BackgroundSubstantial efforts have been made to link the gut bacterial community to many complex human diseases. Nevertheless, the gut phages are often neglected.ResultsIn this study, we used multiple bioinformatic methods to catalog gut phages from whole-community metagenomic sequencing data of fecal samples collected from both type II diabetes (T2D) patients (n = 71) and normal Chinese adults (n = 74). The definition of phage operational taxonomic units (pOTUs) and identification of large phage scaffolds (n = 2567, ≥ 10 k) revealed a comprehensive human gut phageome with a substantial number of novel sequences encoding genes that were unrelated to those in known phages. Interestingly, we observed a significant increase in the number of gut phages in the T2D group and, in particular, identified 7 pOTUs specific to T2D. This finding was further validated in an independent dataset of 116 T2D and 109 control samples. Co-occurrence/exclusion analysis of the bacterial genera and pOTUs identified a complex core interaction between bacteria and phages in the human gut ecosystem, suggesting that the significant alterations of the gut phageome cannot be explained simply by co-variation with the altered bacterial hosts.ConclusionsAlterations in the gut bacterial community have been linked to the chronic disease T2D, but the role of gut phages therein is not well understood. This is the first study to identify a T2D-specific gut phageome, indicating the existence of other mechanisms that might govern the gut phageome in T2D patients. These findings suggest the importance of the phageome in T2D risk, which warrants further investigation.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0410-y) contains supplementary material, which is available to authorized users.

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A novel acidothermophilic archaeon, strain Ar-4 T , was isolated from a sulfuric hot spring in Tengchong, Yunnan, China. Cells of strain T were Gram-staining-negative, irregular cocci and motile by means of flagella. Strain Ar-4 T grew over a temperature range of 55-75 6C(optimum, 65 6C), a pH range of 2.5-5.5 (optimum, pH 3.5) and a NaCl concentration range of 0-1 % (w/v). The novel strain was aerobic and facultatively chemolithoautotrophic. The strain could extract metal ions from sulfidic ore. It was also able to oxidize reduced sulfur compounds. In addition, it was able to use heterogeneous organic materials for organotrophic growth. , respectively. The differences in cell motility, the temperature and pH ranges for growth, the ability to utilize carbon sources, the DNA G+C content, and the low DNA-DNA relatedness values distinguished strain T from recognized species of the genus Metallosphaera. On the basis of these results, it was concluded that strain Ar-4 T represents a novel species of the genus Metallosphaera, for which the name Metallosphaera cuprina is proposed. The type strain is Ar-4

A novel mesophilic and acidophilic Gram-positive bacterium, designated strain TC-34 T , was isolated from solfataric soil. Strain TC-34 T grew aerobically at 17-40 6C and pH 2.0-6.0, and optimally at 28 6C and pH 3.0. Analysis based on 16S rRNA gene sequences showed that strain TC-34 T was phylogenetically related to members of the genus Alicyclobacillus, with the highest similarity (94.8 %) to Alicyclobacillus pomorum. Strain TC-34 T showed a range of phenotypic characteristics that differentiated it from recognized Alicyclobacillus species, including growth temperature, assimilation of carbon sources and production of acids from a range of compounds. Strain TC-34 T was able to oxidize ferrous iron and its growth was correlated with the oxidation of Fe 2+ in culture medium. v-Alicyclic fatty acids were not detected. On the basis of these results, it was concluded that strain TC-34 T represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus ferrooxydans (type strain TC-34The genus Alicyclobacillus was first proposed to accommodate three Bacillus species that contained v-alicyclic fatty acids and were phylogenetically distant from other members of Bacillus (Wisotzkey et al., 1992). Subsequently, the genus was emended by Goto et al. (2003) to include species that did not contain v-alicyclic fatty acids, e.g. Alicyclobacillus pomorum (Goto et al., 2003). Currently, the genus Alicyclobacillus contains 18 species with validly published names, two subspecies and two genomic species ( Fig. 1 and http://www.bacterio.cict.fr/a/alicyclobacillus.html). Most members of the genus Alicyclobacillus are thermoacidophilic, Gram-positive, spore-forming, heterotrophic organisms that often inhabit acidic geothermal environments such as geothermal water (Hiraishi et al., 1997;Nicolaus et al., 1998) and soil (Hippchen et al., 1981;Tsuruoka et al., 2003). Although the majority of Alicyclobacillus species mainly utilize organic compounds, Alicyclobacillus tolerans and Alicyclobacillus disulfidooxidans are able to oxidize ferrous iron, elemental sulfur and sulfides for growth (Kovalenko & Malakhova, 1983;Dufresne et al., 1996). In this report, we describe a novel Alicyclobacillus strain, designated TC-34 T , which grows by means of oxidation of ferrous iron, pyrite, tetrasulfate and thiosulfate.Strain TC-34 T was isolated from solfataric samples (temperature and pH ranges of 48-50 uC and 4.5-5.5, respectively) from Tengchong county (24 u 389-25 u 529 N 98 u 059-98 u 469 E), Yunnan Province, China, using modified Norris broth that contained a mineral salts medium (Norris et al., 1996) supplemented with 14.0 g FeSO 4 . 7H 2 O l 21 and 0.2 g yeast extract l 21. For the preparation of modified Norris solid medium, 14.0 g Gelrite Gellan Gum l 21 (Sigma) was added to the modified broth. The samples collected were first enriched at 30 u C using modified broth. After three enrichments, the enriched culture was serially diluted (10-fold) in tubes containing 0.9 ml modified Norris broth. Aliquots (0.2 ml) of t...

The Acidianus hospitalis W1 genome consists of a minimally sized chromosome of about 2.13 Mb and a conjugative plasmid pAH1 and it is a host for the model filamentous lipothrixvirus AFV1. The chromosome carries three putative replication origins in conserved genomic regions and two large regions where non-essential genes are clustered. Within these variable regions, a few orphan orfB and other elements of the IS200/607/605 family are concentrated with a novel class of MITE-like repeat elements. There are also 26 highly diverse vapBC antitoxin–toxin gene pairs proposed to facilitate maintenance of local chromosomal regions and to minimise the impact of environmental stress. Complex and partially defective CRISPR/Cas/Cmr immune systems are present and interspersed with five vapBC gene pairs. Remnants of integrated viral genomes and plasmids are located at five intron-less tRNA genes and several non-coding RNA genes are predicted that are conserved in other Sulfolobus genomes. The putative metabolic pathways for sulphur metabolism show some significant differences from those proposed for other Acidianus and Sulfolobus species. The small and relatively stable genome of A. hospitalis W1 renders it a promising candidate for developing the first Acidianus genetic systems.

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A novel mesophilic, acidophilic, endospore-forming bacterium, designated strain ZJ-6 T , was isolated from Zi-Jin copper mine in Inner Mongolia, China. Cells of strain ZJ-6 T were rod-shaped, stained Gram-positive or were Gram-variable, and grew aerobically at 25-35 6C (optimum, 30 6C) and pH 2.0-6.0 (optimum, pH 3.5). 16S rRNA gene sequence analysis showed that strain ZJ-6 T was related phylogenetically to members of the genus Alicyclobacillus, with 16S rRNA gene sequence similarities of 89.5-94.2 %. Cells contained MK-7 as the major quinone and the DNA G+C content was 51.2 mol%. Strain ZJ-6 T possessed a number of phenotypic characteristics that differentiated it from recognized Alicyclobacillus species, including its growth temperature, assimilation of various carbon sources, production of acids from a range of compounds, and the ability to grow chemoautotrophically using ferrous iron, elemental sulfur and tetrathionate as electron donors. The predominant cellular fatty acids of strain ZJ-6 T were anteiso-C 15 : 0 (67.1 %), iso-C 16 : 0 (7.7 %) and anteiso-C 17 : 0 (7.4 %); v-alicyclic fatty acids were not found. On the basis of these results, it is concluded that strain ZJ-6 T represents a novel species within the genus Alicyclobacillus, for which the name Alicyclobacillus aeris sp. nov. is proposed; the type strain is ZJ-6 T (5CGMCC 1.7072 T 5NBRC 104953 T ).

The genome of the metal sulfide-oxidizing, thermoacidophilic strain Metallosphaera cuprina Ar-4 has been completely sequenced and annotated. Originally isolated from a sulfuric hot spring, strain Ar-4 grows optimally at 65°C and a pH of 3. Extremely thermoacidophilic archaea play important roles in mobilizing metal sulfide deposits in natural bioleaching environments (5, 9). Due to the ability to oxidize reduced inorganic sulfur compounds (RISCs) under hightemperature conditions, Metallosphaera has attracted increasing interest from the biomining industry (5, 6, 10-13). The bioleaching Metallosphaera sedula was explored at the genomic level (2). Here, we present the complete genome of a newly isolated, bioleaching, and thermoacidophilic Metallosphaera cuprina strain (8).Genomic DNA of M. cuprina Ar-4 was purified from cells grown in modified Allen medium (3). The whole genome was sequenced by a Roche 454 genome sequencer FLX instrument. A total of 295,139 shotgun reads were produced and assembled into 55 contigs, providing 67-fold coverage. Gaps were closed by multiplex PCR and primer-walking methods. The gap-spanning PCR products were sequenced with an ABI 3730 DNA analyzer, and the resulting sequences were assembled using Phred/Phrap/Consed software. The final consensus quality level of each base was above 64. Protein-coding genes were identified with the Glimmer 3.02 program (4). Protein function was predicted by either homology searches in the GenBank and UniProt protein databases, function assignment searches in the CDD (COG) database, or domain/motif searches in the Pfam databases. The KEGG tool was used to reconstruct metabolic pathways. Membrane proteins were predicted by the LipoP, SignalP, and ConPred II programs. The tRNA genes were identified by using the tRNAScan-SE tool, and the rRNA genes were identified by using the RNAmmer 1.2 and BLASTn programs.M. cuprina Ar-4 grew chemolithotrophically on CO 2 with metal sulfide and RISCs as energy sources or chemoheterotrophically on various organics (8). Its genome consisted of a 1,840,348-bp circular chromosome. The genome carried 2,029 open reading frames (ORFs) in total. Genome annotation and metabolic reconstruction supported the idea that M. cuprina lived a facultative life. The M. cuprina strain fixed CO 2 via the 3-hydroxypropionate/4-hydroxybutyrate cycle, and this strain assimilated carbohydrates via the nonphosphorylated Entner-Doudoroff (ED) pathway. It had a complete tricarboxylic acid (TCA) cycle and an incomplete phosphate pentose pathway. Oxidation of RISCs by the heterodisulfide reductase complex, sulfide:quinone oxidoreductase, thiosulfate:quinone oxidoreductase, tetrathionate hydrolase, and sulfite:acceptor oxidoreductase in M. cuprina was proposed. The terminal oxidase complexes of M. cuprina that channel electrons from RISC oxidation to oxygen were similar to those of "Metallosphaera yellowstonensis" (7) and M. sedula (1).The M. cuprina genome was 16% smaller than the M. sedula genome. Analysis indicated that the counterpart genes of abo...