A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes, bioRxiv, 2019-12-06
ABSTRACTAn imbalance of normal bacterial groups such as Bacteroidales within the human gut is correlated with diseases like obesity. A current grand challenge in the microbiome field is to identify factors produced by normal microbiome bacteria that cause these observed health and disease correlations. While identifying factors like a bacterial injection system could provide a missing explanation for why Bacteroidales correlates with host health, no such factor has been identified to date. The lack of knowledge about these factors is a significant barrier to improving therapies like fecal transplants that promote a healthy microbiome. Here we show that a previously ill-defined Contractile Injection System is carried in the gut microbiome of 99% of individuals from the United States and Europe. This type of Contractile Injection System, we name here Bacteroidales Injection System (BIS), is related to the contractile tails of bacteriophage (viruses of bacteria) and have been described to mediate interactions between bacteria and diverse eukaryotes like amoeba, insects and tubeworms. Our findings that BIS are ubiquitous within adult human microbiomes suggest that they shape host health by mediating interactions between Bacteroidales bacteria and the human host or its microbiome.
biorxiv microbiology 0-100-users 2019Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria, bioRxiv, 2019-12-04
AbstractMobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium and, as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. Moreover, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalogue of genes encoded on MGEs, dictating bacterial evolution through HGT.
biorxiv microbiology 100-200-users 2019A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome, bioRxiv, 2019-09-20
AbstractComprehensive reference data is essential for accurate taxonomic and functional characterization of the human gut microbiome. Here we present the Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut. These genomes contain over 625 million protein sequences used to generate the Unified Human Gastrointestinal Protein (UHGP) catalogue, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue. We find that a large portion of the human gut microbiome remains to be fully explored, with over 70% of the UHGG species lacking cultured representatives, and 40% of the UHGP missing meaningful functional annotations. Intra-species genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which were specific to individual human populations. These freely available genomic resources should greatly facilitate investigations into the human gut microbiome.
biorxiv microbiology 200-500-users 2019Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy, bioRxiv, 2019-09-19
AbstractWe recently introduced the Genome Taxonomy Database (GTDB), a phylogenetically consistent, genome-based taxonomy providing rank normalized classifications for nearly 150,000 genomes from domain to genus. However, nearly 40% of the genomes used to infer the GTDB reference tree lack a species name, reflecting the large number of genomes in public repositories without complete taxonomic assignments. Here we address this limitation by proposing 24,706 species clusters which encompass all publicly available bacterial and archaeal genomes when using commonly accepted average nucleotide identity (ANI) criteria for circumscribing species. In contrast to previous ANI studies, we selected a single representative genome to serve as the nomenclatural type for circumscribing each species with type strains used where available. We complemented the 8,792 species clusters with validly or effectively published names with 15,914de novospecies clusters in order to assign placeholder names to the growing number of genomes from uncultivated species. This provides the first complete domain to species taxonomic framework which will improve communication of scientific results.
biorxiv microbiology 200-500-users 2019Peptide-based quorum sensing systems in Paenibacillus polymyxa, bioRxiv, 2019-09-13
AbstractPaenibacillus polymyxa is an agriculturally important plant growth-promoting rhizobacterium. Many Paenibacillus species are known to be engaged in complex bacteria-bacteria and bacteria-host interactions, which in other species were shown to necessitate quorum sensing communication. However, to date no quorum sensing systems have been described in Paenibacillus. Here we show that the type strain P. polymyxa ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the Paenibacillaceae family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.
biorxiv microbiology 0-100-users 2019Myristate as a carbon and energy source for the asymbiotic growth of the arbuscular mycorrhizal fungus Rhizophagus irregularis, bioRxiv, 2019-08-11
AbstractArbuscular mycorrhiza (AM) is one of the most widespread mutualistic symbioses, which is formed between the majority of land plants and soil-borne fungi belonging to Glomeromycotina. AM fungi are obligate symbionts that cannot complete their natural life cycle without a host. Recent evidence suggests that lipids synthesized by a host are transferred to AM fungi that possess no fatty acid synthase genes in their genome and that mutations in lipid biosynthesis-related genes of the host lead the symbiotic interaction to fail (1–3). We hypothesized that lipids derived from plants are crucial for AM fungal growth and reproduction. In this study, we evaluated whether AM fungi can grow on medium supplied with fatty acids under asymbiotic conditions without the host. Myristate led to an extensive hyphal growth of Rhizophagus irregularis and an increase in biomass production. Other examined fatty acids showed no effect on biomass production. Myristate also induced secondary spore formation. The myristate-induced spores can germinate, colonize carrot hairy roots, and form the next generation of mature daughter spores. A fluorescently labeled fatty acid probe was taken up by branched hyphae of AM fungi. Tracer experiments using 13C-labeled myristic acid showed that myristate and its metabolites were utilized for the synthesis of triacylglycerol and cell wall components of AM fungi. Furthermore, myristate activated ATP generation in the fungal hyphae. Here we demonstrate that myristate is utilized as a carbon and energy source for biomass production and sporulation under asymbiotic conditions.
biorxiv microbiology 0-100-users 2019