ABSTRACT
The ecological and genetic changes that underlie the evolution of host-microbe interactions remain elusive, primarily due to challenges in disentangling the variables that alter microbiome composition. To understand the impact of host habitat, host genetics, and evolutionary history on microbial community structure, we examined gut microbiomes of river- and three cave-adapted morphotypes of the Mexican tetra, Astyanax mexicanus, in their natural environments and under controlled laboratory conditions. Field-collected samples were dominated by very few taxa and showed considerable interindividual variation. We found that lab-reared fish exhibited increased microbiome richness and distinct composition compared to their wild counterparts, underscoring the significant influence of habitat. Most notably, however, we found that morphotypes reared on the same diet throughout life developed distinct microbiomes suggesting that genetic loci resulting from cavefish evolution shape microbiome composition. We observed stable differences in Fusobacteriota abundance between morphotypes and demonstrated that this could be used as a trait for quantitative trait loci mapping to uncover the genetic basis of microbial community structure.
ABSTRACT
The family Fusobacteriaceae is a large family within the phylum Fusobacteriota. The reclassification of F. naviforme as Zandiella naviformis gen. nov., comb. nov. is proposed because of the separate and distinct phylogenetic situation on the basis of the results of 16S rRNA gene sequence analysis, the genetic and genomic differences from all other species and subspecies in the Fusobacteriaceae family. The type strain is ATCC 25832; CCUG 50052; NCTC 13121. In phylogenetic trees drawn using complete genome sequences and 16S rRNA gene sequences, F. necrophorum subsp. funduliforme and F. equinum were clades together with F. necrophorum subsp. necrophorum and F. gonidiaformans, respectively. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between themes exceeded the cut-off values for species delineation. Based on these results, F. necrophorum subsp. funduliforme and F. equinum should be reclassified as later heterotypic synonyms of F. necrophorum subsp. necrophorum and F. gonidiaformans, respectively.
Subject(s)
DNA , Fusobacterium , Genomics , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , DNA, Bacterial/chemistryABSTRACT
A novel mesophilic, obligately anaerobic, facultatively sulphur-reducing bacterium, designated strain IC12T, was isolated from a deep-sea hydrothermal field in the Mid-Okinawa Trough, Japan. The cells were Gram-negative, motile, short rods with a single polar flagellum. The ranges and optima of the growth temperature, NaCl concentration and pH of strain IC12T were 15-40 °C (optimum, 30-35 °C), 10-60 g l-1 (optimum, 20-30 g l-1) and pH 4.9-6.7 (optimum, pH 5.8), respectively. Yeast extract was utilized as a sole carbon and energy source for fermentative growth. Major fatty acids of strain IC12T were C14â:â0, C16â:â0 and C16â:â1 ω7. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IC12T was affiliated to the phylum Fusobacteriota and was most closely related to Ilyobacter insuetus VenChi2T (86.5â% sequence similarity). Strain IC12T contained a chromosome of 2.43 Mbp and a large plasmid of 0.30 Mbp. The G+C content of the genomic DNA was 26.4âmol%. The maximum values for average nucleotide identity and in silico DNA-DNA hybridization between strain IC12T and related strains of the phylum Fusobacteriota were 71.4 and 26.4â%, respectively. Phylogenomic, physiological and chemotaxonomic analyses indicate that strain IC12T represents a novel genus and species within the phylum Fusobacteriota, for which the name Haliovirga abyssi gen. nov., sp. nov. is proposed, with strain IC12T (= DSM 112164T=JCM 39166T) as the type strain. We also propose the family Haliovirgaceae fam. nov. to accommodate this novel genus.