Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika.

Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika () is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance.

Integration Host Factor Modulates the Expression and Function of T6SS2 in .

, an emerging foodborne pathogen of increasing public health concern, contains two distinct gene clusters encoding type VI secretion system (T6SS), the most newly discovered secretion pathway in Gram-negative bacteria. Previously we have shown that one of the two T6SS clusters, namely VflT6SS2, is active and associates with anti-bacterial activity. However, how its activity is regulated is not completely understood.

Susceptibility profiles of Nocardia spp. to antimicrobial and antituberculotic agents detected by a microplate Alamar Blue assay.

Nocardia species are ubiquitous in natural environments and can cause nocardiosis. Trimethoprim-sulfamethoxazole has long been the monotherapy treatment of choice, but resistance to this treatment has recently emerged. In this study, we used microplate Alamar Blue assays to determine the antimicrobial susceptibility patterns of 65 standard Nocardia isolates, including 28 type strains and 20 clinical Nocardia isolates, to 32 antimicrobial agents, including 13 little studied drugs.

Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai-Tibet plateau of China.

Escherichia coli is both of a widespread harmless gut commensal and a versatile pathogen of humans. Domestic animals are a well-known reservoir for pathogenic E. coli.

Structural Modulation of Gut Microbiota in Rats with Allergic Bronchial Asthma Treated with Recuperating Lung Decoction.

Objective: To investigate whether recuperating lung decoction (RLD) can modulate the composition of gut microbiota in rats during asthma treatment.

Methods: Fifteen Sprague-Dawley rats were divided randomly and equally into control group, model group, dexamethasone (DEX) group, RLD medium-dose group, and RLD high-dose group. The asthma model was established in all groups, except for the control group.

Data on the phylogenetic typing, integron gene cassette array analysis, multi-drug resistance analysis and correlation between antimicrobial resistance determinants in Klebsiella strains.

The antimicrobial resistance of Klebsiella species in the poultry industry is becoming a public concern. In support our recent publication "Characterization of antimicrobial resistance in Klebsiella species isolated from chicken broilers" (Wu et al., 2016) [1], multilocus sequence typing (MLST) and gyrA PCR-RFLP assays were conducted to identify the genetic relationships between and phylogenetic groups of the 90 antimicrobial resistant Klebsiella species isolated from a commercial broiler slaughter plant in Shandong, China.

Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012-2014, traced by whole genome sequencing.

Background: The rapid spread of Clostridium difficile NAP1/BI/027 (C. difficile 027) has become one of the leading threats of healthcare-associated infections worldwide. However, C.

Genotyping of Nocardia farcinica with multilocus sequence typing.

Nocardia are aerobic Gram-positive saprophytes that are widely distributed in nature, but some species cause nocardiosis, especially opportunistic infections that affect immunocompromised patients mostly. In this study, we developed a multilocus sequence typing (MLST) scheme using seven housekeeping genes (gyrB, hsp65, secA1, rpoB, rpoA, recA, and trpB) for genotyping the most common clinical species, Nocardia farcinica (37 clinical isolates from the patients with nocardiosis and seven from animals in China and 15 reference strains). The results showed that using these loci could perform accurate identification among different species, and high discriminative power within the N.

Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China.

Severe acute respiratory infection (SARI) in children is thought to be mainly caused by infection with various viruses, some of which have been well characterized; however, analyses of respiratory tract viromes among children with SARI versus those without are limited. In this study, nasopharyngeal swabs from children with and without SARI (135 versus 15) were collected in China between 2008 and 2010 and subjected to multiplex metagenomic analyses using a next-generation sequencing platform. The results show that members of the Paramyxoviridae, Coronaviridae, Parvoviridae, Orthomyxoviridae, Picornaviridae, Anelloviridae and Adenoviridae families represented the most abundant species identified (>50% genome coverage) in the respiratory tracts of children with SARI.

Genome sequences of two closely related strains of Escherichia coli K-12 GM4792.

Escherichia coli lab strains K-12 GM4792 Lac(+) and GM4792 Lac(-) carry opposite lactose markers, which are useful for distinguishing evolved lines as they produce different colored colonies. The two closely related strains are chosen as ancestors for our ongoing studies of experimental evolution. Here, we describe the genome sequences, annotation, and features of GM4792 Lac(+) and GM4792 Lac(-).

Repression by H-NS of genes required for the biosynthesis of the Vibrio cholerae biofilm matrix is modulated by the second messenger cyclic diguanylic acid.

Expression of Vibrio cholerae genes required for the biosynthesis of exopolysacchide (vps) and protein (rbm) components of the biofilm matrix is enhanced by cyclic diguanylate (c-di-GMP). In a previous study, we reported that the histone-like nucleoid structuring (H-NS) protein represses the transcription of vpsA, vpsL and vpsT. Here we demonstrate that the regulator VpsT can disrupt repressive H-NS nucleoprotein complexes at the vpsA and vpsL promoters in the presence of c-di-GMP, while H-NS could disrupt the VpsT-promoter complexes in the absence of c-di-GMP.

Helicobacter himalayensis sp. nov. isolated from gastric mucosa of Marmota himalayana.

A Gram-stain-negative, microaerophilic strain, 80(YS1)T, with a spiral-shaped morphology and 1-2 sheathed flagella at each end of the cells was isolated from the gastric mucosa of Marmota himalayana, the animal reservoir of Yersinia pestis in China, on the Qinghai-Tibet Plateau. The strain grew at 30, 35 and 42 °C, but not at 25 °C. Growth was in the form of a thinly spreading film on brain heart infusion agar containing 8 % sheep blood under microaerobic conditions.

RNA-seq analysis identifies new genes regulated by the histone-like nucleoid structuring protein (H-NS) affecting Vibrio cholerae virulence, stress response and chemotaxis.

The histone-like nucleoid structuring protein (H-NS) functions as a transcriptional silencer by binding to AT-rich sequences at bacterial promoters. However, H-NS repression can be counteracted by other transcription factors in response to environmental changes. The identification of potential toxic factors, the expression of which is prevented by H-NS could facilitate the discovery of new regulatory proteins that may contribute to the emergence of new pathogenic variants by anti-silencing.

Rapid Identification of Bacterial Species Associated with Bronchiectasis via Metagenomic Approach.

Bronchiectasis is a chronic lung disorder and a number of bacterial pathogens are involved. However, 30%-40% of sputum and purulent samples in good quality failed to grow any pathogenic bacteria, making it difficult to confirm the pathogen. In this study, we collected bronchoalveolar lavage fluid from a bronchiectasis patient undergoing acute exacerbation, and sent for 16S rDNA pyrosequencing by a 454 GS Junior machine.

Use of genome sequencing to assess nucleotide structure variation of Staphylococcus aureus strains cultured in spaceflight on Shenzhou-X, under simulated microgravity and on the ground.

The extreme environment of space could affect microbial behavior and may increase the risk of infectious disease during spaceflight. However, the molecular genetic changes of methicillin-resistant Staphylococcus aureus (MRSA) in response to the spaceflight environment have not been fully clarified. In the present study, we determined the draft genome sequences for an ancestral S.

[The study of ctxB and rstR variations of toxigenic Vibrio cholerae O1 El Tor strains isolated from 1961 to 2010 in China].

Objective: To understand the ctxB and rstR variations of toxigenic Vibrio cholerae (V.cholerae) O1 El Tor strains isolated from different provinces in China from 1961 to 2010.

Methods: All 385 toxigenic V.

Clonal characteristics of invasive Neisseria meningitidis following initiation of an A + C vaccination program in China, 2005-2012.

Objectives: To reveal the population structure of invasive Neisseria meningitidis isolates after the initiation of an A + C vaccination program in China.

Methods: Multilocus sequence typing (MLST) and PorA typing were used to characterize 238 invasive N. meningitidis isolates collected in China between 2005 and 2012.

[Phenotypic diversity of toxigenic Vibrio cholerae O1 El Tor strains identified in China].

Objective: To understand the phenotypic diversity of toxigenic Vibrio cholerae O1 El Tor strains isolated from different provinces in China during the last 50 years.

Methods: Traditional biotyping testings including susceptibility to polymyxin B, sensitivity to group IV phage, Voges-Proskauer test and haemolysis of sheep erythrocytes were conducted.

Results: Data from Biotype-specific phenotype analysis revealed that only 133 isolates carried the typical El Tor phenotypes while the other 251 isolates displayed atypical El Tor phenotypes.

Sequence variation in tcdA and tcdB of Clostridium difficile: ST37 with truncated tcdA is a potential epidemic strain in China.

Clostridium difficile is a well-known nosocomial infectious pathogen. Research on C. difficile infection has primarily focused on strains such as the hypervirulent PCR ribotype 027 (sequence type 1 [ST1]) emerging in Europe and North America.

Outer membrane protein OmpW is the receptor for typing phage VP5 in the Vibrio cholerae O1 El Tor biotype.

Phage typing is used for the subtyping of clones of epidemic bacteria. In this study, we identified the outer membrane protein OmpW as the receptor for phage VP5, one of the typing phages for the Vibrio cholerae O1 El Tor biotype. A characteristic 11-bp deletion in ompW was observed in all epidemic strains resistant to VP5, suggesting that this mutation event can be used as a tracing marker in cholera surveillance.

Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China.

Background: Helicobacter pylori is well known for its relationship with the occurrence of several severe gastric diseases. The mechanisms of pathogenesis triggered by H. pylori are less well known.

Silent geographical spread of the H7N9 virus by online knowledge analysis of the live bird trade with a distributed focused crawler.

Unlike those infected by H5N1, birds infected by the newly discovered H7N9 virus have no observable clinical symptoms. Public health workers in China do not know where the public health threat lies. In this study, we used a distributed focused crawler to analyze online knowledge of the live bird trade in first-wave provinces, namely, Jiangsu, Zhejiang, Anhui, and Shanghai, to track the new H7N9 virus and predict its spread.