Genomic convergence between Akkermansia muciniphila in different mammalian hosts.

BACKGROUND: Akkermansia muciniphila is a member of the human gut microbiota where it resides in the mucus layer and uses mucin as the sole carbon, nitrogen and energy source. A. muciniphila is the only representative of the Verrucomicrobia phylum in the human gut. However, A. muciniphila 16S rRNA gene sequences have also been found in the intestines of many vertebrates. RESULTS: We detected A. muciniphila-like bacteria in the intestines of animals belonging to 15 out of 16 mammalian orders. In addition, other species belonging to the Verrucomicrobia phylum were detected in fecal samples. We isolated 10 new A. muciniphila strains from the feces of chimpanzee, siamang, mouse, pig, reindeer, horse and elephant. The physiology and genome of these strains were highly similar in comparison to the type strain A. muciniphila MucT. Overall, the genomes of the new strains showed high average nucleotide identity (93.9 to 99.7%). In these genomes, we detected considerable conservation of at least 75 of the 78 mucin degradation genes that were previously detected in the genome of the type strain MucT. CONCLUSIONS: The low genomic divergence observed in the new strains may indicate that A. muciniphila favors mucosal colonization independent of the differences in hosts. In addition, the conserved mucus degradation capability points towards a similar beneficial role of the new strains in regulating host metabolic health.

Luteolibacter ambystomatis sp. nov., isolated from the skin of an Anderson's salamander (Ambystoma andersoni).

A bacterial strain designated 32AT was isolated from the skin of an Anderson's salamander (Ambystoma andersoni) and subjected to a comprehensive taxonomic study. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase- and urease-negative, and catalase-positive. 16S rRNA gene sequence comparisons placed the strain in the genus Luteolibacter with highest sequence similarities to Luteolibacter pohnpeiensis A4T-83T (95.2%), Luteolibacter gellanilyticus CB-286403T (95.1%) and Luteolibacter cuticulihirudinis E100T (94.9%). Genomic sequence analysis revealed a size of 5.3 Mbp, a G+C-content of 62.2 mol% and highest ANI values with Luteolibacter luteus (71.2%), Luteolibacter yonseiensis (71.4%) and L. pohnpeiensis (69.5%). In the polyamine pattern, 1,3-diaminopropane and spermidine were predominant. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system was composed of the major menaquinones MK-9 and MK-10. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, the unidentified aminolipid AL2, the unidentified phospholipid PL2 and the unidentified aminophospholipid APL1. The fatty acid profile contained major amounts of iso-C14:0, iso-C16:0, C16 : 0 and C16 : 1 ω9c. In addition, C14 : 0, C15:0, anteiso-C15 : 0, summed feature 2 (C14 : 0 3OH and/or iso-C16 : 0 I), and the hydroxylated fatty acids iso-C14 : 0 3OH, iso-C16 : 0 3OH and C16 : 0 3-OH were detected. Physiologically, strain 32AT is distinguishable from its next relatives. Based on phylogenetic, genomic, physiological and chemotaxonomic data, strain 32AT represents a novel species of the genus Luteolibacter for which we propose the name Luteolibacter ambystomatis sp. nov. The type strain is 32AT (=CCM 9141T=LMG 32214T).

Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community.

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

Effects of Lactobacillus reuteri supplementation on the gut microbiota in extremely preterm infants in a randomized placebo-controlled trial.

Extremely low birth weight (ELBW) infants often develop an altered gut microbiota composition, which is related to clinical complications, such as necrotizing enterocolitis and sepsis. Probiotic supplementation may reduce these complications, and modulation of the gut microbiome is a potential mechanism underlying the probiotic effectiveness. In a randomized, double-blind, placebo-controlled trial, we assessed the effect of Lactobacillus reuteri supplementation, from birth to post-menstrual week (PMW)36, on infant gut microbiota. We performed 16S amplicon sequencing in 558 stool samples from 132 ELBW preterm infants at 1 week, 2 weeks, 3 weeks, 4 weeks, PMW36, and 2 years. Probiotic supplementation results in increased bacterial diversity and increased L. reuteri abundance during the 1st month. At 1 week, probiotic supplementation also results in a lower abundance of Enterobacteriaceae and Staphylococcaceae. No effects were found at 2 years. In conclusion, probiotics may exert benefits by modulating the gut microbiota composition during the 1st month in ELBW infants.

Structural rearrangement of native and processed pea starches following simulated digestion in vitro and fermentation characteristics of their resistant starch residues using human fecal inoculum.

Pea starches, in both native (NPS) and retrograded-autoclaved forms (RAPS), were subjected to simulated gastrointestinal (GI) digestion in vitro, their multi-scale structural characteristics, morphological features, molecular distribution and thermal properties were characterized. A gradual increase in the short-/long-range crystallinity, melting enthalpy of gelatinization on increasing digestion time was observed for both the native and retrograded-autoclaved pea starch samples based on the X-ray diffraction, Fourier-transform infrared spectra, solid-state 13CNMR and differential scanning calorimetry measurements. It was especially noticed that the growth rate of crystallinity and double helices, as well as the decrease in Mw values were evidently greater for RAPS than for NPS. To investigate how different molecular fine structure of pea starch substrate affects the gut microbiota shifts and dynamic short-chain fatty acid profile, their resistant starch residues obtained from both native and retrograded-autoclaved pea starch after 8 h of simulated GI tract digestion was used as the fermentation substrate. The levels of acetate, propionate and butyrate gradually increased with the increasing fermentation time for NPS and RAPS. In comparison to the blank control (i.e., the group without the addition of carbohydrate), the fermented NPS and RAPS obviously resulted in an increased abundance of Firmicutes and Bacteroidetes, accompanied by a decrease in Proteobacteria, Actinobacteria and Verrucomicrobia. Both NPS and RAPS promoted different shifts in the microbial community at the genus level, with an increase in the abundance of Bacteroides, Megamonas and Bifidobacterium, as well as a reduction in the abundance of Fusobacterium, Faecalibacterium and Lachnoclostridium in comparison to the blank control samples.

Luteolibacter luteus sp. nov., isolated from stream bank soil.

A non-motile, Gram-stain-negative, rod-shaped and yellow-colored bacterium, designated G-1-1-1T was obtained from soil sampled at Gwanggyo stream bank, Gyeonggi-do, Republic of Korea. Cells were aerobic, catalase positive, grew optimally at 25-30 °C and hydrolysed aesculin and casein. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-1-1-1T formed a lineage within the genus Luteolibacter. The closest members were Luteolibacter flavescens GKXT (97.7% sequence similarity) and Luteolibacter arcticus MC 3726T (97.3%). The sequence similarities with other members of the genus Luteolibacter were ≤ 93.9%. The genome of strain G-1-1-1T was 6,412,079 bp long with 5176 protein-coding genes. The diagnostic amino acid of cell-wall peptidoglycan of strain G-1-1-1T was meso-diaminopimelic acid. The only respiratory quinone was menaquinone-9 and the principal polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and unidentified phospholipids. The predominant cellular fatty acids were iso-C14:0, C16:1 ω9c, C16:0, C14:0 and anteiso-C15:0. The DNA G + C content was 61.0 mol%. The anti-SMASH analysis of whole genome showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Based on genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain G-1-1-1T represents a novel species in the genus Luteobacter, for which the name Luteolibacter luteus sp. nov. is proposed. The type strain is G-1-1-1T (= KACC 21614T = NBRC 114341T).

Oceanipulchritudo coccoides gen. nov., sp. nov., isolated from marine sediment within the family Puniceicoccaceae.

A Gram-stain-negative, aerobic coccus, designated CK1056T, was isolated from coastal sediment of Xiaoshi Island, Weihai, PR China. Strain CK1056T was found to grow at 15-37 °C (optimum, 30 °C), with 0.5-6.5 % (w/v) NaCl (optimum, 3.5 %) and displayed alkaliphilic growth within the pH range of pH 6.5-10.0 (optimum, pH 8.0). The major fatty acids identified were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The main polar lipids consisted of aminophosphoglycolipid and phosphatidylethanolamine. The predominant respiratory quinone was MK-7. The G+C content of the genomic DNA was 54.0 mol%. The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this micro-organism to the family Puniceicoccaceae, with Coraliomargarita akajimensis KCTC 12865T as its closest relative with only 88.0 % sequence similarity. From the taxonomic data obtained in this study, we propose that the new marine isolate be placed into a novel species within a novel genus in the family Puniceicoccaceae, phylum Verrucomicrobia, for which the name Oceanipulchritudo coccoides gen. nov., sp. nov. is proposed. The type strain is CK1056T (=KCTC 72798T=MCCC 1H00425T).

Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales.

Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.

Oleiharenicola lentus sp. nov., isolated from irrigation water.

Bacterial strain TWA-58T, isolated from irrigation water in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain TWA-58T formed a phylogenetic lineage in the genus Oleiharenicola of the family Opitutaceae. Strain TWA-58T was most closely related to Oleiharenicola alkalitolerans NVTT with a 96.7 % 16S rRNA gene sequence similarity. Strain TWA-58T showed 75.2 % average nucleotide identity, 70.9 % average amino acid identity and 21.0 % digital DNA-DNA hybridization identity with O. alkalitolerans NVTT. Cells were Gram-stain-negative, aerobic, motile, coccoid-shaped and formed transparent colonies. Optimal growth occurred at 25 °C, pH 6, and 0 % NaCl. The major fatty acids of strain TWA-58T were iso-C15 : 0 and anteiso-C15 : 0. The predominant hydroxy fatty acid was iso-C13 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminophospholipids. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TWA-58T was 65.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TWA-58T should be classified in a novel species of the genus Oleiharenicola, for which the name Oleiharenicola lentus sp. nov. is proposed. The type strain is TWA-58T (=BCRC 81161T=LMG 31019T=KCTC 62872T).

Novel cultivated endophytic Verrucomicrobia reveal deep-rooting traits of bacteria to associate with plants.

Despite the relevance of complex root microbial communities for plant health, growth and productivity, the molecular basis of these plant-microbe interactions is not well understood. Verrucomicrobia are cosmopolitans in the rhizosphere, nevertheless their adaptations and functions are enigmatic since the proportion of cultured members is low. Here we report four cultivated Verrucomicrobia isolated from rice, putatively representing four novel species, and a novel subdivision. The aerobic strains were isolated from roots or rhizomes of Oryza sativa and O. longistaminata. Two of them are the first cultivated endophytes of Verrucomicrobia, as validated by confocal laser scanning microscopy inside rice roots after re-infection under sterile conditions. This extended known verrucomicrobial niche spaces. Two strains were promoting root growth of rice. Discovery of root compartment-specific Verrucomicrobia permitted an across-phylum comparison of the genomic conformance to life in soil, rhizoplane or inside roots. Genome-wide protein domain comparison with niche-specific reference bacteria from distant phyla revealed signature protein domains which differentiated lifestyles in these microhabitats. Our study enabled us to shed light into the dark microbial matter of root Verrucomicrobia, to define genetic drivers for niche adaptation of bacteria to plant roots, and provides cultured strains for revealing causal relationships in plant-microbe interactions by reductionist approaches.

Phragmitibacter flavus gen. nov., sp. nov. a new member of the family Verrucomicrobiaceae.

The Gram-stain-negative, aerobic, non-motile, oxidase- and catalase-positive, rod-shaped yellow-coloured bacterial strain MG-N-17T was isolated from a water sample of Lake Ferto/Neusiedler See (Hungary). Results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain forms a distinct linage within the family Verrucomicrobiaceae of the phylum Verrucomicrobia, and its closest relatives are Verrucomicrobium spinosum DSM 4136T (94.38 %) and Roseimicrobium gellanilyticum DC2a-G7T (91.55 %). The novel bacterial strain prefers a weak alkaline environment and grows optimally between 22-28 °C in the absence of NaCl. The major isoprenoid quinones are MK-10, MK-11, MK-12 and MK-9. The major cellular fatty acids are anteiso-C15 : 0, C16 : 0, C16 : 1ω5c and iso-C14 : 0. The polar lipid profile contains phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified glycolipids. The assembled draft genome of strain MG-N-17T had 44 contigs with an N50 value 348255 nt, 56.5× genome coverage, total length of 5 910 933 bp and G+C content of 56.9 mol%. Strain MG-N-17T (=DSM 106674T=NCAIM B.02643T) is proposed as the type strain of a new genus and species in the family Verrucomicrobiaceae, for which the name Phragmitibacter flavus gen. nov., sp. nov. is proposed.

Effect of mannan oligosaccharides on the microbiota and productivity parameters of Litopenaeus vannamei shrimp under intensive cultivation in Ecuador.

The white leg Litopenaeus vannamei shrimp is of importance to the eastern Pacific fisheries and aquaculture industry but suffer from diseases such as the recently emerged early mortality syndrome. Many bacterial pathogens have been identified but the L. vannamei microbiota is still poorly known. Using a next-generation sequencing (NGS) approach, this work evaluated the impact of the inclusion in the diet of mannan oligosaccharide, (MOS, 0.5% w/w), over the L. vannamei microbiota and production behavior of L. vannamei under intensive cultivation in Ecuador. The MOS supplementation lasted for 60 days, after which the shrimp in the ponds were harvested, and the production data were collected. MOS improved productivity outcomes by increasing shrimp survival by 30%. NGS revealed quantitative differences in the shrimp microbiota between MOS and control conditions. In the treatment with inclusion of dietary MOS, the predominant phylum was Actinobacteria (28%); while the control group was dominated by the phylum Proteobacteria (30%). MOS has also been linked to an increased prevalence of Lactococcus- and Verrucomicrobiaceae-like bacteria. Furthermore, under the treatment of MOS, the prevalence of potential opportunistic pathogens, like Vibrio, Aeromonas, Bergeyella and Shewanella, was negligible. This may be attributable to MOS blocking the adhesion of pathogens to the surfaces of the host tissues. Together, these findings point to the fact that the performance (survival) improvements of the dietary MOS may be linked to the impact on the microbiota, since bacterial lines with pathogenic potential towards shrimps were excluded in the gut.

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition.

Intestinal microbiotas contain beneficial microorganisms that protect against pathogen colonization; treatment with antibiotics disrupts the microbiota and compromises colonization resistance. Here, we determine the impact of exchanging microorganisms between hosts on resilience to the colonization of invaders after antibiotic-induced dysbiosis. We assess the functional consequences of dysbiosis using a mouse model of colonization resistance against Escherichia coli. Antibiotics caused stochastic loss of members of the microbiota, but the microbiotas of co-housed mice remained more similar to each other compared with the microbiotas among singly housed animals. Strikingly, co-housed mice maintained colonization resistance after treatment with antibiotics, whereas most singly housed mice were susceptible to E. coli. The ability to retain or share the commensal Klebsiella michiganensis, a member of the Enterobacteriaceae family, was sufficient for colonization resistance after treatment with antibiotics. K. michiganensis generally outcompeted E. coli in vitro, but in vivo administration of galactitol-a nutrient that supports the growth of only E. coli-to bi-colonized gnotobiotic mice abolished the colonization-resistance capacity of K. michiganensis against E. coli, supporting the idea that nutrient competition is the primary interaction mechanism. K. michiganensis also hampered colonization of the pathogen Salmonella, prolonging host survival. Our results address functional consequences of the stochastic effects of microbiota perturbations, whereby microbial transmission through host interactions can facilitate reacquisition of beneficial commensals, minimizing the negative impact of antibiotics.

Rariglobus hedericola gen. nov., sp. nov., belonging to the Verrucomicrobia, isolated from a temperate freshwater habitat.

The bacterial strain 53C-WASEF was isolated from a small freshwater ditch located in Eugendorf, Austria. Phylogenetic reconstructions with 16S rRNA gene sequences and genome based, with amino acid sequences obtained from 105 single copy genes, suggested that the strain represents a new genus and a new species within the family Opitutaceae, which belongs to the class Opitutae of the phylum Verrucomicrobia. Comparisons of the 16S rRNA gene sequence of strain 53C-WASEF with those of related type strains revealed a highest sequence similarity of 93.5 % to Nibricoccus aquaticus and of 92.9 % to Geminisphaera colitermitum. Interestingly, phylogentic trees indicated the latter as being the closest known relative of the new strain. Phenotypic, chemotaxonomic and genomic traits were investigated. Cells were observed to be small, spherical, motile and unpigmented, and grew chemoorganotrophically and aerobically. The respiratory quinone was MK-7, the predominant fatty acids were anteiso-C15 : 0, C16 : 1ω5c and C16 : 0. The identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genome sequencing revealed genes putatively encoding for flagella synthesis and cellulose degradation. The genome size was 4.1 Mbp and the G+C content 60.6 mol%. For the new genus and the new species, we propose the name Rariglobus hedericola gen. nov., sp. nov. (=CIP 111665T=DSM 109123T).

Regional community assembly drivers and microbial environmental sources shaping bacterioplankton in an alpine lacustrine district (Pyrenees, Spain).

Microbial communities in natural ecosystems are subject to strong ecological rules. The study of local communities along a regional metacommunity can reveal patterns of community assembly, and disentangle the underlying ecological processes. In particular, we seek drivers of community assembly at the regional scale using a large lacustrine dataset (>300 lakes) along the geographical, limnological and physico-chemical gradients in the Pyrenees. By using high throughput amplicon sequencing of the 16S rRNA gene, and inferring environmental sources of bacterial immigrants, we showed that surface aquatic bacterial assemblages were strongly influenced by terrestrial populations from soil, biofilms or sediments, and primarily selected by a pH-alkalinity gradient. Indeed, source proportions explained 27% of the community variation, and chemistry 15% of the total variation, half of it shared with the sources. Major taxonomic groups such as Verrucomicrobia, Actinobacteria and Bacteroidetes showed higher aquatic affinities than Parcubacteria, Gammaproteobacteria, Alphaproteobacteria or Betaproteobacteria, which may be recruited and selected through different hydrographic habitats. A regional fingerprint was observed with lower alpha diversity and higher beta diversity in the central Pyrenees than in both ends. We suggest an ecological succession process, likely influenced by complex interactions of environmental source dispersal and environmental filtering along the mountain range geography.

An Akkermansia muciniphila subtype alleviates high-fat diet-induced metabolic disorders and inhibits the neurodegenerative process in mice.

The prevalence of obesity and diabetes, and their complicating mental disorders, severely affect public health. This study aimed to investigate the long-term effects of an Akkermansia muciniphila subtype (A. muciniphilasub) on high-fat diet-induced obesity and diabetes, and to evaluate whether this subtype can alleviate their complicated mental disorders. Whole genome sequencing and short chain fatty acid production analysis in supernatant of pure culture were performed. Female adult C57BL/6 mice were fed a high-fat diet or a normal chow diet and were gavaged with A. muciniphilasub or phosphate-buffered saline daily for 10 months. Body weight, food consumption and blood glucose were measured. At the end of the treatment period, all mice were subjected to the Y-maze test, sucrose preference test, analyses of serum, fecal microbiota analysis and histological examination. This A. muciniphilasub had 278 unique genes compared to the type strain (A. muciniphila ATCC BAA-835) and produced short chain fatty acids both. A. muciniphilasub administration significantly reduced body weight gain and improved the spatial memory of high-fat diet-fed mice. A. muciniphilasub increased Nissl bodies in neurons of the hippocampus, and restored the high-fat diet-inhibited tryptophan metabolism. The high-fat diet led to decreased serum 5-hydroxytryptamine and induced depression, which were not alleviated by A. muciniphilasub. A. muciniphilasub increased the relative fecal abundance of Bifidobacterium, and was negatively correlated with the fecal abundance of Bacteroides. The present study demonstrated the beneficial effects of this A. muciniphilasub on body weight, blood glucose control and the alleviation of the memory decay caused by a high-fat diet in mice.

Distribution, Interaction and Functional Profiles of Epiphytic Bacterial Communities from the Rocky Intertidal Seaweeds, South Africa.

Interrelations between epiphytic bacteria and macroalgae are multifaceted and complicated, though little is known about the community structure, interaction and functions of those epiphytic bacteria. This study comprehensively characterized the epiphytic bacterial communities associated with eight different common seaweeds collected from a rocky intertidal zone on the Indian Ocean at Cape Vidal, South Africa. High-throughput sequencing analyses indicated that seaweed-associated bacterial communities were dominated by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Energy-dispersive X-ray (EDX) analysis showed the presence of elemental composition in the surface of examined seaweeds, in varying concentrations. Cluster analysis showed that bacterial communities of brown seaweeds (SW2 and SW4) were closely resembled those of green seaweeds (SW1) and red seaweeds (SW7) while those of brown seaweeds formed a separate branch. Predicted functional capabilities of epiphytic bacteria using PICRUSt analysis revealed abundance of genes related to metabolic and biosynthetic activities. Further important identified functional interactions included genes for bacterial chemotaxis, which could be responsible for the observed association and network of elemental-microbes interaction. The study concludes that the diversity of epiphytic bacteria on seaweed surfaces is greatly influenced by algal organic exudates as well as elemental deposits on their surfaces, which triggers chemotaxis responses from epiphytic bacteria with the requisite genes to metabolise those substrates.

Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface.

Bacteria of the phylum Verrucomicrobia are prevalent and are particularly common in soil and freshwater environments. Their cosmopolitan distribution and reported capacity for polysaccharide degradation suggests members of Verrucomicrobia are important contributors to carbon cycling across Earth's ecosystems. Despite their prevalence, the Verrucomicrobia are underrepresented in isolate collections and genome databases; consequently, their ecophysiological roles may not be fully realized. Here, we expand genomic sampling of the Verrucomicrobia phylum by describing a novel genus, "Candidatus Marcellius," belonging to the order Opitutales "Ca. Marcellius" was recovered from a shale-derived produced fluid metagenome collected 313 days after hydraulic fracturing, the deepest environment from which a member of the Verrucomicrobia has been recovered to date. We uncover genomic attributes that may explain the capacity of this organism to inhabit a shale gas well, including the potential for utilization of organic polymers common in hydraulic fracturing fluids, nitrogen fixation, adaptation to high salinities, and adaptive immunity via CRISPR-Cas. To illuminate the phylogenetic and environmental distribution of these metabolic and adaptive traits across the Verrucomicrobia phylum, we performed a comparative genomic analysis of 31 publicly available, nearly complete Verrucomicrobia genomes. Our genomic findings extend the environmental distribution of the Verrucomicrobia 2.3 kilometers into the terrestrial subsurface. Moreover, we reveal traits widely encoded across members of the Verrucomicrobia, including the capacity to degrade hemicellulose and to adapt to physical and biological environmental perturbations, thereby contributing to the expansive habitat range reported for this phylum.IMPORTANCE The Verrucomicrobia phylum of bacteria is widespread in many different ecosystems; however, its role in microbial communities remains poorly understood. Verrucomicrobia are often low-abundance community members, yet previous research suggests they play a major role in organic carbon degradation. While Verrucomicrobia remain poorly represented in culture collections, numerous genomes have been reconstructed from metagenomic data sets in recent years. The study of genomes from across the phylum allows for an extensive assessment of their potential ecosystem roles. The significance of this work is (i) the recovery of a novel genus of Verrucomicrobia from 2.3 km in the subsurface with the ability to withstand the extreme conditions that characterize this environment, and (ii) the most extensive assessment of ecophysiological traits encoded by Verrucomicrobia genomes to date. We show that members of this phylum are specialist organic polymer degraders that can withstand a wider range of environmental conditions than previously thought.

Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species.

BACKGROUND: Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. OBJECTIVE: In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied. METHODS: Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to-Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRUCTURE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands. RESULTS: The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila PytT. CONCLUSION: Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future.

Strain-Specific Anti-inflammatory Properties of Two Akkermansia muciniphila Strains on Chronic Colitis in Mice.

Akkermansia muciniphila is potential probiotic in that its type strain ATCC BAA-835 has beneficial effects upon obesity and diabetes. However, whether A. muciniphila can improve inflammatory bowel diseases (IBD), which is a form of chronic intestinal dysbiosis, is unknown. Hence, we used an isolated murine A. muciniphila strain (designated 139) and A. muciniphila type strain ATCC, to investigate their anti-inflammatory properties in cell models and in Dextran Sulfate Sodium (DSS)-induced chronic colitis of mice. In vitro, the two A. muciniphila strains exerted similar anti-inflammatory properties as they both reduced IL-8 production by TNF-α-stimulated HT-29 cells. However, neither of the strains showed capacity to increase the differentiation of regulatory T (Treg)-cells from CD4+ T cell populations significantly. In vivo, both A. muciniphila strains exerted anti-inflammatory effects on chronic colitis as they improved clinical parameters including spleen weight, colon inflammation index, and colon histological score. They also down-regulated the expression of the pro-inflammatory cytokines including TNF-α and IFN-γ in the colon of mice. However, the anti-inflammatory effects of strain ATCC were stronger than strain 139 in that ATCC significantly reduced spleen weight, colon inflammation index, and fecal lipocalin-2 content in mice with chronic colitis, while strain 139 was not. Dysbiosis of the gut microbiota was observed in mice with chronic colitis. Both A. muciniphila strains facilitated the normalization of the gut microbiota. The specific capacity of strain ATCC to modulate the differentiation of Tregs as well as increase production of short chain fatty acids, demonstrated strain-specific characteristics for these two A. muciniphila strains. This study suggests the potential beneficial effect of A. muciniphila on IBD and the importance of the future study of the function of A. muciniphila at the strain-level.