-
Environmental Microbiology Oct 2022Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key...
Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head-tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near-complete genomes of spindle-shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head-tailed virus-like particles and the presence of spindle-shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.
Topics: Archaea; Archaeal Viruses; Carbon; Formates; Genome, Viral; Isotopes; Metagenomics; Methanobacterium; Viruses
PubMed: 35848130
DOI: 10.1111/1462-2920.16120 -
Scientific Reports Jun 2022In silico prediction of epitopes is a potentially time-saving alternative to experimental epitope identification but is often subject to misidentification of epitopes...
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.
Topics: Adhesins, Bacterial; Algorithms; Animals; Epitope Mapping; Epitopes, T-Lymphocyte; Methanobrevibacter; Mice; Peptides
PubMed: 35729277
DOI: 10.1038/s41598-022-14545-8 -
Microbiology Spectrum Aug 2022Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the...
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 species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent 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 Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861 and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the species indicate potentially different niche adaptation strategies in the human host, which may support the designation of M. intestini as a novel species. 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 Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and . M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different species.
Topics: Feces; Gastrointestinal Microbiome; Humans; Metagenomics; Methanobrevibacter; RNA, Ribosomal, 16S
PubMed: 35699469
DOI: 10.1128/spectrum.00849-22 -
Nature Communications Jun 2022Archaea 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,...
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 H can represent an important fraction of the overall methanogens in many animals. Together with CO-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.
Topics: Animals; Archaea; Bacteria; Dietary Fiber; Euryarchaeota; Mammals; Methanobacteriaceae; Methanobrevibacter; Phylogeny; RNA, Ribosomal, 16S
PubMed: 35688919
DOI: 10.1038/s41467-022-31038-4 -
Frontiers in Veterinary Science 2022Ruminants are a critical human food source and have been implicated as a potentially important source of global methane emissions. Because of their unique digestive...
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.
PubMed: 35664853
DOI: 10.3389/fvets.2022.897996 -
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 -
Frontiers in Microbiology 2022Supplementation with lipids and oils is one of the most efficient strategies for reducing enteric methane emission. However, high costs and adverse impacts on fiber...
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 ( = 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 ( = 0.15) and CP ( = 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 ( < 0.001) than in CTR. In the CON group, body weight gain (kg, = 0.02) and average daily gain (g, = 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 ( = 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 ( < 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 , , and . The long-term supplementation of oil did not induce any significant change in the rumen archaeal community, whereas minor species such as exhibited differing abundance among the groups. , irrespective of treatment, was the largest genus, while was the dominant species. Oil supplementation in CON and INT compared with CTR decreased ( < 0.01) the numbers of total protozoa (× 10 cells/ml), (× 10 cells/ml), and (× 10 cells/ml). SWPO continuous supplementation (CON group) resulted in the largest reduction in enteric methane emission and relatively higher body weight gain ( = 0.02) in sheep.
PubMed: 35369442
DOI: 10.3389/fmicb.2022.780073 -
Poultry Science Feb 2022The aim of this study was to investigate the effects of different probiotic fermented diets on production performance and intestinal health of laying hens. A total of...
The aim of this study was to investigate the effects of different probiotic fermented diets on production performance and intestinal health of laying hens. A total of 360 healthy 22-wk-age Jingfen No. 6 layers were randomly divided into 4 treatments: basal diet (CON); supplemented with 6% Clostridium butyricum fermented feed (CB); supplemented with 6% Lactobacillus crispatus fermented feed (LC); supplemented with 6% Lactobacillus salivarius fermented feed (LS). The experiment lasted for 8 wk. The results showed that the levels of crude fiber, β-glucan and pH of feed decreased significantly after fermentation (P < 0.05). Compared with CON group, the feed conversion ratio (FCR) was decreased significantly (P < 0.05), and albumen height and Haugh unit in LC group and LS group were increased significantly (P < 0.05). Fermented feed supplementation significantly improved villus height (VH) of the jejunum and the ratio of villus height to crypt depth (VH/CD) of the ileum (P < 0.05). Additionally, the VH and VH/CD of the duodenum were significantly increased in LS group (P < 0.05). Furthermore, the ACE and chao1 indexes in LS group were extremely significant higher than that in the other 3 groups (P < 0.05). In addition, compared with CON group, the abundance of Rikenellaceae and Methanobacteriaceae was significantly decreased at the family level in LC group and LS group (P < 0.05), while the abundance of Ruminocaceae was significantly higher (P < 0.05). Collectively, feeding Lactobacillus salivarius and Lactobacillus crispatus fermented feed improved the FCR, albumen height and Haugh unit of laying hens, and Lactobacillus salivarius fermented feed supplementation could improve intestinal health by ameliorating intestinal morphology, altering microbial composition and enhancing microbial community richness.
Topics: Animal Feed; Animal Nutritional Physiological Phenomena; Animals; Chickens; Diet; Dietary Supplements; Female; Probiotics
PubMed: 34852968
DOI: 10.1016/j.psj.2021.101570 -
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 -
Archaea (Vancouver, B.C.) 2021Methane 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...
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 . 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 spp including , 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 , a major methane-producing archaeon found in the rumen of cattle.
METHODS
M1 (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 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.
Topics: Animals; Anti-Bacterial Agents; Archaea; Cattle; Greenhouse Gases; Humulus; Methane; Methanobrevibacter; Rumen; Tuberculosis, Bovine
PubMed: 34776791
DOI: 10.1155/2021/5510063