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Microorganisms
2020 Nov 27;812:. doi: 10.3390/microorganisms8121874.
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Genomic Characterization of a Novel Tenericutes Bacterium from Deep-Sea Holothurian Intestine.
Zhu FC
,
Lian CA
,
He LS
.
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Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and immunity of animals, but little is known about the composition and function of intestinal microbiota in deep-sea invertebrates. In this study, the intestinal microbiota of six holothurian Molpadia musculus were investigated, showing that their midguts were predominantly occupied by Izemoplasmatales bacteria. Using metagenomic sequencing, a draft genome of 1,822,181 bp was successfully recovered. After comparison with phylogenetically related bacteria, genes involved in saccharide usage and de novo nucleotide biosynthesis were reduced. However, a set of genes responsible for extracellular nucleoside utilization and 14 of 20 amino acid synthesis pathways were completely retained. Under oligotrophic condition, the gut-associated bacterium may make use of extracellular DNA for carbon and energy supplement, and may provide essential amino acids to the host. The clustered regularly interspaced short palindromic repeat (CRISPR) and restriction-modification (RM) systems presented in the genome may provide protection against invading viruses. A linear azol(in)e-containing peptide gene cluster for bacteriocin synthesize was also identified, which may inhibit the colonization and growth of harmful bacteria. Known virulence factors were not found by database searching. On the basis of its phylogenetic position and metabolic characteristics, we proposed that the bacterium represented a novel genus and a novel family within the Izemoplasmatales order and suggested it be named "Candidatus Bathyoplasma sp. NZ". This was the first time describing host-associated Izemoplasmatales.
2018YFC0309804 National Key Research and Development Program of China, 2016YFC0302504 National Key Research and Development Program of China, 2016YFC0304905 National Key Research and Development Program of China
Figure 1. The bacterial composition in (A) the intestine and (B) its content of Molpadia musculus. The amplicon sequence variants (ASVs) are classified at the phylum level. BP1 and BP2 indicate two sampling sites in the Bay of Plenty. There are three individuals for each site. The hindgut of BP2-3 sample failed to amplify the 16S rRNA gene fragments. A phylum with a percentage less than 1% is classified into minor groups. Bac, Bacteria; Arc, Archaea.
Figure 2. Maximum-likelihood phylogenetic tree based on (A) 16S rRNA genes and (B) 21 concatenated conserved proteins. Three Bacillus (Firmicutes) bacteria are used as outgroups. The species in bold blue comes from this study. Bacteria belonging to the Izemoplasmatales order are masked by orange background. Bootstrap values are indicated on the branches, and accession numbers are labeled in parentheses. The species number in each collapsed node is also labeled. The tree scale bar represents the number of expected substitutions per site.
Figure 3. Comparison of gene numbers in different metabolic pathways. Gene numbers in each Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of BNZ and reference genomes are counted and normalized using z-score. Heatmap is generated using R.
Figure 4. The predicted model of metabolism in Ca. Bathyoplasma sp. NZ. Absent elements of metabolic pathways and transporters are shown in dotted lines. Enzymes that were retained and lost in the genome of BNZ are presented in blue and green, respectively. Abbreviation: GAP, glyceraldehyde 3-phosphate; DHAP, dihydroxyacetone phosphate; 3PG, 3-phosphoglycerate; PEP, phosphoenolpyruvate; PRPP, phosphoribosyl pyrophosphate; IPP, isopentenyl diphosphate; FPP, farnesyl diphosphate; DPP, dimethylallyl diphosphate; Und-P, bactoprenol phosphate; GlcNAc, N-acetylglucosamine; MurNAc, N-acetylmuramic acid; GlpF, glycerol uptake facilitator protein; NCS2, nucleobase cation symporter-2; GK, glucokinase; GPI, glucose-6-phosphate isomerase; LDH, L-lactate dehydrogenase; PFO, pyruvate:ferredoxin (flavodoxin) oxidoreductase; PTA, phosphate acetyltransferase; ACK, acetate kinase; PNP, purine nucleoside phosphorylase; PDP, pyrimidine-nucleoside phosphorylase; ADE, adenine deaminase; GuaD, guanine deaminase; XDH, xanthine dehydrogenase/oxidase; DeoB, phosphopentomutase; DeoC, deoxyribose-phosphate aldolase; PRPS, ribose-phosphate pyrophosphokinase; CDD, cytidine deaminase; FDPS, farnesyl diphosphate synthase; APRTase, adenine phosphoribosyltransferase; HGPRT, hypoxanthine-guanine phosphoribosyltransferase.
Figure 5. The linear azol(in)e-containing peptide synthesis gene cluster in Ca. Bathyoplasma sp. NZ. tBLASTx searches were performed against the listeriolysin S synthesis gene cluster in Enterococcus durans and the streptolysin O synthesis gene cluster in Streptococcus pyogenes with an e-value of 1e-5. Homologous regions are indicated with gray frames. The loci for the putative bacteriocin precursor, core enzymes, ABC transporter-related proteins, membrane-associated proteins, and other related proteins are shown in red, pink, green, orange, and blue, respectively. SagA~I, streptolysin associated protein A~I.
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