (July 1, 2005): 73–78. http://dx.doi.org/10.2166/wst.2005.0500.
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Microbial properties of a methanogenic granular phenol-degrading sludge were characterized using the 16S rRNA/DNA-based techniques, including polymerase chain reaction (PCR) amplification, cloning, DNA sequencing, and fluorescence in situ hybridization (FISH). The sludge was sampled from an upflow anaerobic sludge blanket reactor, which removed 98% of phenol (up to 1260 mg/l) in wastewater at 26°C with 12 hours of hydraulic retention. Based on DNA analysis, the Eubacteria in the sludge was composed of 13 operational taxonomy units (OTUs). Two OTUs, one resembling Clostridium and the other remotely resembling Desulfotomaculum, were likely responsible for the conversion of phenol to benzoate, which was further degraded by five Syntrophus-resembling OTUs to acetate and H2/CO2; methanogens lastly converted acetate and H2/CO2 into methane. The role of six remaining OTUs remains unclear. Overall, the sludge was composed of 26±6% Eubacteria and 74±9% methanogens, of which 54±6% were acetotrophic Methanosaetaceae, 14±3% and 3±2% were hydrogenotrophic Methanomicrobiales and Methanobacteriaceae, respectively.
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Ziganshin, Ayrat M., Elvira E. Ziganshina, Sabine Kleinsteuber, and Marcell Nikolausz. "Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters." Archaea 2016 (2016): 1–12. http://dx.doi.org/10.1155/2016/3401272.
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Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, andJatrophapress cake) was carried out by analysis of the methyl coenzyme-M reductaseα-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genusMethanoculleuspositively correlated with the relative methane content, whereas opposite correlations were found forMethanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genusMethanoculleuspositively correlated with the ammonia level, whereas the prevalence ofMethanocorpusculum,Methanobacterium, andMethanosaetawas negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors.
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Lueders, Tillmann, and Michael Friedrich. "Archaeal Population Dynamics during Sequential Reduction Processes in Rice Field Soil." Applied and Environmental Microbiology 66, no. 7 (July 1, 2000): 2732–42. http://dx.doi.org/10.1128/aem.66.7.2732-2742.2000.
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ABSTRACT The population dynamics of Archaea after flooding of an Italian rice field soil were studied over 17 days. Anoxically incubated rice field soil slurries exhibited a typical sequence of reduction processes characterized by reduction of nitrate, Fe3+, and sulfate prior to the initiation of methane production. Archaeal population dynamics were followed using a dual approach involving molecular sequence retrieval and fingerprinting of small-subunit (SSU) rRNA genes. We retrieved archaeal sequences from four clone libraries (30 each) constructed for different time points (days 0, 1, 8, and 17) after flooding of the soil. The clones could be assigned to known methanogens (i.e., Methanosarcinaceae,Methanosaetaceae, Methanomicrobiaceae, andMethanobacteriaceae) and to novel euryarchaeotal (rice clusters I, II, and III) and crenarchaeotal (rice clusters IV and VI) lineages previously detected in anoxic rice field soil and on rice roots (R. Grosskopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983–4989, 1998). During the initiation of methanogenesis (days 0 to 17), we detected significant changes in the frequency of individual clones, especially of those affiliated with theMethanosaetaceae and Methanobacteriaceae. However, these findings could not be confirmed by terminal restriction fragment length polymorphism (T-RFLP) analysis of SSU rDNA amplicons. Most likely, the fluctuations in sequence composition of clone libraries resulted from cloning bias. Clonal SSU rRNA gene sequences were used to define operational taxonomic units (OTUs) for T-RFLP analysis, which were distinguished by group-specific TaqI restriction sites. Sequence analysis showed a high degree of conservation of TaqI restriction sites within the different archaeal lineages present in Italian rice field soil. Direct T-RFLP analysis of archaeal populations in rice field soil slurries revealed the presence of all archaeal lineages detected by cloning with a predominance of terminal restriction fragments characteristic of rice cluster I (389 bp), Methanosaetaceae (280 bp), andMethanosarcinaceae/rice cluster VI (182 bp). In general, the relative gene frequency of most detected OTUs remained rather constant over time during the first 17 days after flooding of the soil. Most minor OTUs (e.g., Methanomicrobiaceae and rice cluster III) and Methanosaetaceae did not change in relative frequency. Rice cluster I (37 to 30%) and to a lesser extent rice cluster IV as well as Methanobacteriaceae decreased over time. Only the relative abundance of Methanosarcinaceae(182 bp) increased, roughly doubling from 15 to 29% of total archaeal gene frequency within the first 11 days, which was positively correlated to the dynamics of acetate and formate concentrations. Our results indicate that a functionally dynamic ecosystem, a rice field soil after flooding, was linked to a relatively stable archaeal community structure.
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Khan, Munawwar A., Poojabahen G. Patel, Arpitha G. Ganesh, Naushad Rais, Sultan M. Faheem, and Shams T. Khan. "Assessing Methanogenic Archaeal Community in Full Scale Anaerobic Sludge Digester Systems in Dubai, United Arab Emirates." Open Microbiology Journal 12, no. 1 (April 30, 2018): 123–34. http://dx.doi.org/10.2174/1874285801812010123.
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Introduction:Anaerobic digestion for methane production comprises of an exceptionally diverse microbial consortium, a profound understanding about which is still constrained. In this study, the methanogenic archaeal communities in three full-scale anaerobic digesters of a Municipal Wastewater Treatment Plant were analyzed by Fluorescencein situhybridization and quantitative real-time Polymerase Chain Reaction (qPCR) technique.Methods & Materials:Fluorescencein situhybridization (FISH) was performed to detect and quantify the methanogenicArchaeain the sludge samples whereas qPCR was carried out to support the FISH analysis. Multiple probes targeting domain archaea, different orders and families of Archaea were used for the studies.Results and Discussion:In general, the aceticlastic organisms(Methanosarcinaceae & Methanosaetaceae)were more abundant than the hydrogenotrophic organisms(Methanobacteriales, Methanomicrobiales, Methanobacteriaceae & Methanococcales). Both FISH and qPCR indicated that familyMethanosaetaceaewas the most abundant suggesting that aceticlastic methanogenesis is probably the dominant methane production pathway in these digesters.Conclusion:Future work involving high-throughput sequencing methods and correlating archaeal communities with the main operational parameters of anaerobic digesters will help to obtain a better understanding of the dynamics of the methanogenic archaeal community in wastewater treatment plants in United Arab Emirates (UAE) which in turn would lead to improved performance of anaerobic sludge digesters.
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Montenegro, M. A. P., J. C. Araujo, and R. F. Vazoller. "Microbial community evaluation of anaerobic granular sludge from a hybrid reactor treating pentachlorophenol by using fluorescence in situ hybridization." Water Science and Technology 48, no. 6 (September 1, 2003): 65–73. http://dx.doi.org/10.2166/wst.2003.0359.
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We used in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotide probes concurrently with microscopic examinations and methane measurements to characterize the microbial community of an anaerobic hybrid reactor treating pentachlorophenol (PCP) with a mixture of fatty acids (propionic, butyric, acetic and lactic) and methanol. Archaeal cells detected with probe ARC915 prevailed in anaerobic granular sludge without and with the addition of PCP in a range of 2.0 to 21.0 mg/L to the reactor. This group accounted for 81 and 90% of the DAPI-stained cells before and after the addition of 21 mg/L of PCP, respectively. In these conditions, cells detected with the Methanosarcinales specific probe (MSMX860) were the only methanogenic Archaea found and accounted for 59 to 87.6% of the DAPI-stained cells. No cells were detected by the Methanomicrobiales (MG1200), Methanobacteriaceae (MB1174) and Methanococcaceae (MC1109) specific probes. Bacterial cells detected with probe EUB338 were found in very low numbers, which ranged from 5.7 to 1.0% of the DAPI-stained cells. This finding agrees with the scanning electron microscope examinations, in which cells morphologically resembling Methanosaeta and Methanosarcina were predominantly observed in the granular sludge. Results contributed to the investigation of the importance of the methanogens during PCP degradation.
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Hamberger, Alexandra, Marcus A. Horn, Marc G. Dumont, J. Colin Murrell, and Harold L. Drake. "Anaerobic Consumers of Monosaccharides in a Moderately Acidic Fen." Applied and Environmental Microbiology 74, no. 10 (March 31, 2008): 3112–20. http://dx.doi.org/10.1128/aem.00193-08.
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ABSTRACT 16S rRNA-based stable isotope probing identified active xylose- and glucose-fermenting Bacteria and active Archaea, including methanogens, in anoxic slurries of material obtained from a moderately acidic, CH4-emitting fen. Xylose and glucose were converted to fatty acids, CO2, H2, and CH4 under moderately acidic, anoxic conditions, indicating that the fen harbors moderately acid-tolerant xylose- and glucose-using fermenters, as well as moderately acid-tolerant methanogens. Organisms of the families Acidaminococcaceae, Aeromonadaceae, Clostridiaceae, Enterobacteriaceae, and Pseudomonadaceae and the order Actinomycetales, including hitherto unknown organisms, utilized xylose- or glucose-derived carbon, suggesting that highly diverse facultative aerobes and obligate anaerobes contribute to the flow of carbon in the fen under anoxic conditions. Uncultured Euryarchaeota (i.e., Methanosarcinaceae and Methanobacteriaceae) and Crenarchaeota species were identified by 16S rRNA analysis of anoxic slurries, demonstrating that the acidic fen harbors novel methanogens and Crenarchaeota organisms capable of anaerobiosis. Fermentation-derived molecules are conceived to be the primary drivers of methanogenesis when electron acceptors other than CO2 are absent, and the collective findings of this study indicate that fen soils harbor diverse, acid-tolerant, and novel xylose-utilizing as well as glucose-utilizing facultative aerobes and obligate anaerobes that form trophic links to novel moderately acid-tolerant methanogens.
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Bomberg, Malin, Mari Nyyssönen, Petteri Pitkänen, Anne Lehtinen, and Merja Itävaara. "Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland." BioMed Research International 2015 (2015): 1–17. http://dx.doi.org/10.1155/2015/979530.
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Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland) using bacterial and archaeal 16S rRNA,dsrB, andmcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296–798 m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ) at 250–350 m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizingε-proteobacteria (Sulfurimonassp.) dominated in the SMMZ andγ-proteobacteria (Pseudomonasspp.) below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG) were more common at 415–559 m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea,α-,β- andδ-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths.DsrB genes were most numerous and most actively transcribed in the SMMZ while themcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems.
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Hudson, André O., Charles Gilvarg, and Thomas Leustek. "Biochemical and Phylogenetic Characterization of a Novel Diaminopimelate Biosynthesis Pathway in Prokaryotes Identifies a Diverged Form of ll-Diaminopimelate Aminotransferase." Journal of Bacteriology 190, no. 9 (February 29, 2008): 3256–63. http://dx.doi.org/10.1128/jb.01381-07.
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ABSTRACT A variant of the diaminopimelate (DAP)-lysine biosynthesis pathway uses an ll-DAP aminotransferase (DapL, EC 2.6.1.83) to catalyze the direct conversion of l-2,3,4,5-tetrahydrodipicolinate to ll-DAP. Comparative genomic analysis and experimental verification of DapL candidates revealed the existence of two diverged forms of DapL (DapL1 and DapL2). DapL orthologs were identified in eubacteria and archaea. In some species the corresponding dapL gene was found to lie in genomic contiguity with other dap genes, suggestive of a polycistronic structure. The DapL candidate enzymes were found to cluster into two classes sharing approximately 30% amino acid identity. The function of selected enzymes from each class was studied. Both classes were able to functionally complement Escherichia coli dapD and dapE mutants and to catalyze ll-DAP transamination, providing functional evidence for a role in DAP/lysine biosynthesis. In all cases the occurrence of dapL in a species correlated with the absence of genes for dapD and dapE representing the acyl DAP pathway variants, and only in a few cases was dapL coincident with ddh encoding meso-DAP dehydrogenase. The results indicate that the DapL pathway is restricted to specific lineages of eubacteria including the Cyanobacteria, Desulfuromonadales, Firmicutes, Bacteroidetes, Chlamydiae, Spirochaeta, and Chloroflexi and two archaeal groups, the Methanobacteriaceae and Archaeoglobaceae.
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Rocchetti, Maria Teresa, Biagio Raffaele Di Iorio, Mirco Vacca, Carmela Cosola, Stefania Marzocco, Ighli di Bari, Francesco Maria Calabrese, Roberto Ciarcia, Maria De Angelis, and Loreto Gesualdo. "Ketoanalogs’ Effects on Intestinal Microbiota Modulation and Uremic Toxins Serum Levels in Chronic Kidney Disease (Medika2 Study)." Journal of Clinical Medicine 10, no. 4 (February 18, 2021): 840. http://dx.doi.org/10.3390/jcm10040840.
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Nutritional therapy (NT) is a therapeutic option in the conservative treatment of chronic kidney disease (CKD) patients to delay the start of dialysis. The aim of this study was to evaluate the specific effect of ketoanalogs (KA)-supplemented diets for gut microbiota modulation. In a previous study we observed that the Mediterranean diet (MD) and a KA-supplemented very-low-protein diet (VLPD) modulated beneficially gut microbiota, reducing indoxyl- and p-cresyl-sulfate (IS, PCS) serum levels, and ameliorating the intestinal permeability in CKD patients. In the current study, we added a third diet regimen consisting of KA-supplemented MD. Forty-three patients with CKD grades 3B–4 continuing the crossover clinical trial were assigned to six months of KA-supplemented MD (MD + KA). Compared to MD, KA-supplementation in MD + KA determined (i) a decrease of Clostridiaceae, Methanobacteriaceae, Prevotellaceae, and Lactobacillaceae while Bacteroidaceae and Lachnospiraceae increased; (ii) a reduction of total and free IS and PCS compared to a free diet (FD)—more than the MD, but not as effectively as the VLPD. These results further clarify the driving role of urea levels in regulating gut integrity status and demonstrating that the reduction of azotemia produced by KA-supplemented VLPD was more effective than KA-supplemented MD in gut microbiota modulation mainly due to the effect of the drastic reduction of protein intake rather than the effect of KA.
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Purkamo, Lotta, Malin Bomberg, Riikka Kietäväinen, Heikki Salavirta, Mari Nyyssönen, Maija Nuppunen-Puputti, Lasse Ahonen, Ilmo Kukkonen, and Merja Itävaara. "Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids." Biogeosciences 13, no. 10 (May 30, 2016): 3091–108. http://dx.doi.org/10.5194/bg-13-3091-2016.
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Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible “keystone” genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.
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Reyer, Henry, Per J. R. Sjöberg, Michael Oster, Aisanjiang Wubuli, Eduard Murani, Siriluck Ponsuksili, Petra Wolf, and Klaus Wimmers. "Mineral Phosphorus Supply in Piglets Impacts the Microbial Composition and Phytate Utilization in the Large Intestine." Microorganisms 9, no. 6 (June 1, 2021): 1197. http://dx.doi.org/10.3390/microorganisms9061197.
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A sufficient supply of phosphorus (P) to pigs in livestock farming is based on the optimal use of plant-based phytate and mineral P supplements to ensure proper growth processes and bone stability. However, a high P supplementation might bear the risk of higher environmental burden due to the occurrence of excess P and phytate degradation products in manure. In this context, the intestinal microbiota is of central importance to increase P solubility, to employ non-mineral P by the enzymatic degradation of phytate, and to metabolize residual P. A feeding experiment was conducted in which piglets were fed diets with different P levels, resulting in three groups with low, medium (covering requirements), and high concentrations of available P. Samples from caecum and colon digesta were analysed for microbial composition and phytate breakdown to estimate the microbial contribution to metabolize P sources. In terms of identified operational taxonomic units (OTU), caecum and colon digesta under the three feeding schemes mainly overlap in their core microbiome. Nevertheless, different microbial families correlate with increased dietary P supply. Specifically, microbes of Desulfovibrionaceae, Pasteurellaceae, Anaerovoracaceae, and Methanobacteriaceae were found significantly differentially abundant in the large intestine across the dietary treatments. Moreover, members of the families Veillonellaceae, Selenomonadaceae, and Succinivibrionaceae might contribute to the observed phytate degradation in animals fed a low P diet. In this sense, the targeted manipulation of the intestinal microbiota by feeding measures offers possibilities for the optimization of intestinal phytate and P utilization.
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Kim, Chungwoo, Denver I. Walitang, Aritra Roy Choudhury, Yi Lee, Sanghun Lee, Hyenchung Chun, Tae-Young Heo, Kido Park, and Tongmin Sa. "Changes in Soil Chemical Properties Due to Long-Term Compost Fertilization Regulate Methane Turnover Related Gene Abundances in Rice Paddy." Applied Sciences 12, no. 5 (March 4, 2022): 2652. http://dx.doi.org/10.3390/app12052652.
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Maintaining rice yield, soil function, and fertility are essential components of long-term compost fertilization. However, paddy fields are major sources of anthropogenic methane emissions. The aim of the study is to evaluate the changes in soil chemical properties and their concurrent impact on the abundance of methanogenesis (mcrA) and methane oxidation (pmoA) related genes among compost (Com), NPK+Compost (NPKCom), and unfertilized (NF) fallow paddy fields under long-term compost fertilization. Results showed that compost and NPK+Compost fertilization altered the soil chemical properties of paddy fields with a significant increase in the functional gene abundance potentially associated with Methanobacteriaceae for mcrA (1.23 × 106 to 3.84 × 106 copy number g−1 dry soil) and methane oxidizing bacteria such as Methylomonas and Methylobacter for pmoA (1.65 × 106 to 4.3 × 106 copy number g−1 dry soil). Ordination plots visualized these changes, where treatments clustered distinctly indicating that Com and NPKCom treatments were characterized by paddy soils with elevated OM, TN, K and P content and higher abundances of methanogenesis and methane oxidation related genes. The study showed that long-term compost fertilization resulted in paddy fields with high nutrient content and high gene abundance, attributed to methanogens and methane oxidizing bacteria that responded well with compost fertilization. These results indicated the potential of these fallow paddy fields for methane emission and methane oxidation and that they are ‘primed’, potentially influencing subsequent paddy field responses to long-term compost application.
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Inglis, G. Douglas, Benjamin D. Wright, Stephanie A. Sheppard, D. Wade Abbott, Matt A. Oryschak, and Tony Montina. "Expeller-Pressed Canola (Brassica napus) Meal Modulates the Structure and Function of the Cecal Microbiota, and Alters the Metabolome of the Pancreas, Liver, and Breast Muscle of Broiler Chickens." Animals 11, no. 2 (February 23, 2021): 577. http://dx.doi.org/10.3390/ani11020577.
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The inoculation of one-day-old broiler chicks with the cecal contents from a mature broiler breeder resulted in a highly diverse and uniform cecal bacterial community. CM did not affect feed consumption, weight gain, nor the richness, evenness, or diversity of the cecal bacterial community. However, the structure of the bacterial community was altered in birds fed the CM diet. Although the CM diet was formulated to contain equivalent metabolizable energy to the control diet, it contained more dietary fiber. The abundance of bacterial families, including those that are known to contain species able to metabolize fiber was altered (e.g., bacteria within the families, Methanobacteriaceae, Atopobiaceae, Prevotellaceae, Clostridiales Family XIII, Peptostreptococcaceae, and Succinivibrionaceae), and concentrations of SCFAs were higher in the ceca of birds fed the CM diet. Moreover, concentrations of isoleucine, isobutyrate, glutamate, and 2-oxoglutarate were higher, whereas concentrations of phenyllactic acid, indole, glucose, 3-phenylpropionate, and 2-oxobutyrate were lower in the digesta of chickens that were fed CM. The metabolic profiles of pancreas, liver, and breast muscle tissues of birds fed the CM diet differed from control birds. Metabolites that were associated with energy production, protection against oxidative stress, and pathways of amino acid and glycerophospholipid metabolism had altered concentrations in these tissues. Some of the observed changes in metabolite levels may indicate an increased disease risk in birds fed the CM diet (e.g., pancreatitis), and others suggested that birds mounted metabolic response to offset the adverse impacts of CM (e.g., oxidative stress in the liver).
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Park, Hyung Soo, Indranil Chatterjee, Xiaoli Dong, Sheng-Hung Wang, Christoph W. Sensen, Sean M. Caffrey, Thomas R. Jack, Joe Boivin, and Gerrit Voordouw. "Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline." Applied and Environmental Microbiology 77, no. 19 (August 19, 2011): 6908–17. http://dx.doi.org/10.1128/aem.05891-11.
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ABSTRACTPipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) ofPseudomonasnot found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereasDeltaproteobacteriaof the generaDesulfomicrobiumandDesulfocapsawere not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) ofMethanobacteriaceaearchaea but increased fractions of sulfate-reducingDesulfomicrobium(18% and 48%) and of bisulfite-disproportionatingDesulfocapsa(35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters.
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Calli, B., B. Mertoglu, N. Tas, B. Inanc, O. Yenigun, and I. Ozturk. "Investigation of variations in microbial diversity in anaerobic reactors treating landfill leachate." Water Science and Technology 48, no. 4 (August 1, 2003): 105–12. http://dx.doi.org/10.2166/wst.2003.0232.
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A young landfill leachate containing elevated total ammonia concentrations frequently as high as 2,700 mg/l was anaerobically treated for 1,015 days in two different laboratory-scale anaerobic reactors configured as sludge blanket and hybrid bed. In this paper, the last 265 days of this long-term anaerobic treatability study are presented. Effects of high ammonia concentrations on reactor performances were correlated to the variations in microbial diversity by identifying the dominant microorganisms with FISH (fluorescent in-situ hybridization), cloning, DGGE (denaturing gradient gel electrophoresis) and morphological analysis. The results have indicated that the high ammonia landfill leachate can be treated successfully by using either an UASB or a hybrid bed reactor if temporary pH adjustments in the reactor influents are made when high ammonia concentrations are experienced. Consequently, COD removal efficiency is independent of microbial diversity and reactor configuration and it depends on the biodegradable portion of the leachate. Under this circumstance, stability of the reactors with low levels of acetate was supported by the abundance of Methanosaeta population. In both of the reactors, some populations of Methanobacteriaceae were also detected while other methanogenic species were virtually absent. However, after the termination of pH adjustment at Day 860, reactors immediately became unstable due to the sudden increase in free ammonia concentration up to 400 mg/l. COD removal efficiency decreased to 42% in the hybrid bed and to 48% in the UASB reactor. The durations of inhibitions were not long enough to severely deteriorate the massive Methanosaeta cells; therefore, many of them were again identified after two free ammonia inhibitions. However, subsequently, long filamentous morphologies of Methanosaeta cells shifted to shorter filaments and they lost their aggregating property.
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Sun, Xiaoge, Shu Zhang, Erdan Wang, Na Lu, Wei Wang, and Shengli Li. "505 Late-Breaking: Ruminal Microbiota, Inflammation Cytokines, and Performance of High-yield Dairy Cows Supplemented with Saccharomyces Cerevisiae Culture." Journal of Animal Science 99, Supplement_3 (October 8, 2021): 179–80. http://dx.doi.org/10.1093/jas/skab235.327.
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Abstract Dramatic increases in milk yields in recent decades have created challenges in terms of rumen pH and microbial health which ultimately impact dairy cow health. The objective of this study was to assess the effects on ruminal pH, Volatile Fatty Acid (VFA), microbiota, inflammation, and performance of high-yield dairy cows by supplementing Saccharomyces cerevisiae culture (SC). Forty Holstein cows were divided into two groups based on their milk yield, days of milk, and parity fed the same basal ration diet that did or did not contain 100 g of SC /cow per day. Individual dry matter intake (DMI) and milk yield were recorded each day. Rumen fluid and milk samples were collected after 2 hours of morning feeding at intervals of 15 days during the experiment period. The data showed that rumen pH was increased by 0.19 (P = 0.09) when SC was supplemented than no SC was provided. SC-supplemented cow consumed 0.28 kg (P < 0.05) extra DM/d. Those supplemented with SC produced 1.36 kg (P < 0.05) more milk/cow per day than did non-supplemented cows. Milk fat percentage was higher (4.11 vs. 3.96%) for cows receiving SC. There were no differences in milk protein percentage. Rumen fluid VFA concentration was not statistically affected by SC but was numerically higher acetic and lower propionic for supplemented cows. The blood of the SC group with lower inflammation cytokines and somatic cell count (SCC). SC-supplemented cows had a greater relative abundance of Prevotellaceae, Succinivibrionaceae, Fibrobacteraceae, Lactobacillaceae, and lower relative abundance of Spirochaetaceae, Methanobacteriaceae, Enterobacteriaceae than the unsupplemented cows. It had greater functions on xylanolysis, fermentation, cellulolysis in the rumen in terms of the KEGG function prediction analysis. This study demonstrated that high-yield lactation cows receiving supplemental SC produced more milk and potentially reduced the inflammation and enhanced rumen cellulolysis bacteria growth.
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Zhang, Kun, Yan-Ling Zhang, Xin Ouyang, Jun-Peng Li, Jun-Jie Liao, Ao You, Xiu Yue, Guang-Jian Xie, Jie-Liang Liang, and Jin-Tian Li. "Genome-Centered Metagenomics Analysis Reveals the Microbial Interactions of a Syntrophic Consortium during Methane Generation in a Decentralized Wastewater Treatment System." Applied Sciences 10, no. 1 (December 23, 2019): 135. http://dx.doi.org/10.3390/app10010135.
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The application of anaerobic digestors to decentralized wastewater treatment systems (DWTS) has gained momentum worldwide due to their ease of operation, high efficiency, and ability to recycle wastewater. However, the microbial mechanisms responsible for the high efficiency and ability of DWTS to recycle wastewater are still unclear. In this study, the microbial community structure and function of two different anaerobic bioreactors (a primary sludge digestor, PSD, and anaerobic membrane bioreactor, AnMBR) of a DWTS located in Germany was investigated using 16S rRNA gene amplicon and metagenomic sequencing, respectively. The results showed that the microbial community structure was remarkably different in PSD and AnMBR. Methanobacteriaceae and Syntrophaceae were identified as the families that significantly differed in abundance between these two bioreactors. We also used genome-centered metagenomics to predict the microbial interactions and methane-generating pathway, which yielded 21 near-complete assembled genomes (MAGs) (average completeness of 93.0% and contamination of 2.9%). These MAGs together represented the majority of the microbial community. MAGs affiliated with methanogenic archaea, including Methanobacterium sp., Methanomicrobiales archaea, Methanomassiliicoccales archaea, and Methanosaeta concilii, were recruited, along with other syntrophic bacterial MAGs associated with anaerobic digestion. Key genes encoding enzymes involved in specific carbohydrate-active and methanogenic pathways in MAGs were identified to illustrate the microbial functions and interactions that occur during anaerobic digestion in the wastewater treatment. From the MAG information, it was predicted that bacteria affiliated with Bacteroidetes, Prolixibacteraceae, and Synergistaceae were the key bacteria involved in anaerobic digestion. In the methane production step, Methanobacterium sp. performed hydrogenotrophic methanogenesis, which reduced carbon dioxide to methane with hydrogen as the primary electron donor. Taken together, our findings provide a clear understanding of the methane-generating pathways and highlight the syntrophic interactions that occur during anaerobic digestion in DWTS.
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Cheng, Xi, Jiawei Wang, Liu Gong, Yong Dong, Jiawei Shou, Hongming Pan, Zhaonan Yu, and Yong Fang. "Composition of the Gut Microbiota Associated with the Response to Immunotherapy in Advanced Cancer Patients: A Chinese Real-World Pilot Study." Journal of Clinical Medicine 11, no. 18 (September 18, 2022): 5479. http://dx.doi.org/10.3390/jcm11185479.
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Background: The composition of the gut microbiota is associated with the response to immunotherapy for different cancers. However, the majority of previous studies have focused on a single cancer and a single immune checkpoint inhibitor. Here, we investigated the relationship between the gut microbiota and the clinical response to anti-programmed cell death protein 1 (PD-1) immunotherapy in patients with advanced cancers. Method: In this comprehensive study, 16S rRNA sequencing was performed on the gut microbiota of pre-immunotherapy and post-immunotherapy, of 72 advanced cancer patients in China. Results: At the phylum level, Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the main components of the microbiota in the 72 advanced cancer patients. At the genus level, Bacteroides and Prevotella were the dominant microbiota among these 72 patients. The PD_whole_tree, Chao1, Observed_species and Shannon indices of R.0 and R.T were higher than those of NR.0 and NR.T. The results of LEfSe showed that Archaea, Lentisphaerae, Victivallaceae, Victivallales, Lentisphaeria, Methanobacteriaceae, Methanobacteria, Euryarchaeota, Methanobrevibacter, and Methanobacteriales were significantly enriched in the response group before immunotherapy (R.0), and the Clostridiaceae was significantly enriched in the non-response group before immunotherapy (NR.0) (p < 0.05). Lachnospiraceae and Thermus were significantly enriched in the response group after immunotherapy (R.T), and Leuconostoc was significantly enriched in R.0 (p < 0.05). ROC analysis showed that the microbiota of R.T (AUC = 0.70) had obvious diagnostic value in differentiating Chinese cancer patients based on their response to immunotherapy. Conclusions: We demonstrated that the gut microbiota was associated with the clinical response to anti-PD-1 immunotherapy in cancer patients. Taxonomic signatures enriched in responders were effective biomarkers to predict the clinical response. Our findings provide a new strategy to improve the efficiency of responses to immunotherapy among cancer patients.
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Silva, Kaliu G. Scaranto, Igor Gomes Favero, Kaue Tonelli Nardi, Lucas Barbosa Kondratovich, Carly A. Hoffmann, Jordan K. Hinds, Nathaniel Hall, Darren D. Henry, and Jhones Onorino Sarturi. "PSVI-4 Effects of exogenous fibrolytic enzymes on beef cattle fed growing diets: Ruminal microbiome." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 425–26. http://dx.doi.org/10.1093/jas/skaa278.741.
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Abstract The effect of pre-treatment with fibrolytic enzymes [cellulase/xylanase (Trichoderma ressie)] of growing diets (high quality and low-quality) on ruminal microbiome relative abundance (RA) were evaluated. Ruminally cannulated beef steers (n = 5; BW = 520 ± 30 kg) were used in a 5×4 unbalanced Latin square design using a 2×2 factorial arrangement of treatments: (a) growing diet quality [high (HQ) and low (LQ)] and (b) enzyme inclusion (0 or 0.75 mL/kg of diet DM). Steers were individually fed ad libitum throughout four 21-d periods consisting of 14-d of adaptation and 7-d of collections. Ruminal fluid samples (100 mL) were collected on d-5 of each collection-period, at 6 h post feeding for DNA extraction and determination of microbial RA. Microbiome data were sequenced by Illumnia® NovaSeq™ 6000 (16S rRNA). Regardless of enzyme×diet quality interaction (P ≥ 0.11) or pre-treatment with enzyme (P ≥ 0.12), Domain RA was affected (P ≤ 0.04), in which LQ diets increased RA of Bacteria (93.25 vs. 86.80%) and decreased Archaea (6.75 vs. 13.20%). In Phylum, LQ diets decreased RA (P ≤ 0.04) of Euryarchaeota (6.75 vs. 13.21%), and increased Bacteroidetes (11.22 vs. 2.26%). Within Class, LQ diets decreased RA (P ≤ 0.04) of Clostridia (38.66 vs. 51.40%), Methanobacteria (6.75 vs. 13.21%), and increased Bacteroidia (10.62 and 1.47%). Within Order LQ diets, decreased RA (P ≤ 0.04) of Clostridiales (38.47 vs. 51.29%), Methanobacteriales (6.75 vs. 13.21%), and increased Bacteroidales (10.62 vs. 1.47%). In Family, LQ diets showed decreased RA (P ≤ 0.04) of Methanobacteriaceae (6.75 vs. 13.21%), Ruminococcaceae (6.71 vs. 2.18%), and increased Prevotellaceae (9.83 vs. 1.17%). In Genus, LQ diets showed increased RA (P ≤ 0.03) of Prevotella (9.61 vs. 1.10%). The dietary pre-treatment with fibrolytic enzymes seems to not dramatically affect RA of ruminal microbiome, while growing diet quality greatly influenced ruminal microbiome RA.
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Egert, Markus, Bianca Wagner, Thorsten Lemke, Andreas Brune, and Michael W. Friedrich. "Microbial Community Structure in Midgut and Hindgut of the Humus-Feeding Larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae)." Applied and Environmental Microbiology 69, no. 11 (November 2003): 6659–68. http://dx.doi.org/10.1128/aem.69.11.6659-6668.2003.
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ABSTRACT The guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. In a companion paper (T. Lemke, U. Stingl, M. Egert, M. W. Friedrich, and A. Brune, Appl. Environ. Microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle Pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and the presence of a diverse, yet unstudied microbial community. Here, we report on the community structure of bacteria and archaea in the midgut, hindgut, and food soil of P. ephippiata larvae, determined with cultivation-independent techniques. Clone libraries and terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed that the intestines of P. ephippiata larvae contain a complex gut microbiota that differs markedly between midgut and hindgut and that is clearly distinct from the microbiota in the food soil. The bacterial community is dominated by phylogenetic groups with a fermentative metabolism (Lactobacillales, Clostridiales, Bacillales, and Cytophaga-Flavobacterium-Bacteroides [CFB] phylum), which is corroborated by high lactate and acetate concentrations in the midgut and hindgut and by the large numbers of lactogenic and acetogenic bacteria in both gut compartments reported in the companion paper. Based on 16S rRNA gene frequencies, Actinobacteria dominate the alkaline midgut, while the hindgut is dominated by members of the CFB phylum. The archaeal community, however, is less diverse. 16S rRNA genes affiliated with mesophilic Crenarchaeota, probably stemming from the ingested soil, were most frequent in the midgut, whereas Methanobacteriaceae-related 16S rRNA genes were most frequent in the hindgut. These findings agree with the reported restriction of methanogenesis to the hindgut of Pachnoda larvae.
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Fadeeva, M. V., A. V. Kudryavtseva, G. S. Krasnov, M. R. Skhirtladze, and V. T. Ivashkin. "Intestinal Microbiota in Patients with Chronic Heart Failure and Systolic Dysfunction." Russian Journal of Gastroenterology, Hepatology, Coloproctology 30, no. 2 (May 6, 2020): 35–44. http://dx.doi.org/10.22416/1382-4376-2020-30-2-35-44.
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Aim. To study the composition of the intestinal microbiota in patients with chronic heart failure (CHF), as well as a relationship between the features of the CHF clinical course and changes in the microbial composition of the colon.Materials and methods. The study included 60 heart failure patients with systolic dysfunction diagnosed according to the results of echocardiographic examination. The control group consisted of 20 patients comparable to the main group by gender, age and underlying diseases in the absence of CHF. In all patients, the severity of CHF symptoms was assessed using a clinical assessment scale. The levels of the N-terminal fragment of the cerebral natriuretic peptide (NT-proBNP) and C-reactive protein (CRP) were determined. Echocardiographic examination and, if indicated, Holter ECG monitoring were performed. The intestinal microbiota in stool samples was studied by sequencing the 16S gene of ribosomal RNA (rRNA).Results. In comparison with the control group, CHF patients showed a decrease in the relative content of Tenericutes (p = 0.02, Mann—Whitney test) and an increase in the proportion of Euryarchaeota (p = 0.02) and Firmicutes (p = 0.03). At the family level, an increase in the proportion of Methanobacteriaceae (p = 0.03) and a decrease in the proportion of Pseudomonadaceae (p = 0.01) and Moraxellaceae (p = 0.01) were noted. No dependence of the intestinal microflora composition on the functional class of heart failure was observed. However, a correlation was revealed between the relative number of certain bacterial families and the severity of impaired contractile function, the level of the inflammatory marker and the biochemical marker of heart failure.Conclusions. The obtained data indicate differences in the intestinal microbiota composition in patients with and without heart failure. A correlation between the number of some bacterial families and various laboratory and instrumental indicators assessed in heart failure patients was revealed. Further research into the effect of intestinal microbiota on the course of heart failure appears to be promising for improving treatment methods.
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Fey, Axel, and Ralf Conrad. "Effect of Temperature on Carbon and Electron Flow and on the Archaeal Community in Methanogenic Rice Field Soil." Applied and Environmental Microbiology 66, no. 11 (November 1, 2000): 4790–97. http://dx.doi.org/10.1128/aem.66.11.4790-4797.2000.
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ABSTRACT Temperature is an important factor controlling CH4production in anoxic rice soils. Soil slurries, prepared from Italian rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37°C or in a temperature gradient block covering the same temperature range at intervals of 1°C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH4 production rates increased with temperature, with an apparent activation energy of 61 kJ mol−1. Steady-state partial pressures of the methanogenic precursor H2 also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H2 plus CO2-dependent methanogenesis was kept at −20 to −25 kJ mol of CH4 −1 over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 μM. Simultaneously, the relative contribution of H2 as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to 14CH4, so that the carbon and electron flow to CH4 was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal Methanobacteriaceae,Methanomicrobiaceae, Methanosaetaceae,Methanosarcinaceae, and Rice clusters I, III, IV, V, and VI, which were all present in the rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I andMethanosaetaceae were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring Methanosarcinaceae decreased and the more modest Methanosaetaceae increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.
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Nilusha, Rathmalgodage Thejani, and Yuansong Wei. "New Insights into the Microbial Diversity of Cake Layer in Yttria Composite Ceramic Tubular Membrane in an Anaerobic Membrane Bioreactor (AnMBR)." Membranes 11, no. 2 (February 3, 2021): 108. http://dx.doi.org/10.3390/membranes11020108.
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Cake layer formation is an inevitable challenge in membrane bioreactor (MBR) operation. The investigations on the cake layer microbial community are essential to control biofouling. This work studied the bacterial and archaeal communities in the cake layer, the anaerobic sludge, and the membrane cleaning solutions of anaerobic membrane bioreactor (AnMBR) with yttria-based ceramic tubular membrane by polymerase chain reaction (PCR) amplification of 16S rRNA genes. The cake layer resistance was 69% of the total membrane resistance. Proteins and soluble microbial by-products (SMPs) were the dominant foulants in the cake layer. The pioneering archaeal and bacteria in the cake layer were mostly similar to those in the anaerobic bulk sludge. The dominant biofouling bacteria were Proteobacteria, Bacteroidetes, Firmicutes, and Chloroflexi and the dominant archaeal were Methanosaetacea and Methanobacteriacea at family level. This finding may help to develop antifouling membranes for AnMBR treating domestic wastewater.
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Ruaud, Albane, Sofia Esquivel-Elizondo, Jacobo de la Cuesta-Zuluaga, Jillian L. Waters, Largus T. Angenent, Nicholas D. Youngblut, and Ruth E. Ley. "Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut." mBio 11, no. 1 (February 4, 2020). http://dx.doi.org/10.1128/mbio.03235-19.
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ABSTRACT Across human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae cooccur and are enriched in individuals with a lean, compared to an obese, body mass index (BMI). Whether these association patterns reflect interactions between metabolic partners, as well as whether these associations play a role in the lean host phenotype with which they associate, remains to be ascertained. Here, we validated previously reported cooccurrence patterns of the two families and their association with a lean BMI with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Furthermore, we report positive associations at the genus and species levels between Christensenella spp. and Methanobrevibacter smithii, the most abundant methanogen of the human gut. By coculturing three Christensenella spp. with M. smithii, we show that Christensenella spp. efficiently support the metabolism of M. smithii via H2 production far better than Bacteroides thetaiotaomicron does. Christensenella minuta forms flocs colonized by M. smithii even when H2 is in excess. In culture with C. minuta, H2 consumption by M. smithii shifts the metabolic output of C. minuta’s fermentation toward acetate rather than butyrate. Together, these results indicate that the widespread cooccurrence of these microorganisms is underpinned by both physical and metabolic interactions. Their combined metabolic activity may provide insights into their association with a lean host BMI. IMPORTANCE The human gut microbiome is made of trillions of microbial cells, most of which are Bacteria, with a subset of Archaea. The bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae are widespread in human guts. They correlate with each other and with a lean body type. Whether species of these two families interact and how they affect the body type are unanswered questions. Here, we show that species within these families correlate with each other across people. We also demonstrate that particular species of these two families grow together in dense flocs, wherein the bacteria provide hydrogen gas to the archaea, which then make methane. When the archaea are present, the ratio of bacterial products (which are nutrients for humans) is changed. These observations indicate that when these species grow together, their products have the potential to affect the physiology of their human host.
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Pinnell, Lee J., Arquimides A. Reyes, Cory A. Wolfe, Maggie D. Weinroth, Jessica L. Metcalf, Robert J. Delmore, Keith E. Belk, Paul S. Morley, and Terry E. Engle. "Bacteroidetes and Firmicutes Drive Differing Microbial Diversity and Community Composition Among Micro-Environments in the Bovine Rumen." Frontiers in Veterinary Science 9 (May 19, 2022). http://dx.doi.org/10.3389/fvets.2022.897996.
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Ruminants are a critical human food source and have been implicated as a potentially important source of global methane emissions. Because of their unique digestive physiology, ruminants rely upon a symbiotic relationship with the complex and rich community of microorganism in the foregut to allow digestion of complex carbohydrates. This study used 16S rRNA gene sequencing to investigate the composition of microbial communities from three rumen micro-environments of cattle fed identical diets: (1) free fluid, (2) the fibrous pack, and (3) the mucosa. Community composition analysis revealed that while a phylogenetic core including the most abundant and most common ruminal taxa (members of Bacteroidetes and Firmicutes) existed across micro-environments, the abundances of these taxa differed significantly between fluid- and mucosa-associated communities, and specific lineages were discriminant of individual micro-environments. Members of Firmicutes, specifically Clostridiales, Lachnospiraceae, Mogibacteriaceae, Christenellaceae, and Erysipelotrichaceae were significantly more abundant in fluid communities, while members of Bacteroidetes, namely Muribaculaceae and Prevotellaceae were more abundant in mucosa-associated communities. Additionally, Methanobacteriaceae, a family of methanogenic Archaea, was more abundant in fluid-associated communities. A set of four more diverse lineages were discriminant of pack-associated communities that included Succinivibrionaceae, RFP12 (Verruco-5), Fibrobacteraceae, and Spirochaetaceae. Our findings indicate that different ecological niches within each micro-environment have resulted in significant differences in the diversity and community structure of microbial communities from rumen fluid, pack, and mucosa without the influence of diet that will help contextualize the influence of other environmental factors.
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Huws, Sharon A., Joan E. Edwards, Wanchang Lin, Francesco Rubino, Mark Alston, David Swarbreck, Shabhonam Caim, et al. "Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches." Microbiome 9, no. 1 (June 21, 2021). http://dx.doi.org/10.1186/s40168-021-01087-w.
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Abstract Background Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. Results Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be ‘cheating’ in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. Conclusions In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants.
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Ngetich, Denis, Rawlynce Bett, Charles Gachuiri, and Felix Kibegwa. "Factors influencing Euryarchaeal gut methanogens distribution in dairy cattle in smallholding farms." East African Journal of Science, Technology and Innovation 2, no. 4 (September 25, 2021). http://dx.doi.org/10.37425/eajsti.v2i4.377.
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Guts of ruminants contain symbiotic domains (Eubacteria, Archaea and Eukarya) that aid in the breakdown of consumed carbohydrates from plants to simple molecules that can be absorbed into the ruminant’s bloodstream. Methanogenesis occurs during the gut fermentation and methane gas is released in the final step of biomass degradation from the fermentation chambers. The Archaea that play a major role critical for methane emissions are methanogens and are found freely in the ruminants’ gut. Methane production from ruminants has attracted global attention due to their input on the Green House Gases effect, contribution to global warming and negative effects on farmers’ productivity. The objective of this study was to determine the factors contributing to the methanogens’ gut distribution in dairy cows from smallholder farms using next generation sequencing techniques. A total of 48 samples from smallholding dairy farms were used during this study and were collected from Kenya (Kiambu county) and Tanzania (Lushoto and Rungwe). The collected data samples from the experimental animals were from both the rumen fluid (6) and fecal (42). Samples were analyzed using metagenomic approaches and statistical analysis was undertaken using IBM SPSS statistics software version 28.0.0.0. Results showed that the gut site along the gastrointestinal tract and the feeding regime significantly contributed to the distribution and presence of various methanogenic species (P<0.1). The herd and the genotype had no statistical effect. A total of 12 families were identified. The family Methanobacteriaceae was identified with the leading number (8) of the methanogenic species. A third of the identified families showed presence for at least two methanogenic species with Methanobrevibacter ruminantium being abundant. For proper curbing mechanisms, efforts to reduce methane release should be channeled to the whole gastrointestinal tract and advanced studies carried out on any potential interspecies presence facilitation and/or elimination.
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Ahmed, Eslam, Rintaro Yano, Miho Fujimori, Deepashree Kand, Masaaki Hanada, Takehiro Nishida, and Naoki Fukuma. "Impacts of Mootral on Methane Production, Rumen Fermentation, and Microbial Community in an in vitro Study." Frontiers in Veterinary Science 7 (January 22, 2021). http://dx.doi.org/10.3389/fvets.2020.623817.
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Methane mitigation strategies have a two-sided benefit for both environment and efficient livestock production. This preliminary short-term in vitro trial using Mootral (garlic and citrus extracts), a novel natural feed supplement, was conducted to evaluate its efficacy on rumen fermentation characteristics, methane production, and the bacterial and archaeal community. The experiment was performed as a batch culture using rumen fluid collected from sheep, and Mootral was supplemented in three concentrations: 0% (Control), 10%, and 20% of the substrate (50% Grass:50% Concentrate). The rumen fermentation data and alpha diversity of microbial community were analyzed by ordinary one-way analysis of variance. The relative abundance and statistical significance of families and operational taxonomic units (OTUs) among the groups were compared by Kruskal–Wallis H test using Calypso software. After 24-h incubation at 39°C, Mootral in a dose-dependent manner improved the production of total volatile fatty acids and propionate while it reduced the acetate proportion and acetate/propionate ratio. The total produced gas was two times higher in the Mootral-supplemented groups than control (P < 0.01), while the proportion of methane in the produced gas was reduced by 22% (P < 0.05) and 54% (P < 0.01) for 10 and 20% Mootral, respectively. Mootral did not change pH, digestibility, and ammonia-nitrogen. Microbial community analyses showed that Mootral effectively changed the ruminal microbiome. The bacterial community showed an increase of the relative abundance of the propionate-producing family such as Prevotellaceae (P = 0.014) and Veillonellaceae (P = 0.030), while there was a decrease in the relative abundance of some hydrogen-producing bacteria by Mootral supplementation. In the archaeal community, Methanobacteriaceae was decreased by Mootral supplementation compared with control (P = 0.032), while the Methanomassiliicoccaceae family increased in a dose-dependent effect (P = 0.038). The results of the study showed the efficacy of the new mixture to alter the ruminal microbial community, produce more propionate, and reduce microbial groups associated with methane production, thus suggesting that Mootral is a promising natural mixture for methane reduction from ruminants.
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Ranchou-Peyruse, Magali, Marion Guignard, Franck Casteran, Maïder Abadie, Clémence Defois, Pierre Peyret, David Dequidt, et al. "Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer." Frontiers in Microbiology 12 (October 13, 2021). http://dx.doi.org/10.3389/fmicb.2021.688929.
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Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L−1 and a phosphate content of 0.02mg.L−1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria (“Candidatus Acetothermia”) with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.
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Klinsoda, Jutamat, Julia Vötterl, Qendrim Zebeli, and Barbara U. Metzler-Zebeli. "Alterations of the Viable Ileal Microbiota of the Gut Mucosa-Lymph Node Axis in Pigs Fed Phytase and Lactic Acid-Treated Cereals." Applied and Environmental Microbiology 86, no. 4 (November 22, 2019). http://dx.doi.org/10.1128/aem.02128-19.
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ABSTRACT The gut-lymph node axis is a critical player in the symbiotic relationship between gut microbiota and the host. However, little is known about the impact of diet-related bacterial shifts in the gut lumen on bacterial translocation into lymph nodes. Here, we (i) characterized changes in the viable microbiota composition along the ileal digesta-mucosa-lymph node axis and (ii) examined the effect of dietary phytase supplementation and lactic acid (LA) soaking of cereals on the bacterial taxonomy along this axis, together with their effect on the mucosal expression of innate immune and barrier function genes in pigs (n = 8/diet). After 18 days on diets, ileal digesta, mucosa, and ileocecal lymph nodes (ICLNs) were collected for RNA isolation and 16S rRNA-based high-resolution community profiling. Bacterial communities were dominated by Lactobacillaceae and Clostridiaceae, with clearly distinguishable profiles at the three sampling sites. Specific bacterial subsampling was indicated by enrichment of the ICLNs with Lactobacillaceae, Lachnospiraceae, Veillonellaceae, and Methanobacteriaceae and less Clostridiaceae, Pasteurellaceae, Helicobacteraceae, and Enterobacteriaceae compared to that of the mucosa. LA treatment of cereals reduced proteolytic taxa in the lumen, including pathobionts like Helicobacteraceae, Campylobacteraceae, and Fusobacteriaceae. When combined, phytase- and LA-treated cereals largely increased species richness, while the single treatments reduced Actinobacteria and Bacteroidetes in ICLNs and increased mucosal MUC2 expression. In contrast, phytase reduced mucosal CDH1 expression, indicating altered barrier function with potential effects on bacterial translocation. Overall, both treatments, although often differently, changed the viable microbiome along the digesta-mucosa-lymph node axis in the ileum, probably due to altered substrate availability and microbial-host interactions. IMPORTANCE A host’s diet largely determines the gut microbial composition and therefore may influence bacterial translocation into ICLNs. Due to its importance for cell metabolism, the intestinal phosphorus availability, which was modified here by phytase and LA treatment of cereals, affects the intestinal microbiota. Previous studies mainly focused on bacteria in the lumen. The novelty of this work resides mainly in that we report diet-microbe effects along the digesta-mucosa-ICLN axis and linked those effects to mucosal expression of barrier function genes as crucial components for host health. Lymph nodes can serve as reservoir of pathobionts; therefore, present diet-microbiome-host interactions have implications for food safety.
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Li, Long-Ping, Lei Qu, and Tuo Li. "Supplemental dietary Selenohomolanthionine affects growth and rumen bacterial population of Shaanbei white cashmere wether goats." Frontiers in Microbiology 13 (October 20, 2022). http://dx.doi.org/10.3389/fmicb.2022.942848.
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Selenium (Se) is an important trace element for all livestock growth. However, little is known about the dietary supplementation of Selenohomolanthionine (SeHLan) effect on growth and rumen microbiota of cashmere goats. In this study, thirty-two growing Shaanbei white cashmere wether goats with mean body weight (26.18 ± 2.71) kg were randomly assigned into 4 treatments, each with 8 replicates. The goats in 4 experimental groups were fed the basal diet (0.016 mg/kg Se) added with organic Se in the form of SeHLan, namely, control group (CG, added 0 mg/kg Se), low Se group (LSE, added 0.3 mg/kg Se), medium Se group (MSE, added 0.6 mg/kg Se), and high Se group (HSE, added 1.2 mg/kg Se). The feed experiment lasted for 70 days including 10-day adaptation, followed by 11 days digestibility trial including 7-day adaptation and 4-day collection period. On the last day of feeding experiment, rumen fluid was collected for microbial community analysis. The feed, orts, and fecal samples were collected for chemical analysis during digestibility trial. The results showed that average daily feed intake (ADFI) and the apparent digestibility of crude protein (CP) were both quadratic ally increased with increased SeHLan supply (Pquadratic < 0.05), while average daily gain (ADG) and feed conversion ratio (FCR) showed a linear response (Plinear < 0.05). The ADFI and ADG were all highest in the MSE group, which also had the lowest FCR (P < 0.05). Alpha diversity indices of the microbial community did not differ among four treatments. While principal coordinates analysis (PCoA) showed that rumen bacterial population differed among four groups. Taxonomic analysis revealed that Bacteroidetes, Firmicutes, and Euryarchaeota were the dominant phyla. The dominant families were Prevotellaceae, Selenomonadaceae, Methanobacteriaceae, and Bifidobacteriaceae. The significantly different rumen bacterial genera were found to be Methanobrevibacter, Quinella, Christensenellaceae_R-7_group, Veillonellaceae_UCG-001, and Succinivibrionaceae_UCG-002 (P < 0.05). In addition, Tax4fun analysis revealed that SeHLan supplemented groups enhanced the enrichment of genes related to energy metabolism, amino acid metabolism, carbohydrate metabolism, and enzymes. Twenty-eight pathways showed significant differences among four treatment groups (P < 0.05). In conclusion, dietary supplementation of medium SeHLan significantly affects rumen bacterial composition and ultimately promotes Shaanbei white cashmere wether goats nutrient digestibility and growth.
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Thirumalaisamy, Govindasamy, Pradeep Kumar Malik, Shraddha Trivedi, Atul Purushottam Kolte, and Raghavendra Bhatta. "Effect of Long-Term Supplementation With Silkworm Pupae Oil on the Methane Yield, Ruminal Protozoa, and Archaea Community in Sheep." Frontiers in Microbiology 13 (March 8, 2022). http://dx.doi.org/10.3389/fmicb.2022.780073.
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Supplementation with lipids and oils is one of the most efficient strategies for reducing enteric methane emission. However, high costs and adverse impacts on fiber degradation restrict the use of conventional oils. Silkworm pupae, a non-conventional oil source rarely used for human consumption in India, could be one of the cheaper alternatives for methane mitigation. The objective of this study was to investigate the effect on sheep of long-term supplementation (180 days) of silkworm pupae oil (SWPO) with two distinct supplementation regimes (daily and biweekly) on daily enteric methane emission, methane yield, nutrient digestibility, rumen fermentation, ruminal archaea community composition, and protozoal population. The effect of the discontinuation of oil supplementation on enteric methane emission was also investigated. Eighteen adult male sheep, randomly divided into three groups (n = 6), were provisioned with a mixed diet consisting of 10.1% crude protein (CP) and 11.7 MJ/kg metabolizable energy formulated using finger millet straw and concentrate in a 55:45 ratio. SWPO was supplemented at 2% of dry matter intake (DMI) in test groups either daily (CON) or biweekly (INT), while no oil was supplemented in the control group (CTR). DMI (p = 0.15) and CP (p = 0.16) in the CON and INT groups were similar to that of the CTR group; however, the energy intake (MJ/kg) in the supplemented groups (CON and INT) was higher (p < 0.001) than in CTR. In the CON group, body weight gain (kg, p = 0.02) and average daily gain (g, p = 0.02) were both higher than in the CTR. The daily methane emission in the CON (17.5 g/day) and INT (18.0 g/day) groups was lower (p = 0.01) than the CTR group (23.6 g/day), indicating a reduction of 23–25% due to SWPO supplementation. Similarly, compared with the CTR group, methane yields (g/kg DMI) in test groups were also significantly lower (p < 0.01). The transient nature of the anti-methanogenic effect of SWPO was demonstrated in the oil discontinuation study, where daily methane emission reverted to pre-supplementation levels after a short period. The recorded methanogens were affiliated to the families Methanobacteriaceae, Methanomassilliicoccaceae, and Methanosarcinaceae. The long-term supplementation of oil did not induce any significant change in the rumen archaeal community, whereas minor species such as Group3b exhibited differing abundance among the groups. Methanobrevibacter, irrespective of treatment, was the largest genus, while Methanobrevibacter gottschalkii was the dominant species. Oil supplementation in CON and INT compared with CTR decreased (p < 0.01) the numbers of total protozoa (× 107 cells/ml), Entodiniomorphs (× 107 cells/ml), and Holotrichs (× 106 cells/ml). SWPO continuous supplementation (CON group) resulted in the largest reduction in enteric methane emission and relatively higher body weight gain (p = 0.02) in sheep.