Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota

Abstract

SUMMARY Many microbial phyla that are widely distributed in open environments have few or no representatives within animal-associated microbiota. Among them, the Chloroflexi comprises taxonomically and physiologically diverse lineages adapted to a wide range of aquatic and terrestrial habitats. A distinct group of uncultured chloroflexi related to free-living anaerobic Anaerolineae inhabits the mammalian gastrointestinal tract and includes low-abundance human oral bacteria that appear to proliferate in periodontitis. Using a single-cell genomics approach we obtained the first draft genomic reconstruction for these organisms and compared their inferred metabolic potential with free-living chloroflexi. Genomic data suggest that oral chloroflexi are anaerobic heterotrophs, encoding abundant carbohydrate transport and metabolism functionalities, similar to those seen in environmental Anaerolineae isolates. The presence of genes for a unique phosphotransferase system and N-acetylglucosamine metabolism suggests an important ecological niche for oral chloroflexi in scavenging material from lysed bacterial cells and the human tissue. The inferred ability to produce sialic acid for cell membrane decoration may enable them to evade the host defense system and colonize the subgingival space. As with other low-abundance but persistent members of the microbiota, discerning community and host factors that influence the proliferation of oral chloroflexi may help understand the emergence of oral pathogens and the microbiota dynamics in health and disease states.

Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge

“…This is in agreement with the results showing most of the B45-related isolates in the classes Anaerolineae and Caldilineae can grow by fermentation of carbohydrates or amino acids (see Supplementary Table S4) as well as with the genome annotation data of related uncultured Chloroflexi species (Hug et al, 2013;Campbell et al, 2014). Other Chloroflexi members in activated sludge have also been reported as being able to ferment sugars.…”

“…The generation of further genome sequences is required to resolve the taxonomy of the remaining classes, along with the precise phylogenetic position of members of the B45 genus. Metagenomic approaches, as applied here and in other Chloroflexi studies (Hug et al, 2013;Campbell et al, 2014), will be important in providing coverage of members of the phylogenetic tree presently recalcitrant to isolation into pure culture.…”

Marine sponges as Chloroflexi hot-spots: Genomic insights and high resolution visualization of an abundant and diverse symbiotic clade

“…In the present study, we focused our metagenomic analyses on Chloroflexi as abundant and characteristic, yet understudied members of HMA sponge microbiomes. The phylum Chloroflexi comprises taxonomically and physiologically highly diverse lineages that populate a wide range of habitats (22–25) including the deep sea (26), uranium-contaminated aquifers (27) and the human oral cavity and gut (28, 29). Chloroflexi metabolism is very diverse, ranging from anxoxygenic photosynthesis, obligate aerobic/anaerobic heterotrophs, thermophiles, halophiles, clades capable of reductive halogenation, and even predators with gliding motility.…”

Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi

“…nov. The type strain of Flexilinea flocculi is strain TC1 T (5JCM 30897 T 5CGMCC 1.5202Cultivation-independent 16S rRNA gene and metagenome surveys have significantly broadened the spectrum of known phylogenetic diversity of the bacterial phylum Chloroflexi (Campbell et al, 2014;Speirs et al, 2015;Yamada & Sekiguchi, 2009 The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain TC1 T is LC049585. …”

“…Cultivation-independent 16S rRNA gene and metagenome surveys have significantly broadened the spectrum of known phylogenetic diversity of the bacterial phylum Chloroflexi (Campbell et al, 2014;Speirs et al, 2015;Yamada & Sekiguchi, 2009). More than 20 putative subphylum-level lineages can be discerned in the Greengenes database (release 05_13; McDonald et al, 2012).…”