RESUMO
The human gut virome, which is mainly composed of bacteriophages, also includes viruses infecting archaea, yet their role remains poorly understood due to lack of isolates. Here, we characterize a temperate archaeal virus (MSTV1) infecting Methanobrevibacter smithii, the dominant methanogenic archaeon of the human gut. The MSTV1 genome is integrated in the host chromosome as a provirus which is sporadically induced, resulting in virion release. Using cryo-electron tomography, we capture several intracellular virion assembly intermediates and confirm that only a small fraction of the host population actively produces virions in vitro. Similar low frequency of induction is observed in a mouse colonization model, using mice harboring a stable consortium of 12 bacterial species (OMM12). Transcriptomic analysis suggests a regulatory lysogeny-lysis switch involving an interplay between viral proteins to maintain virus-host equilibrium, ensuring host survival and viral persistence. Thus, our study sheds light on archaeal virus-host interactions and highlights similarities with bacteriophages in establishing stable coexistence with their hosts in the gut.
Assuntos
Vírus de Archaea , Microbioma Gastrointestinal , Methanobrevibacter , Animais , Humanos , Methanobrevibacter/genética , Methanobrevibacter/metabolismo , Camundongos , Vírus de Archaea/genética , Vírus de Archaea/fisiologia , Vírus de Archaea/ultraestrutura , Genoma Viral/genética , Vírion/ultraestrutura , Lisogenia , FemininoRESUMO
The study aimed to investigate the effect of supplementing polyclonal antibodies (PAP) of avian origin against the ruminal methanogens Methanobrevibacter gottschalkii Ho (PAP-Ho) and M. ruminantium M1 (PAP-M1) on ruminal fermentation profile and methane production in Angus crossbred cattle (13 steers and 1 heifer). The experiment was conducted using a randomized block design with a 3â ×â 2â +â 1 factorial arrangement, replicated in 3 periods. The factors included proportions of PAP against Ho and M1 in the mixture (100:0, 50:50, and 0:100 Ho:M1) and level of each mixture (3- or 6-mL per d). Cattle in control treatment did not receive PAP supplementation. Ruminal fluid was collected from the animals on days 0, 14, and 21 of treatment to determine of ruminal fermentation profile and ex vivo methane production. There was no effect of level of inclusion on ex vivo methane production. Supplementation with PAP-M1, either alone or in combination with PAP-Ho, decreased ex vivo methane output compared to the control group. Furthermore, in vivo molar proportion of propionate tended to be greater with PAP-M1, alone or combined with PAP-Ho, when compared with the control group. The study concluded that polyclonal antibodies against ruminal methanogens have the potential to decrease enteric methane emissions in cattle. The research provided important insights into the potential use of PAP as a strategy for reducing greenhouse gas emissions from cattle. Further research is needed to confirm these findings and to determine the practicality and feasibility of using PAP.
Methane is produced by methanogens, a type of microorganism that inhabits environments with low or no oxygen, for instance, the rumen of cattle. Methane is a greenhouse gas, and its emission contributes to climate change. Antibodies are proteins produced by the immune system when foreign bodies, called antigens, enter the body. Antibodies bind antigens and inhibit their negative actions. This study aimed to determine if oral supplementation of cattle with antibodies produced against 2 species of ruminal methanogens can decrease methane emissions from cattle. Different mixtures and doses of the 2 antibodies were supplemented to Angus crossbred animals for 21 d. Ruminal fluid from each animal was collected and incubated for 48 h to determine methane production and concentration of fermentation metabolites. There was no difference between supplementing low or high levels of antibodies. Supplementation with antibodies can result in up to 13% lower methane emissions and, in addition, production of fermentation metabolites was also affected. In summary, even a low dose of antibodies against methanogens could potentially decrease methane emissions from cattle and could become a technology to mitigate the negative effects of methane on climate.
Assuntos
Ração Animal , Dieta , Suplementos Nutricionais , Fermentação , Metano , Methanobrevibacter , Rúmen , Animais , Bovinos , Rúmen/microbiologia , Metano/metabolismo , Masculino , Ração Animal/análise , Suplementos Nutricionais/análise , Dieta/veterinária , Anticorpos , Feminino , AvesRESUMO
Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.
Assuntos
Fezes , Microbioma Gastrointestinal , Genoma Arqueal , Methanobrevibacter , Methanobrevibacter/genética , Methanobrevibacter/isolamento & purificação , Methanobrevibacter/metabolismo , Humanos , Fezes/microbiologia , Microbioma Gastrointestinal/genética , Metano/metabolismo , Filogenia , Adulto , Masculino , Feminino , Trato Gastrointestinal/microbiologiaRESUMO
Two protocols involving batch cultures were used to investigate the bioaugmentation of methane production by Pecoramyces ruminantium, and Methanobrevibacter thaueri. Protocol I examined the effect of altering the proportion of the microbial constituents in inoculum on alfalfa stalk fermentations and showed a 25 % improvement in dry matter loss in cultures where the inoculum contained just 30 % of co-culture and 70 % of fungal monoculture. Protocol II involved consecutive cultures and alternating inoculations. This protocol resulted in 17-22 mL/g DM methane production with co-cultures a 30 % increase in methane relative to the fungal monoculture. Both protocols indicate that the co-culture rapidly dominated and was more resilient than the monoculture. Synergistic interaction between fungus and methanogen, promoted more efficient lignocellulose degradation and higher methane yield. This study highlighted the potential of microbial co-cultures for enhancing methane production from lignocellulosic biomass, offering a promising bioaugmentation strategy for improving biogas yields and waste valorization.
Assuntos
Técnicas de Cocultura , Lignina , Medicago sativa , Metano , Methanobrevibacter , Metano/metabolismo , Lignina/metabolismo , Medicago sativa/metabolismo , Methanobrevibacter/metabolismo , Fermentação , Biodegradação AmbientalRESUMO
The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms, signifying alterations in microbiota composition and bile acid (BA) metabolism in IBS and ulcerative colitis (UC). Luminal oxygen concentration is a key factor in the gastrointestinal (GI) ecosystem and might be increased in IBS and UC. Here we analyzed the role of archaea as a marker for hypoxia in mucosal biofilms and GI homeostasis. The effects of archaea on microbiome composition and metabolites were analyzed via amplicon sequencing and untargeted metabolomics in 154 stool samples of IBS-, UC-patients and controls. Mucosal biofilms were collected in a subset of patients and examined for their bacterial, fungal and archaeal composition. Absence of archaea, specifically Methanobrevibacter, correlated with disrupted GI homeostasis including decreased microbial diversity, overgrowth of facultative anaerobes and conjugated secondary BA. IBS-D/-M was associated with absence of archaea. Presence of Methanobrevibacter correlated with Oscillospiraceae and epithelial short chain fatty acid metabolism and decreased levels of Ruminococcus gnavus. Absence of fecal Methanobrevibacter may indicate a less hypoxic GI environment, reduced fatty acid oxidation, overgrowth of facultative anaerobes and disrupted BA deconjugation. Archaea and Ruminococcus gnavus could distinguish distinct subtypes of mucosal biofilms. Further research on the connection between archaea, mucosal biofilms and small intestinal bacterial overgrowth should be performed.
Assuntos
Archaea , Bactérias , Biofilmes , Fezes , Microbioma Gastrointestinal , Humanos , Biofilmes/crescimento & desenvolvimento , Archaea/classificação , Archaea/metabolismo , Archaea/genética , Archaea/isolamento & purificação , Adulto , Pessoa de Meia-Idade , Feminino , Masculino , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Bactérias/isolamento & purificação , Fezes/microbiologia , Colo/microbiologia , Methanobrevibacter/metabolismo , Methanobrevibacter/genética , Methanobrevibacter/crescimento & desenvolvimento , Methanobrevibacter/isolamento & purificação , Colite Ulcerativa/microbiologia , Colite Ulcerativa/metabolismo , Síndrome do Intestino Irritável/microbiologia , Síndrome do Intestino Irritável/metabolismo , Idoso , Mucosa Intestinal/microbiologia , Mucosa Intestinal/metabolismo , Íleo/microbiologia , Ácidos Graxos Voláteis/metabolismo , Adulto Jovem , Ácidos e Sais Biliares/metabolismoRESUMO
OBJECTIVES: Methanogenic archaea are a minor component of human oral microbiota. Due to their relatively low abundance, the detection of these neglected microorganisms is challenging. This study concerns the presence of methanogens in salivary samples collected from Tunisian adults to evaluate their prevalence and burden using a polyphasic molecular approach. METHODS: A total of 43 saliva samples were included. Metagenomic and standard 16S rRNA sequencing were performed as an initial screening to detect the presence of methanogens in the oral microbiota of Tunisian adults. Further investigations were performed using specific quantitative real-time PCR targeting Methanobrevibacter oralis and Methanobrevibacter smithii. RESULTS: Methanobrevibacter was detected in 5/43 (11.62 %) saliva samples after metagenomic 16S rRNA data analysis. The presence of M. oralis was confirmed in 6/43 samples by standard 16S rRNA sequencing. Using real-time PCR, methanogens were detected in 35/43 (81.39 %) samples, including 62.79 % positive for M. oralis and 76.74 % positive for M. smithii. These findings reflect the high prevalence of both methanogens, revealed by the high sensitivity of the real-time PCR approach. Interestingly, we also noted a significant statistical association between the detection of M. smithii and poor adherence to a Mediterranean diet, indicating the impact of diet on M. smithii prevalence. CONCLUSION: Our study showed the presence of methanogens in the oral microbiota of Tunisian adults with an unprecedented relatively high prevalence. Choice of methodology is also central to picturing the real prevalence and diversity of such minor taxa in the oral microbiota.
Assuntos
Microbiota , Saliva , Adulto , Humanos , RNA Ribossômico 16S/genética , Methanobrevibacter/genética , Archaea/genéticaRESUMO
The human gut microbiota is a complex ecosystem that affects a range of human physiology. In order to explore the dynamics of the human gut microbiota, we used a system of ordinary differential equations to model mathematically the biomass of three microorganism populations: Bacteroides thetaiotaomicron, Eubacterium rectale, and Methanobrevibacter smithii. Additionally, we modeled the concentrations of relevant nutrients necessary to sustain these populations over time. Our model highlights the interactions and the competition among these three species. These three microorganisms were specifically chosen due to the system's end product, butyrate, which is a short chain fatty acid that aids in developing and maintaining the intestinal barrier in the human gut. The basis of our mathematical model assumes the gut is structured such that bacteria and nutrients exit the gut at a rate proportional to its volume, the rate of volumetric flow, and the biomass or concentration of the particular population or nutrient. We performed global sensitivity analyses using Sobol' sensitivities to estimate the relative importance of model parameters on simulation results.
Assuntos
Bacteroides thetaiotaomicron , Humanos , Eubacterium , Methanobrevibacter , Ecossistema , Bacteroides , Modelos TeóricosRESUMO
Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each other remains largely unknown. This in vitro study cocultured Blautia hydrogenotrophica (reductive acetogen), Desulfovibrio piger (sulfate reducer) and Methanobrevibacter smithii (methanogen). Results revealed that these three species coexisted and did not compete for hydrogen in the early phase of incubations. Sulfate reduction was not affected by B. hydrogenotrophica and M. smithii. D. piger inhibited the growth of B. hydrogenotrophica and M. smithii after 10 h incubations, and the inhibition on M. smithii was associated with increased sulfide concentration. Remarkably, M. smithii growth lag phase was shortened by coculturing with B. hydrogenotrophica and D. piger. Formate was rapidly used by M. smithii under high acetate concentration. Overall, these findings indicated that the interactions of the hydrogenotrophic microbes are condition-dependent, suggesting their interactions may vary in gut ecosystems.
Assuntos
Microbioma Gastrointestinal , Methanobrevibacter , Methanobrevibacter/fisiologia , Ecossistema , Hidrogênio , SulfatosRESUMO
Non-alcoholic fatty liver (NAFLD), and its complicated form, non-alcoholic steatohepatitis (NASH), have been associated with gut dysbiosis with specific signatures. Endogenous ethanol production by Klebsiella pneumoniae or yeasts has been identified as a potential physio-pathological mechanism. A species-specific association between Lactobacillus and obesity and metabolic diseases has been reported. In this study, the microbial composition of ten cases of NASH and ten controls was determined using v3v4 16S amplicon sequencing as well as quantitative PCR (qPCR). Using different statistical approaches, we found an association of Lactobacillus and Lactoccocus with NASH, and an association of Methanobrevibacter, Faecalibacterium and Romboutsia with controls. At the species level, Limosilactobacillus fermentum and Lactococcus lactis, two species producing ethanol, and Thomasclavelia ramosa, a species already associated with dysbiosis, were associated with NASH. Using qPCR, we observed a decreased frequency of Methanobrevibacter smithii and confirmed the high prevalence of L. fermentum in NASH samples (5/10), while all control samples were negative (p = 0.02). In contrast, Ligilactobacillus ruminis was associated with controls. This supports the critical importance of taxonomic resolution at the species level, notably with the recent taxonomic reclassification of the Lactobacillus genus. Our results point towards the potential instrumental role of ethanol-producing gut microbes in NASH patients, notably lactic acid bacteria, opening new avenues for prevention and treatment.
Assuntos
Lactococcus lactis , Limosilactobacillus fermentum , Hepatopatia Gordurosa não Alcoólica , Humanos , Hepatopatia Gordurosa não Alcoólica/complicações , Hepatopatia Gordurosa não Alcoólica/epidemiologia , Hepatopatia Gordurosa não Alcoólica/patologia , Methanobrevibacter/genética , Lactococcus lactis/metabolismo , Disbiose/microbiologia , EtanolRESUMO
Methanobrevibacter smithii (M. smithii), the most prevalent and abundant gut methanogen, detoxifies hydrogen into methane and is, therefore, of paramount importance for the equilibrium of the gut microbiota. The isolation by culture of M. smithii has routinely relied upon hydrogencarbon dioxide-enriched, oxygen-deprived atmospheres. In this study, we developed a medium referred to as "GG", which allowed for M. smithii growth and isolation by culture in an oxygen-deprived atmosphere, with no supply of either hydrogen or carbon dioxide, making it easier to detect M. smithii by culture in clinical microbiology laboratories.
Assuntos
Microbioma Gastrointestinal , Methanobrevibacter , Dióxido de Carbono , Bactérias Anaeróbias , HidrogênioRESUMO
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.
Assuntos
Euryarchaeota , Microbioma Gastrointestinal , Humanos , Archaea/genética , Methanobrevibacter/genética , Metano , Doença CrônicaRESUMO
Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the human gut. However, the gut methanogen diversity of human populations in many global regions remains poorly investigated. Here, we report the abundance and diversity of gut methanogenic Archaea in a multi-ethnic cohort of healthy Singaporeans by using a concerted approach of metagenomic sequencing, 16S rRNA gene amplicon sequencing, and quantitative PCR. Our results indicate a mutual exclusion of Methanobrevibacter species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent Candidatus Methanobrevibacter intestini in more than 80% of the samples when using an amplicon sequencing-based approach. Leveraging on this finding, we were able to select a fecal sample to isolate a representative strain, TLL-48-HuF1, for Candidatus Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861T and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the Methanobrevibacter species indicate potentially different niche adaptation strategies in the human host, which may support the designation of Candidatus M. intestini as a novel species. IMPORTANCE Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents. While Methanobrevibacter smithii is the most prevalent and abundant methanogen in the human gut of local subjects, the recently proposed Candidatus Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and Ca. M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different Methanobrevibacter species.
Assuntos
Microbioma Gastrointestinal , Methanobrevibacter , Fezes , Humanos , Metagenômica , Methanobrevibacter/genética , RNA Ribossômico 16S/genéticaRESUMO
Archaea are common constituents of the gut microbiome of humans, ruminants, and termites but little is known about their diversity and abundance in other animals. Here, we analyse sequencing and quantification data of archaeal and bacterial 16S rRNA genes from 250 species of animals covering a large taxonomic spectrum. We detect the presence of archaea in 175 animal species belonging to invertebrates, fish, amphibians, birds, reptiles and mammals. We identify five dominant gut lineages, corresponding to Methanobrevibacter, Methanosphaera, Methanocorpusculum, Methanimicrococcus and "Ca. Methanomethylophilaceae". Some archaeal clades, notably within Methanobrevibacter, are associated to certain hosts, suggesting specific adaptations. The non-methanogenic lineage Nitrososphaeraceae (Thaumarchaeota) is frequently present in animal samples, although at low abundance, but may have also adapted to the gut environment. Host phylogeny, diet type, fibre content, and intestinal tract physiology are major drivers of the diversity and abundance of the archaeome in mammals. The overall abundance of archaea is more influenced by these factors than that of bacteria. Methanogens reducing methyl-compounds with H2 can represent an important fraction of the overall methanogens in many animals. Together with CO2-reducing methanogens, they are influenced by diet and composition of gut bacteria. Our results provide key elements toward our understanding of the ecology of archaea in the gut, an emerging and important field of investigation.
Assuntos
Archaea , Euryarchaeota , Animais , Archaea/genética , Bactérias/genética , Fibras na Dieta , Euryarchaeota/genética , Mamíferos/genética , Methanobacteriaceae , Methanobrevibacter/genética , Filogenia , RNA Ribossômico 16S/genéticaRESUMO
In silico prediction of epitopes is a potentially time-saving alternative to experimental epitope identification but is often subject to misidentification of epitopes and may not be useful for proteins from archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigen from the methanogen Methanobrevibacter ruminantium M1, the Big_1 domain (AdLP-D1, amino acids 19-198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cover the Big_1 domain. Peptide-specific antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specific T-cell responses. Overall, five peptides of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validated epitopes were found in the outside region of the protein, with loop like secondary structures reflecting their flexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identified by in silico predictions were not comparable to those determined empirically.
Assuntos
Adesinas Bacterianas , Methanobrevibacter , Adesinas Bacterianas/metabolismo , Algoritmos , Animais , Mapeamento de Epitopos , Epitopos de Linfócito T , Methanobrevibacter/metabolismo , Camundongos , Peptídeos/metabolismoRESUMO
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 B12, 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. IMPORTANCE 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.
Assuntos
Microbioma Gastrointestinal , Methanobrevibacter , Bacteroides/metabolismo , Fermentação , Humanos , Methanobrevibacter/metabolismo , Interações MicrobianasRESUMO
The aetiology of appendicular abscess is predominantly microbial with aerobic and anaerobic bacteria from gut flora. In this study, by using specific laboratory tools, we co-detected Methanobrevibacter oralis and Methanobrevibacter smithii among a mixture of enterobacteria including Escherichia coli, Enterococcus faecium and Enterococcus avium in four unrelated cases of postoperative appendiceal abscesses. These unprecedented observations raise a question on the role of methanogens in peri-appendicular abscesses, supporting antibiotics as an alternative therapeutic option for appendicitis, including antibiotics active against methanogens such as metronidazole or fusidic acid.
Assuntos
Abscesso/diagnóstico , Abscesso/microbiologia , Apendicite/complicações , Methanobrevibacter/classificação , Abscesso/tratamento farmacológico , Adolescente , Adulto , Antibacterianos/uso terapêutico , Apendicite/diagnóstico , Apendicite/tratamento farmacológico , Hemocultura , Gerenciamento Clínico , Suscetibilidade a Doenças , Feminino , Humanos , Masculino , Methanobrevibacter/genética , Methanobrevibacter/isolamento & purificação , Methanobrevibacter/ultraestrutura , Pessoa de Meia-Idade , Tipagem Molecular , RNA Ribossômico 16S/genética , Tomografia Computadorizada por Raios X , Adulto JovemRESUMO
BACKGROUND: Methane emissions from agriculture are responsible for over 40% of the world's greenhouse gas emissions. In the past, antibiotics were used to control methane production by animals, but concerns over the emergence and spread of antibiotic-resistant bacteria to humans have prompted a search for alternative approaches. Hops are the flowers of the hop plant Humulus lupulus. They have been used to feed cattle for many years and are known to contain antibacterial compounds, and their extracts have been shown to kill members of the Mycobacterium spp including Mycobacterium bovis, the causative agent of bovine tuberculosis as well as a number of human pathogens. In this study, hop extracts were studied for their ability to inhibit methane production from Methanobrevibacter ruminantium, a major methane-producing archaeon found in the rumen of cattle. METHODS: Methanobrevibacter ruminantium M1T (DSM 1093) was grown at 37°C for 30 days, and the amount of methane produced at different time points during this period was measured using gas chromatography. The archaeon was exposed to commercial hop extracts (tetra-hydro-iso-alpha acid and beta acid) and to aqueous hop extracts of a range of hop variants, and their effect on methane production was determined. RESULTS: All of the extracts reduced the level of methane production of M. ruminantium over the 30-day period compared to the negative control (sterile distilled water). The commercial hop extracts were the most effective at inhibiting methane production over the course of the experiment in contrast to the aqueous extracts, which showed a gradual reduction of inhibition with time. CONCLUSIONS: Hops contain compounds which inhibit methane production. Given that hops can be safely fed to cattle, this raises the possibility of rationally designing a feed strategy which could reduce greenhouse gas emissions and protect against bovine tuberculosis. This study recommends that further research be undertaken to further identifying bioactive components from hops and their efficacy against a range of archaea.
Assuntos
Gases de Efeito Estufa , Humulus , Tuberculose Bovina , Animais , Antibacterianos/farmacologia , Archaea , Bovinos , Humulus/química , Metano , Methanobrevibacter , Rúmen/microbiologiaRESUMO
BACKGROUND: Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE). RESULTS: We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. CONCLUSIONS: We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.
Assuntos
Archaea , Metagenoma , Archaea/genética , Cálculos Dentários , Humanos , Methanobrevibacter/genética , Pessoa de Meia-Idade , FilogeniaRESUMO
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 (CH4 breath content 5-75 ppm) and low emitters (CH4 < 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.
Assuntos
Metano , Methanobrevibacter , Adulto , Animais , Feminino , Formiatos , Trato Gastrointestinal , Humanos , Masculino , Metagenômica , Methanobrevibacter/genética , Rúmen , Adulto JovemRESUMO
Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.