-
Microbiome Sep 2021Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human...
BACKGROUND
Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been associated with abdominal pain, bloating, constipation, IBD, CRC or other conditions. Twenty percent of the (healthy) Western populations innately exhale substantially higher amounts (>5 ppm) of this gas. The underlying principle for differential methane emission and its effect on human health is not sufficiently understood.
RESULTS
We assessed the breath methane content, the gastrointestinal microbiome, its function and metabolome, and dietary intake of one-hundred healthy young adults (female: n = 52, male: n = 48; mean age =24.1). On the basis of the amount of methane emitted, participants were grouped into high methane emitters (CH breath content 5-75 ppm) and low emitters (CH < 5 ppm). The microbiomes of high methane emitters were characterized by a 1000-fold increase in Methanobrevibacter smithii. This archaeon co-occurred with a bacterial community specialized on dietary fibre degradation, which included members of Ruminococcaceae and Christensenellaceae. As confirmed by metagenomics and metabolomics, the biology of high methane producers was further characterized by increased formate and acetate levels in the gut. These metabolites were strongly correlated with dietary habits, such as vitamin, fat and fibre intake, and microbiome function, altogether driving archaeal methanogenesis.
CONCLUSIONS
This study enlightens the complex, multi-level interplay of host diet, genetics and microbiome composition/function leading to two fundamentally different gastrointestinal phenotypes and identifies novel points of therapeutic action in methane-associated disorders. Video Abstract.
Topics: Adult; Animals; Female; Formates; Gastrointestinal Tract; Humans; Male; Metagenomics; Methane; Methanobrevibacter; Rumen; Young Adult
PubMed: 34560884
DOI: 10.1186/s40168-021-01130-w -
Scientific Reports Jun 2018The oral fluid microbiome comprises an important bacterial diversity, yet the presence of archaea has not been reported so far. In order to quest for the presence of... (Clinical Trial)
Clinical Trial
The oral fluid microbiome comprises an important bacterial diversity, yet the presence of archaea has not been reported so far. In order to quest for the presence of methanogenic archaea (methanogens) in oral fluid, we used a polyphasic approach including PCR-sequencing detection, microscopic observation by fluorescence in-situ hybridization, isolation and culture, molecular identification and genotyping of methanogens in 200 oral fluid specimens. In the presence of negative controls, 64/200 (32%) prospectively analysed oral fluid specimens were PCR-positive for methanogens, all identified as Methanobrevibacter oralis by sequencing. Further, fluorescence in-situ hybridization detected methanogens in 19/48 (39.6%) investigated specimens; with morphology suggesting M. oralis in 10 cases and co-infecting Methanobrevibacter smithii in nine cases. M. oralis was cultured from 46/64 (71.8%) PCR-positive specimens and none of PCR-negative specimens; and one M. smithii isolate was co-cultured with M. oralis in one specimen. Multispacer Sequence Typing found one M. oralis genotype per specimen and a total of five different genotypes with 19/46 (41%) of isolates all belonging to spacer-type four. Statistical analyses showed a significant correlation between the PCR-detection of methanogens in oral fluid and tobacco smoking. These data indicate that M. oralis and M. smithii are oral fluid-borne methanogens in tobacco smokers. Both methanogens could be transmitted during intimate contacts such as mother-to-child contacts and kissing.
Topics: Cross-Sectional Studies; Female; Humans; Male; Methanobrevibacter; Microbiota; Mouth; Tobacco Smoking
PubMed: 29907776
DOI: 10.1038/s41598-018-27372-7 -
PloS One 2015In previous studies, the abundance and diversity of methanogenic archaea in the dental microbiota have been analysed by the detection of specific DNA sequences by...
In previous studies, the abundance and diversity of methanogenic archaea in the dental microbiota have been analysed by the detection of specific DNA sequences by PCR-based investigations and metagenomic studies. Few data issued regarding methanogens actually living in dental plaque. We collected dental plaque specimens in 15 control individuals and 65 periodontitis patients. Dental plaque specimens were cultured in an anoxic liquid medium for methanogens in the presence of negative control tubes. Dental plaque methanogens were cultured from 1/15 (6.67%) control and 36/65 (55.38%) periodontitis patient samples (p<0.001). The cultures yielded Methanobrevibacter oralis in one control and thirty-one patients, Methanobrevibacter smithii in two patients and a potential new species named Methanobrevibacter sp. strain N13 in three patients with severe periodontitis. Our observations of living methanogens, strengthen previous observations made on DNA-based studies regarding the role of methanogens, in periodontitis.
Topics: Adult; Aged; Case-Control Studies; DNA, Archaeal; Dental Plaque; Female; Humans; Male; Methanobrevibacter; Middle Aged; Molecular Sequence Data; Molecular Typing; Periodontitis; Phylogeny; RNA, Ribosomal, 16S; Young Adult
PubMed: 25830311
DOI: 10.1371/journal.pone.0121565 -
BMC Research Notes May 2012The methanogenic Archaea Methanosphaera stadtmanae has been detected in the human gut microbiota by both culture and culture-independent methods. Its growth reaches an...
BACKGROUND
The methanogenic Archaea Methanosphaera stadtmanae has been detected in the human gut microbiota by both culture and culture-independent methods. Its growth reaches an exponential phase after 5 to 7-day culture in medium 322 (10% vol). Our recent successful isolation of Methanomassiliicoccus luminyensis, a tungstate-selenite-requiring Archaea sharing similar metabolism characteristics with M. stadtmanae prompted us to study the effects of tungsten and selenium on M. stadtmanae growth.
FINDINGS
Addition of 0.2 mg/L sodium tungstate to medium 322 yielded, 48 hours after inoculation, a growth rate equivalent to that obtained after 6 days with control culture as measured by methane monitoring and optical density measurement. Addition of 50 μg/mL sodium selenate had no effect on M. stadtmanae growth. Quantitative real-time PCRs targeting the M. stadtmanae 16S rRNA confirmed these data.
CONCLUSIONS
These data provide new information regarding the poorly known nutritional requirements of the human gut colonizing organismsM. stadtmanae. Adding sodium tungstate to basal medium may facilitate phenotypic characterization of this organism and additionally aid the isolation of new Archaea from complex host microbiota.
Topics: Gastrointestinal Tract; Humans; Methane; Methanobacteriaceae; RNA, Archaeal; RNA, Ribosomal, 16S; Real-Time Polymerase Chain Reaction; Selenic Acid; Selenium Compounds; Time Factors; Tungsten Compounds
PubMed: 22587398
DOI: 10.1186/1756-0500-5-238 -
Nucleic Acids Research May 1998A novel method of cumulative diagrams shows that the nucleotide composition of a microbial chromosome changes at two points separated by about a half of its length....
A novel method of cumulative diagrams shows that the nucleotide composition of a microbial chromosome changes at two points separated by about a half of its length. These points coincide with sites of replication origin and terminus for all bacteria where such sites are known. The leading strand is found to contain more guanine than cytosine residues. This fact is used to predict origin and terminus locations in other bacterial and archaeal genomes. Local changes, visible as diagram distortions, may represent recent genome rearrangements, as demonstrated for two strains of Escherichia coli . Analysis of the diagrams of viral and mitochondrial genomes suggests a link between the base composition bias and the time spent by DNA in a single stranded state during replication.
Topics: Bacteria; Base Composition; Chromosomes, Archaeal; Chromosomes, Bacterial; DNA Replication; DNA, Archaeal; DNA, Bacterial; Gene Rearrangement; Genome; Genome, Bacterial; Methanobacterium; Methanococcus
PubMed: 9580676
DOI: 10.1093/nar/26.10.2286 -
Journal of Bacteriology Dec 2018Coenzyme F plays a key role in the redox metabolisms of various archaea and bacteria, including In , F-dependent reactions have been linked to several virulence...
Coenzyme F plays a key role in the redox metabolisms of various archaea and bacteria, including In , F-dependent reactions have been linked to several virulence factors. F carries multiple glutamate residues in the side chain, forming F- species (, number of glutamate residues), and the length of this side chain impacts cellular physiology. strains with F species carrying shorter side chains exhibit resistance to delamanid and pretomanid, two new tuberculosis (TB) drugs. Thus, the process of polyglutamylation of F is of great interest. It has been known from genetic analysis that in mycobacteria an F-0 γ-glutamyl ligase (FbiB) introduces up to seven glutamate residues into F However, purified FbiB of (FbiB) is either inefficient or incapable of incorporating more than two glutamates. We found that, , FbiB synthesized side chains containing up to seven glutamate residues if F was presented to the enzyme in a two-electron reduced state (FH). Our genetic analysis in BCG and and an analysis of literature data on revealed that in these mycobacteria the polyglutamylation process requires the assistance of F-dependent glucose-6-phosphate dehydrogenase (Fgd) which reduces F to FH We hypothesize that, starting with F-0H, the amino-terminal domain of FbiB builds F-2H, which is then transferred to the carboxy-terminal domain for further glutamylation; F-2H modifies the carboxy-terminal domain structurally to accommodate longer glutamyl chains. This system is analogous to folylpolyglutamate synthase, which introduces more than one glutamate residue into folate only after this vitamin is reduced to tetrahydrofolate. Coenzyme F-dependent reactions of , which causes tuberculosis, potentially contributes to the virulence of this bacterium. The coenzyme carries a glutamic acid-derived tail, the length of which influences the metabolism of Mutations that eliminate the production of F with longer tails make resistant to two new tuberculosis drugs. This report describes that the synthesis of longer glutamyl tails of F requires concerted actions of two enzymes, one of which reduces the coenzyme prior to the action of the other, which catalyzes polyglutamylation. This knowledge will help to develop more effective tuberculosis (TB) drugs. Remarkably, the introduction of multiple glutamate residues into the sidechain of folate (vitamin B) requires similar concerted actions, where one enzyme reduces the vitamin to tetrahydrofolate and the other catalyzes polyglutamylation; folate is required for DNA and amino acid synthesis. Thus, the reported research has also revealed a key similarity between two important cellular systems.
Topics: Antitubercular Agents; Bacterial Proteins; Drug Resistance, Bacterial; Glucosephosphate Dehydrogenase; Ligases; Methanobacteriaceae; Mycobacterium tuberculosis; Nitroimidazoles; Oxazoles; Polyglutamic Acid; Recombinant Proteins; Riboflavin; Tetrahydrofolates
PubMed: 30249701
DOI: 10.1128/JB.00375-18 -
Microbial Biotechnology Jul 2020Glycerol-rich waste streams produced by the biodiesel, bioethanol and oleochemical industries can be treated and valorized by anaerobic microbial communities to produce...
Glycerol-rich waste streams produced by the biodiesel, bioethanol and oleochemical industries can be treated and valorized by anaerobic microbial communities to produce methane. As current knowledge of the microorganisms involved in thermophilic glycerol conversion to methane is scarce, thermophilic glycerol-degrading methanogenic communities were enriched. A co-culture of Thermoanaerobacter and Methanothermobacter species was obtained, pointing to a non-obligately syntrophic glycerol degradation. This hypothesis was further studied by incubating Thermoanaerobacter brockii subsp. finnii and T. wiegelii with glycerol (10 mM) in pure culture and with different hydrogenotrophic methanogens. The presence of the methanogen accelerated glycerol fermentation by the two Thermoanaerobacter strains up to 3.3 mM day , corresponding to 12 times higher volumetric glycerol depletion rates in the methanogenic co-cultures than in the pure bacterial cultures. The catabolic pathways of glycerol conversion were identified by genome analysis of the two Thermoanaerobacter strains. NADH and reduced ferredoxin formed in the pathway are linked to proton reduction, which becomes thermodynamically favourable when the hydrogen partial pressure is kept low by the hydrogenotrophic methanogenic partner.
Topics: Anaerobiosis; Glycerol; Methane; Methanobacteriaceae; Thermoanaerobacter
PubMed: 32154666
DOI: 10.1111/1751-7915.13506 -
MBio Dec 2021Thermophilic spp. are used as model microbes to study the physiology and biochemistry of the conversion of molecular hydrogen and carbon dioxide into methane (i.e.,...
Thermophilic spp. are used as model microbes to study the physiology and biochemistry of the conversion of molecular hydrogen and carbon dioxide into methane (i.e., hydrogenotrophic methanogenesis). Yet, a genetic system for these model microbes was missing despite intensive work for four decades. Here, we report the successful implementation of genetic tools for Methanothermobacter thermautotrophicus ΔH. We developed shuttle vectors that replicated in Escherichia coli and ΔH. For ΔH, a thermostable neomycin resistance cassette served as the selectable marker for positive selection with neomycin, and the cryptic plasmid pME2001 from Methanothermobacter marburgensis served as the replicon. The shuttle-vector DNA was transferred from E. coli into ΔH via interdomain conjugation. After the successful validation of DNA transfer and positive selection in ΔH, we demonstrated heterologous gene expression of a thermostable β-galactosidase-encoding gene () from Geobacillus stearothermophilus under the expression control of four distinct synthetic and native promoters. In quantitative enzyme activity assay, we found significantly different β-galactosidase activity with these distinct promoters. With a formate dehydrogenase operon-encoding shuttle vector, we allowed growth of ΔH on formate as the sole growth substrate, while this was not possible for the empty-vector control. The world economies are facing permanently increasing energy demands. At the same time, carbon emissions from fossil sources need to be circumvented to minimize harmful effects from climate change. The power-to-gas platform is utilized to store renewable electric power and decarbonize the natural gas grid. The microbe Methanothermobacter thermautotrophicus is already applied as the industrial biocatalyst for the biological methanation step in large-scale power-to-gas processes. To improve the biocatalyst in a targeted fashion, genetic engineering is required. With our shuttle-vector system for heterologous gene expression in , we set the cornerstone to engineer the microbe for optimized methane production but also for production of high-value platform chemicals in power-to-x processes.
Topics: Bacterial Proteins; Conjugation, Genetic; Escherichia coli; Galactosidases; Gene Expression; Genetic Vectors; Geobacillus; Methane; Methanobacteriaceae
PubMed: 34809461
DOI: 10.1128/mBio.02766-21 -
EBioMedicine May 2019Urinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context.
BACKGROUND
Urinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context.
METHODS
In two different university hospital centres we used specific laboratory methods for the detection and culture of archaeal methanogens in 383 urine specimens prospectively collected for diagnosing urinary tract infection (UTI).
FINDINGS
Methanobrevibacter smithii was detected by quantitative PCR and sequencing in 34 (9%) of the specimens collected from 34 patients. Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Enterococcus faecium and mixed cultures were detected along with M. smithii in eighteen, six, three, one and six urine samples, respectively. Interestingly, using our specific culture method for methanogens, we also isolated M. smithii in 31 (91%) of the 34 PCR positive urine samples. Genotyping the 31 isolates using multispacer sequence typing revealed three different genotypes which have been previously reported in intestinal microbiota. Antibiotic susceptibility testing found the 31 isolates to be in vitro susceptible to metronidazole (MIC: 1 mg/L) but resistant to fosfomycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanate and ofloxacin, commonly used to treat bacterial UTI. Finally, 19 (54%) of the 34 patients in whose urine samples M. smithii was detected were diagnosed with UTIs, including cystitis, pyelonephritis and prostatitis.
INTERPRETATION
Our results show that M. smithii is part of the urinary microbiota of some individuals and could play a role in community-acquired UTI in association with enteric bacteria. FUND: This study was supported by IHU Méditerranée Infection, Marseille, France.
Topics: Adult; Aged; Bacteriological Techniques; Coculture Techniques; Enterobacteriaceae; Female; Humans; Male; Methanobrevibacter; Middle Aged; Retrospective Studies; Urinalysis; Urinary Tract Infections
PubMed: 31072770
DOI: 10.1016/j.ebiom.2019.04.037 -
BMC Microbiology Jan 2017Pea fiber (PF) is a potential fibrous supplement in swine production. The influence of dietary PF on microbial community in the colon of pigs remains largely unexplored....
Dietary pea fiber increases diversity of colonic methanogens of pigs with a shift from Methanobrevibacter to Methanomassiliicoccus-like genus and change in numbers of three hydrogenotrophs.
BACKGROUND
Pea fiber (PF) is a potential fibrous supplement in swine production. The influence of dietary PF on microbial community in the colon of pigs remains largely unexplored. Methanogens in the hindgut of monogastric animals play important roles in degradation of dietary fibers and efficient removal of microbial metabolic end product H. Understanding the impact of dietary PF on the structure of colonic methanogens may help understand the mechanisms of microbe-mediated physiological functions of PF. This study investigated the influence of PF on the diversity and quantity and/or activity of colonic methanongens of piglets and finishing pigs. Four archaeal 16S rRNA clone libraries were constructed for piglets and finishers fed with control (Piglet-C and Finisher-C) or PF diet (Piglet-P and Finisher-P).
RESULTS
There were 195, 190, 194 and 196 clones obtained from the library Piglet-C, Piglet-P, Finisher-C and Finisher-P, respectively, with corresponding 12, 11, 11 and 16 OTUs (operational taxonomic units). Significant differences of Shannon Index among the four libraries were found (P < 0.05). Libshuff analysis showed that the archaeal community structure among the four libraries were significantly different (P < 0.0001). The predominant methanogens shifted from Methanobrevibacter to Methanobrevibacter and Methanomassiliicoccus-like genus as a result of dietary PF. Supplementation of PF significantly increased the copy numbers of mcrA and dsrA genes (P < 0.05).
CONCLUSIONS
Alteration of methanogenic community structure may lead to functional transition from utilization of H/CO to employment of both H/CO and methanol/CO. Quantification of three functional genes (mcrA, dsrA and fhs) of methanogens, sulfate-reducing bacteria (SRB) and acetogens revealed that dietary PF also increased the activity of methanogens and SRB,probably associated with increased proportion of Methanomassiliicoccus luminyensis-species. Further study is required to examine the interaction between specific methanogens and SRB during fermentation of dietary PF.
Topics: Animal Feed; Animals; Archaea; Biodiversity; Carbon Dioxide; Colon; DNA, Archaeal; Diet; Dietary Fiber; Euryarchaeota; Fermentation; Gastrointestinal Tract; Hydrogen; Methanobrevibacter; Methanol; Pisum sativum; Phylogeny; RNA, Ribosomal, 16S; Swine
PubMed: 28095773
DOI: 10.1186/s12866-016-0919-9