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Science (New York, N.Y.) Jun 2005The human endogenous intestinal microflora is an essential "organ" in providing nourishment, regulating epithelial development, and instructing innate immunity; yet,...
The human endogenous intestinal microflora is an essential "organ" in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features remain poorly described. We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity. A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms. We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease.
Topics: Adult; Bacteria; Bacteroidetes; Biodiversity; Colon; DNA, Ribosomal; Ecosystem; Feces; Genes, Archaeal; Genes, Bacterial; Genes, rRNA; Genetic Variation; Humans; Intestinal Mucosa; Methanobrevibacter; Middle Aged; Molecular Sequence Data; Phylogeny; Polymerase Chain Reaction; RNA, Ribosomal, 16S
PubMed: 15831718
DOI: 10.1126/science.1110591 -
Nature Jun 2021Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome....
Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000-2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.
Topics: Anti-Bacterial Agents; Bacteria; Biodiversity; Biological Evolution; Chronic Disease; Developed Countries; Developing Countries; Diet, Western; Feces; Gastrointestinal Microbiome; Genome, Bacterial; History, Ancient; Host Microbial Interactions; Humans; Industrial Development; Methanobrevibacter; Mexico; Sedentary Behavior; Southwestern United States; Species Specificity; Symbiosis
PubMed: 33981035
DOI: 10.1038/s41586-021-03532-0 -
Biochimica Et Biophysica Acta Aug 2016Life arose in a world without oxygen and the first organisms were anaerobes. Here we investigate the gene repertoire of the prokaryote common ancestor, estimating which... (Review)
Review
Life arose in a world without oxygen and the first organisms were anaerobes. Here we investigate the gene repertoire of the prokaryote common ancestor, estimating which genes it contained and to which lineages of modern prokaryotes it was most similar in terms of gene content. Using a phylogenetic approach we found that among trees for all 8779 protein families shared between 134 archaea and 1847 bacterial genomes, only 1045 have sequences from at least two bacterial and two archaeal groups and retain the ancestral archaeal-bacterial split. Among those, the genes shared by anaerobes were identified as candidate genes for the prokaryote common ancestor, which lived in anaerobic environments. We find that these anaerobic prokaryote common ancestor genes are today most frequently distributed among methanogens and clostridia, strict anaerobes that live from low free energy changes near the thermodynamic limit of life. The anaerobic families encompass genes for bifunctional acetyl-CoA-synthase/CO-dehydrogenase, heterodisulfide reductase subunits C and A, ferredoxins, and several subunits of the Mrp-antiporter/hydrogenase family, in addition to numerous S-adenosyl methionine (SAM) dependent methyltransferases. The data indicate a major role for methyl groups in the metabolism of the prokaryote common ancestor. The data furthermore indicate that the prokaryote ancestor possessed a rotor stator ATP synthase, but lacked cytochromes and quinones as well as identifiable redox-dependent ion pumping complexes. The prokaryote ancestor did possess, however, an Mrp-type H(+)/Na(+) antiporter complex, capable of transducing geochemical pH gradients into biologically more stable Na(+)-gradients. The findings implicate a hydrothermal, autotrophic, and methyl-dependent origin of life. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
Topics: Anaerobiosis; Archaea; Archaeal Proteins; Bacterial Proteins; Biological Evolution; Clostridiales; Coenzyme A Ligases; Ferredoxins; Hydrogenase; Metabolic Networks and Pathways; Methanobacteriaceae; Methyltransferases; Molecular Sequence Annotation; Origin of Life; Phylogeny; Protein Biosynthesis; Ribosomes
PubMed: 27150504
DOI: 10.1016/j.bbabio.2016.04.284 -
International Journal of Molecular... May 2020The microbial cell membrane is affected by physicochemical parameters, such as temperature and pH, but also by the specific growth rate of the host organism.... (Review)
Review
The microbial cell membrane is affected by physicochemical parameters, such as temperature and pH, but also by the specific growth rate of the host organism. Homeoviscous adaption describes the process of maintaining membrane fluidity and permeability throughout these environmental changes. Archaea, and thereby, spp. exhibit a unique lipid composition of ether lipids, which are altered in regard to the ratio of diether to tetraether lipids, number of cyclopentane rings and type of head groups, as a coping mechanism against environmental changes. The main biotechnological application of the membrane lipids of spp. are so called archaeosomes. Archaeosomes are liposomes which are fully or partly generated from archaeal lipids and harbor the potential to be used as drug delivery systems for vaccines, proteins, peptides and nucleic acids. This review summarizes the influence of environmental parameters on the cell membrane of spp. and the biotechnological applications of their membrane lipids.
Topics: Biotechnology; Cell Membrane; Cyclopentanes; Drug Delivery Systems; Hydrogen-Ion Concentration; Liposomes; Membrane Lipids; Membranes, Artificial; Methanobacterium; Natronococcus; Peptides; Sulfolobus; Temperature; Viscosity
PubMed: 32486295
DOI: 10.3390/ijms21113935 -
Animal : An International Journal of... Jan 2021The greenhouse gases (GHGs) derived from agriculture include carbon dioxide, nitrous oxide, and methane (CH). Of these GHGs, CH, in particular, constitutes a major... (Review)
Review
The greenhouse gases (GHGs) derived from agriculture include carbon dioxide, nitrous oxide, and methane (CH). Of these GHGs, CH, in particular, constitutes a major component of the GHG emitted by the agricultural sector. Along with environmental concerns, CH emission also leads to losses in gross energy intake with economic implications. While ruminants are considered the main source of CH from agriculture, nonruminant animals also contribute substantially, and the CH emission intensity of nonruminants remains comparable to that of ruminants. Means of mitigating CH emissions from enteric fermentation have therefore been sought. Methane is produced by methanogens-archaeal microorganisms that inhabit the digestive tracts of animals and participate in fermentation processes. As the diversity of methanogen communities is thought to be responsible for the differences in CH production among nonruminant animals, it is necessary to investigate the archaeal composition of specific animal species. Methanogens play an important role in energy metabolism and adipose tissue deposition in animals. Higher abundances of methanogens, along with their higher diversity, have been reported to contribute to lean phenotype in pigs. In particular, a greater abundance of Methanosphaera spp. and early dominance of Methanobrevibacter smithii have been reported to correlate with lower body fat formation in pigs. Besides the contribution of methanogens to the metabolic phenotype of their hosts, CH release reduces the productivity that could be achieved through other hydrogen (H) disposal pathways. Enhanced participation of acetogenesis in H disposal, leading to acetate formation, could be a more favorable direction for animal production and the environment. Better knowledge and understanding of the archaeal communities of the gastrointestinal tract (GIT), including their metabolism and interactions with other microorganisms, would thus allow the development of new strategies for inhibiting methanogens and shifting toward acetogenesis. There are a variety of approaches to inhibiting methanogens and mitigating methanogenesis in ruminants, which can find an application for nonruminants, such as nutritional changes through supplementation with biologically active compounds and management changes. We summarize the available reports and provide a comprehensive review of methanogens living in the GIT of various nonruminants, such as swine, horses, donkeys, rabbits, and poultry. This review will help in a better understanding of the populations and diversity of methanogens and the implications of their presence in nonruminant animals.
Topics: Animals; Animals, Domestic; Horses; Methane; Methanobrevibacter; Rabbits; Rumen; Ruminants; Swine
PubMed: 33516013
DOI: 10.1016/j.animal.2020.100060 -
NPJ Biofilms and Microbiomes Sep 2022A meta-analysis approach was used, to study the microbiomes of biofilms and planktonic communities underpinning microbial electrosynthesis (MES) cells. High-throughput... (Meta-Analysis)
Meta-Analysis
A meta-analysis approach was used, to study the microbiomes of biofilms and planktonic communities underpinning microbial electrosynthesis (MES) cells. High-throughput DNA sequencing of 16S rRNA gene amplicons has been increasingly applied to understand MES systems. In this meta-analysis of 22 studies, we find that acetogenic and methanogenic MES cells share 80% of a cathodic core microbiome, and that different inoculum pre-treatments strongly affect community composition. Oxygen scavengers were more abundant in planktonic communities, and several key organisms were associated with operating parameters and good cell performance. We suggest Desulfovibrio sp. play a role in initiating early biofilm development and shaping microbial communities by catalysing H production, to sustain either Acetobacterium sp. or Methanobacterium sp. Microbial community assembly became more stochastic over time, causing diversification of the biofilm (cathodic) community in acetogenic cells and leading to re-establishment of methanogens, despite inoculum pre-treatments. This suggests that repeated interventions may be required to suppress methanogenesis.
Topics: Methane; Methanobacterium; Microbiota; Oxygen; RNA, Ribosomal, 16S
PubMed: 36138044
DOI: 10.1038/s41522-022-00337-5 -
Anaerobe Oct 2022Archaea comprise a unique domain of organisms with distinct biochemical and genetic differences from bacteria. Methane-forming archaea, methanogens, constitute the... (Review)
Review
Archaea comprise a unique domain of organisms with distinct biochemical and genetic differences from bacteria. Methane-forming archaea, methanogens, constitute the predominant group of archaea in the human gut microbiota, with Methanobrevibacter smithii being the most prevalent. However, the effect of methanogenic archaea and their methane production on chronic disease remains controversial. As perturbation of the microbiota is a feature of chronic conditions, such as cardiovascular disease, neurodegenerative diseases and chronic kidney disease, assessing the influence of archaea could provide a new clue to mitigating adverse effects associated with dysbiosis. In this review, we will discuss the putative role of archaea in the gut microbiota in humans and the possible link to chronic diseases.
Topics: Humans; Archaea; Gastrointestinal Microbiome; Methanobrevibacter; Euryarchaeota; Methane; Chronic Disease
PubMed: 35985606
DOI: 10.1016/j.anaerobe.2022.102629 -
Microbiology Spectrum Jun 2022Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the...
Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the Gram-negative heterotrophic bacterium Bacteroides thetaiotaomicron and the methanogenic archaeon Methanobrevibacter smithii, are proposed to have a synergistic metabolic relationship. Both organisms play vital roles in human gut health; B. thetaiotaomicron assists the host by fermenting dietary polysaccharides, whereas M. smithii consumes end-stage fermentation products and is hypothesized to relieve feedback inhibition of upstream microbes such as B. thetaiotaomicron. To study their metabolic interactions, we defined and optimized a coculture system and used software testing techniques to analyze growth under a range of conditions representing the nutrient environment of the host. We verify that B. thetaiotaomicron fermentation products are sufficient for M. smithii growth and that accumulation of fermentation products alters secretion of metabolites by B. thetaiotaomicron to benefit M. smithii. Studies suggest that B. thetaiotaomicron metabolic efficiency is greater in the absence of fermentation products or in the presence of M. smithii. Under certain conditions, B. thetaiotaomicron and M. smithii form interspecies granules consistent with behavior observed for syntrophic partnerships between microbes in soil or sediment enrichments and anaerobic digesters. Furthermore, when vitamin B, hematin, and hydrogen gas are abundant, coculture growth is greater than the sum of growth observed for monocultures, suggesting that both organisms benefit from a synergistic mutual metabolic relationship. The human gut functions through a complex system of interactions between the host human tissue and the microbes which inhabit it. These diverse interactions are difficult to model or examine under controlled laboratory conditions. We studied the interactions between two dominant human gut microbes, B. thetaiotaomicron and M. smithii, using a seven-component culturing approach that allows the systematic examination of the metabolic complexity of this binary microbial system. By combining high-throughput methods with machine learning techniques, we were able to investigate the interactions between two dominant genera of the gut microbiome in a wide variety of environmental conditions. Our approach can be broadly applied to studying microbial interactions and may be extended to evaluate and curate computational metabolic models. The software tools developed for this study are available as user-friendly tutorials in the Department of Energy KBase.
Topics: Bacteroides; Fermentation; Gastrointestinal Microbiome; Humans; Methanobrevibacter; Microbial Interactions
PubMed: 35536023
DOI: 10.1128/spectrum.01067-22 -
Cold Spring Harbor Perspectives in... Nov 2013The eukaryotic replicative helicase, the minichromosome maintenance (MCM) complex, is composed of six distinct, but related, subunits MCM(2-7). The relationship between... (Review)
Review
The eukaryotic replicative helicase, the minichromosome maintenance (MCM) complex, is composed of six distinct, but related, subunits MCM(2-7). The relationship between the sequences of the subunits indicates that they are derived from a common ancestor and indeed, present-day archaea possess a homohexameric MCM. Recent progress in the biochemical and structural studies of both eukaryal and archaeal MCM complexes are beginning to shed light on the mechanisms of action of this key component of the replisome.
Topics: Animals; Archaea; Archaeal Proteins; Cell-Free System; DNA Helicases; Drosophila melanogaster; Methanobacteriaceae; Minichromosome Maintenance Proteins; Models, Molecular; Plasmids; Protein Conformation; Protein Structure, Secondary; Protein Structure, Tertiary; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Xenopus
PubMed: 23881943
DOI: 10.1101/cshperspect.a012807 -
Scientific Reports Jun 2018Methanogens have already been described in periodontitis but not in peri-implantitis. Thirty peri-implantitis samples and 28 control samples were collected in 28...
Methanogens have already been described in periodontitis but not in peri-implantitis. Thirty peri-implantitis samples and 28 control samples were collected in 28 consenting peri-implantitis patients. PCR-sequencing of the 16S rRNA gene was used as a broad-spectrum screening method and results were further confirmed by real-time quantitative PCR targeting the mcrA genes. Results showed a methanogen community dominated by Methanobrevibacter oralis in 31/58 (51%) samples including 16/28 (57%) control samples and 15/30 (50%) peri-implantitis samples. Methanobrevibacter massiliense was detected in 5/58 (8.6%) samples including 3/28 (1%) control samples and 2/30 (6.7%) peri-implantitis samples. The prevalence of M. oralis or M. massiliense did not significantly differ in peri-implantitis and control samples (exact Fisher test, P = 0.61 and P = 0.67, respectively). Further ponderation of the methanogen load by the real-time quantitative PCR for actin human gene again indicated non-significant difference (Wilcoxon-Mann-Whitney test, P = 0.48 and P = 0.40, respectively). These data show that the prevalence of methanogens does not differ in peri-implantitis lesions and healthy sites, when individuals are their own control. These data do not allow assigning a specific pathogenic role to methanogens in peri-implantitis; methanogens rather are part of the commensal and normal flora of the oral cavity.
Topics: Adult; Aged; Aged, 80 and over; Female; Humans; Male; Methanobrevibacter; Microbiota; Middle Aged; Peri-Implantitis
PubMed: 29930395
DOI: 10.1038/s41598-018-27862-8