Mice are widely used as experimental models for gut microbiome (GM) studies, yet the majority of mouse GM members remain uncharacterized. Here, we report the construction of a mouse gut microbial ...biobank (mGMB) that contains 126 species, represented by 244 strains that have been deposited in the China General Microorganism Culture Collection. We sequence and phenotypically characterize 77 potential new species and propose their nomenclatures. The mGMB includes 22 and 17 species that are significantly enriched in ob/ob and wild-type C57BL/6J mouse cecal samples, respectively. The genomes of the 126 species in the mGMB cover 52% of the metagenomic nonredundant gene catalog (sequence identity ≥ 60%) and represent 93-95% of the KEGG-Orthology-annotated functions of the sampled mouse GMs. The microbial and genome data assembled in the mGMB enlarges the taxonomic characterization of mouse GMs and represents a useful resource for studies of host-microbe interactions and of GM functions associated with host health and diseases.
Abstract
Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K ...prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.
Influenza A (H7N9) virus has been causing human infections in China since February 2013, raising serious concerns of potential pandemics. Previous studies demonstrate that human infection is directly ...linked to live animal markets, and that the internal genes of the virus are derived from H9N2 viruses circulating in the Yangtze River Delta area in Eastern China. Here following analysis of 109 viruses, we show a much higher genetic heterogeneity of the H7N9 viruses than previously reported, with a total of 27 newly designated genotypes. Phylogenetic and genealogical inferences reveal that genotypes G0 and G2.6 dominantly co-circulate within poultry, with most human isolates belonging to the genotype G0. G0 viruses are also responsible for the inter- and intra-province transmissions, leading to the genesis of novel genotypes. These observations suggest the province-specific H9N2 virus gene pools increase the genetic diversity of H7N9 via dynamic reassortments and also imply that G0 has not gained overwhelming fitness and the virus continues to undergo reassortment.
Pan‐genomics is one of the most powerful means to study genomic variation and obtain a sketch of genes within a defined clade of species. Though there are a lot of computational tools to achieve ...this, an integrated framework to evaluate their performance and offer the best choice to users has never been achieved. To ease the process of large‐scale prokaryotic genome analysis, we introduce Integrated Prokaryotes Genome and pan‐genome Analysis (IPGA), a one‐stop web service to analyze, compare, and visualize pan‐genome as well as individual genomes, that rids users of installing any specific tools. IPGA features a scoring system that helps users to evaluate the reliability of pan‐genome profiles generated by different packages. Thus, IPGA can help users ascertain the profiling method that is most suitable for their data set for the following analysis. In addition, IPGA integrates several downstream comparative analysis and genome analysis modules to make users achieve diverse targets.
Integrated Prokaryotes Genome and pan‐genome Analysis (IPGA) serves as a free and easy‐to‐use web‐based system that could provide up‐to‐date pan‐genome analysis service for non‐bioinformaticians. IPGA offers users the most reliable pan‐genome profile which enables users to perform additional comparative genomic analysis. IPGA provides a series of downstream analysis modules such as phylogenetic inference, synteny inference, and target genome annotation.
Highlights
IPGA serves as a free and easy‐to‐use web‐based system that could provide up‐to‐date pan‐genome analysis service for non‐bioinformaticians.
IPGA offers users the most reliable pan‐genome profile which enables users to perform additional comparative genomic analysis.
IPGA provides a series of downstream analysis modules such as phylogenetic inference, synteny inference, and target genome annotation.
Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly ...increasing in some countries. Exploring their receptor binding and interspecies transmission risk is urgently needed. Herein, we examine the binding capacities of human and other 28 animal ACE2 orthologs covering nine orders towards S proteins of these sub-variants. The binding affinities between hACE2 and these sub-variants remain in the range as that of previous variants of concerns (VOCs) or interests (VOIs). Notably, R493Q reverse mutation enhances the bindings towards ACE2s from humans and many animals closely related to human life, suggesting an increased risk of cross-species transmission. Structures of S/hACE2 or RBD/hACE2 complexes for these sub-variants and BA.2 S binding to ACE2 of mouse, rat or golden hamster are determined to reveal the molecular basis for receptor binding and broader interspecies recognition.
Laboratory information management system (LIMS) has been widely used to facilitate laboratory activities. However, the current LIMSs do not contain functions to improve the safety of laboratory work, ...which is the major concern of biosafety laboratories (BSLs). With tons of biosafety information that need to be managed and an increasing number of biosafety-related research projects under way, it is worthy of expanding the current framework of LIMS and building a system that is more suitable for BSL usage. Such a system should carefully trade off between the safety and efficiency of regular lab activities, allowing the laboratory staff to conduct their research as free as possible while ensuring their and the environment’s safety. In order to achieve this goal, the information on the research contents, laboratory personnel, experimental materials and experimental equipment need to be well collected and fully utilized by a centralized system and its databases.
Two strains of moderately halophilic, Gram-stain-positive and spore-forming rods, designated as SKP4-8
T
and SKP8-2
T
isolated from shrimp paste (
Ka-pi
), were taxonomic studied based on polyphasic ...approach. Strain SKP4-8
T
grew at pH 6.0–9.0 (optimum 7.0), at 25–45 °C (optimum 37 °C) and in 1–16% (w/v) NaCl (optimum 5–10%). Strain SKP8-2
T
grew at pH 6.0–9.0 (optimum 8.0), at 25–45 °C (optimum 37 °C) and in 0–20% (w/v) NaCl (optimum 3–10%). The strains contained
meso
-diaminopimelic acid in cell-wall peptidoglycan and the major menaquinone was MK-7. Strain SKP4-8
T
contained iso-C
15:0
, anteiso-C
15:0
and iso-C
17:0
; and strain SKP8-2
T
contained anteiso-C
15:0
, iso-C
15:0
, iso-C
16:0
and antesio-C
17:0
as major cellular fatty acids. Phosphatidylglycerol, diphosphatidylglycerol, unknown phospholipids and an unknown glycolipid were detected as major polar lipids. On the basis of 16S rRNA gene sequence analysis, strains SKP4-8
T
and SKP8-2
T
belonged to the genus
Allobacillus
and were closely related to
Allobacillus halotolerans
LMG 24826
T
with 98.8% and 99.3% similarity, respectively. The comparative genome analysis based on average nucleotide identity (ANI) and digital DNA–DNA hybridization revealed that both strains showed the values below 95 and 70%, from each other and from
Allobacillus halotolerans
LMG 24826
T
, respectively. Based on the data from this polyphasic study, strains SKP4-8
T
and SKP8-2
T
represent novel species of the genus
Allobacillus
and the name
Allobacillus salarius
sp. nov. was proposed for SKP4-8
T
(= KCTC 33905
T
= LMG 30016
T
= TISTR 2499
T
); and
Allobacillus saliphilus
sp. nov. for SKP8-2
T
(= KCTC 33906
T
= LMG 29682
T
= TISTR 2558
T
).
Infections caused by linezolid-resistant enterococci (LRE) are clinically difficult to treat and threaten patient health. However, there is a lack of studies on long time-span LRE strains in China. ...For this reason, our study comprehensively revealed the resistance mechanisms of LRE strains collected in a Chinese tertiary care hospital from 2011 to 2022.
Enterococcal strains were screened and verified after retrospective analysis of microbial data. Subsequently, 65 LRE strains (61 Enterococcus faecalis and 4 Enterococcus faecium, MIC ≥ 8 µg/ml), 1 linezolid-intermediate Enterococcus faecium (MIC = 4 µg/ml) and 1 linezolid-susceptible Enterococcus faecium (MIC = 1.5 µg/ml) were submitted for whole-genome sequencing (WGS) analysis and bioinformatics analysis.
The optrA gene was found to be the most common linezolid resistance mechanism in our study. We identified the wild-type OptrA and various OptrA variants in 98.5% of LRE strains (61 Enterococcus faecalis and 3 Enterococcus faecium). We also found one linezolid-resistant Enterococcus faecium strain carried both optrA and cfr(D) gene, while one linezolid-resistant Enterococcus faecium only harbored the poxtA gene. Most optrA genes (55/64) were located on plasmids, with impB-fexA-optrA, impB-fexA-optrA-erm(A), fexA-optrA-erm(A), and fexA-optrA segments. A minority of optrA genes (9/64) were found on chromosomes with the Tn6674-like platform. Besides, other possible linezolid resistance-associated mechanisms (mutations in the rplC and rplD genes) were also found in 26 enterococcal strains.
Our study suggested that multiple mechanisms of linezolid resistance exist among clinical LRE strains in China.
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