Articles

WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates

Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate the localiz...

Authors: Astrid P. Heikema, Rick Jansen, Saskia D. Hiltemann, John P. Hays and Andrew P. Stubbs

Patterns of yeast diversity distribution and its drivers in rhizosphere soil of Hami melon orchards in different regions of Xinjiang

The unique climatic conditions of the Xinjiang region nurture rich melon and fruit resources, the melon and fruit sugar sources provide sufficient nutrients for the survival of yeast, and the diverse habitats ...

Authors: ShanShan Zhu, YongHui Lei, Chong Wang, YuMei Wei, ChunCheng Wang and YanFei Sun

Lactic acid bacteria that activate immune gene expression in Caenorhabditis elegans can antagonise Campylobacter jejuni infection in nematodes, chickens and mice

Campylobacter jejuni is the major micro-bacillary pathogen responsible for human coloenteritis. Lactic acid bacteria (LAB) have been shown to protect against Campylobacter infection. However, LAB with a good abil...

Authors: Xing Jin, Yufeng He, Yonghua Zhou, Xiaohua Chen, Yuan-kun Lee, Jianxin Zhao, Hao Zhang, Wei Chen and Gang Wang

Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses

Significant progress has been made in advancing and standardizing tools for human genomic and biomedical research. Yet, the field of next-generation sequencing (NGS) analysis for microorganisms (including mult...

Authors: Delphine Larivière, Laura Wickham, Kenneth Keiler and Anton Nekrutenko

A high-throughput screening assay based on automated microscopy for monitoring antibiotic susceptibility of Mycobacterium tuberculosis phenotypes

Efficient high-throughput drug screening assays are necessary to enable the discovery of new anti-mycobacterial drugs. The purpose of our work was to develop and validate an assay based on live-cell imaging wh...

Authors: Sadaf Kalsum, Blanka Andersson, Jyotirmoy Das, Thomas Schön and Maria Lerm

Effects of S24–7 on the weight of progeny rats after exposure to ceftriaxone sodium during pregnancy

Antibiotic exposure during pregnancy will adversely affect the growth of offspring; however, this remains controversial and the mechanism is poorly understood. To study this phenomenon, we added ceftriaxone so...

Authors: Xin Yang, Ting Tang, Jing Wen, Mengchun Li, Jie Chen, Tingyu Li, Ying Dai and Qian Cheng

Lactobacillus rhamnosus GG modifies the metabolome of pathobionts in gnotobiotic mice

Lactobacillus rhamnosus GG (LGG) is the most widely used probiotic, but the mechanisms underlying its beneficial effects remain unresolved. Previous studies typically inoculated LGG in hosts with established gut ...

Authors: Jinhee Kim, Iyshwarya Balasubramanian, Sheila Bandyopadhyay, Ian Nadler, Rajbir Singh, Danielle Harlan, Amanda Bumber, Yuling He, Lee J. Kerkhof, Nan Gao, Xiaoyang Su and Ronaldo P. Ferraris

Distribution of fluoroquinolone resistance determinants in Carbapenem-resistant Klebsiella pneumoniae clinical isolates associated with bloodstream infections in China

The rate of fluoroquinolone (FQ) resistance among carbapenem-resistant Klebsiella pneumoniae (CRKP) is high. The present study aimed to investigate the distribution of fluoroquinolone resistance determinants in c...

Authors: Qing Zhan, Yanlei Xu, Bingjie Wang, Jingyi Yu, Xiaofei Shen, Li Liu, Xingwei Cao, Yinjuan Guo and Fangyou Yu

Human microbiota modulation via QseC sensor kinase mediated in the Escherichia coli O104:H4 outbreak strain infection in microbiome model

The intestinal microbiota plays a crucial role in human health, adjusting its composition and the microbial metabolites protects the gut against invading microorganisms. Enteroaggregative E. coli (EAEC) is an imp...

Authors: Tamara Renata Machado Ribeiro, Mateus Kawata Salgaço, Maria Angela Tallarico Adorno, Miriam Aparecida da Silva, Roxane Maria Fontes Piazza, Katia Sivieri and Cristiano Gallina Moreira

Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study

Human well-being has been linked to the composition and functional capacity of the intestinal microbiota. As regular exercise is known to improve human health, it is not surprising that exercise was previously...

Authors: Lucas Moitinho-Silva, Michelle Wegener, Sandra May, Florian Schrinner, Awais Akhtar, Teide J. Boysen, Eva Schaeffer, Clint Hansen, Timo Schmidt, Malte C. Rühlemann, Matthias Hübenthal, Philipp Rausch, Mustafa T. Kondakci, Walter Maetzler, Stephan Weidinger, Matthias Laudes…

Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome

SAPHO syndrome is a group of symptoms consisting of synovitis, acne, pustulosis, hyperostosis and osteosis. There is no specific laboratory index assist in the diagnosis of SAPHO because of its highly heteroge...

Authors: Jianhua Zhen, Yuxiu Sun, Pengfei Zhao, Chen Li, Hesong Wang, Yini Li, Lu Zhao, Li Wang, Guangrui Huang and Anlong Xu

Antisense yycG modulates the susceptibility of Staphylococcus aureus to hydrogen peroxide via the sarA

The infectious pathogen Staphylococcus aureus (S. aureus) is primarily associated with osteomyelitis. Hydrogen peroxide drainage is an effective antimicrobial treatment that has been adopted to combat S. aureus i...

Authors: Shizhou Wu, Yunjie Liu, Lei Lei and Hui Zhang

Diversity and prevalence of ANTAR RNAs across actinobacteria

Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory syst...

Authors: Dolly Mehta and Arati Ramesh

Optimisation of sample storage and DNA extraction for human gut microbiota studies​

New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut mic...

Authors: Jekaterina Kazantseva, Esther Malv, Aleksei Kaleda, Aili Kallastu and Anne Meikas

Distribution and Clonality of drug-resistant tuberculosis in South Africa

Studies have shown that drug-resistant tuberculosis (DR-TB) in South Africa (SA) is clonal and is caused mostly by transmission. Identifying transmission chains is important in controlling DR-TB. This study re...

Authors: Halima Said, John Ratabane, Linda Erasmus, Yasmin Gardee, Shaheed Omar, Andries Dreyer, Farzana Ismail, Zaheda Bhyat, Tiisetso Lebaka, Minty van der Meulen, Thabisile Gwala, Adeboye Adelekan, Karidia Diallo and Nazir Ismail

Potential of fecal microbiota for detection and postoperative surveillance of colorectal cancer

Colorectal cancer (CRC) is one of the most common cancers. In recent studies, the gut microbiota has been reported to be potentially involved in aggravating or favoring CRC development. However, little is know...

Authors: Qiulin Yao, Meifang Tang, Liuhong Zeng, Zhonghua Chu, Hui Sheng, Yuyu Zhang, Yuan Zhou, Hongyun Zhang, Huayan Jiang and Mingzhi Ye

Diversity and antibacterial activity of fungal endophytes from Eucalyptus exserta

Eucalyptus bacterial wilt caused by Ralstonia solanacearum is an important eucalyptus disease. Endophytic fungi, an important source of natural active substances, provide a new breakthrough for the control of pla...

Authors: Ziling Mao, Weihao Zhang, Chunyin Wu, Hao Feng, Yuanhang Peng, Hamza Shahid, Zining Cui, Ping Ding and Tijiang Shan

The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal

Bifidobacteria are commensal microbes of the mammalian gastrointestinal tract. In this study, we aimed to identify the intestinal colonization mechanisms and key metabolic pathways implemented by Bifidobacterium ...

Authors: Melinda A. Engevik, Heather A. Danhof, Anne Hall, Kristen A. Engevik, Thomas D. Horvath, Sigmund J. Haidacher, Kathleen M. Hoch, Bradley T. Endres, Meghna Bajaj, Kevin W. Garey, Robert A. Britton, Jennifer K. Spinler, Anthony M. Haag and James Versalovic

Investigation of the invasion mechanism mediated by the outer membrane protein PagN of Salmonella Typhimurium

Salmonella can invade host cells via a type three secretion system called T3SS-1 and its outer membrane proteins, PagN and Rck. However, the mechanism of PagN-dependent invasion pathway used by Salmonella enteric...

Authors: Emilie Barilleau, Mégane Védrine, Michael Koczerka, Julien Burlaud-Gaillard, Florent Kempf, Olivier Grépinet, Isabelle Virlogeux-Payant, Philippe Velge and Agnès Wiedemann

Microbiome characterization of defensive tissues in the model anemone Exaiptasia diaphana

Coral reefs are among the most diverse and productive ecosystems on Earth. This success relies on the coral’s association with a wide range of microorganisms, including dinoflagellates of the family Symbiodini...

Authors: Justin Maire, Linda L. Blackall and Madeleine J. H. van Oppen

Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts

Inter-individual variations in gut microbiota composition are observed even among healthy populations. The gut microbiota may exhibit a unique composition depending on the country of origin and race of individ...

Authors: Jonguk Park, Kumiko Kato, Haruka Murakami, Koji Hosomi, Kumpei Tanisawa, Takashi Nakagata, Harumi Ohno, Kana Konishi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Jin-zhong Xiao, Toshitaka Odamaki, Jun Kunisawa, Kenji Mizuguchi and Motohiko Miyachi

Correction to: Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium

Authors: Ying Zhang, Qingsong Yang, Juan Ling, Lijuan Long, Hui Huang, Jianping Yin, Meilin Wu, Xiaoyu Tang, Xiancheng Lin, Yanying Zhang and Junde Dong

The potential and effects of saline-alkali alfalfa microbiota under salt stress on the fermentation quality and microbial

The objective of this study was to evaluate the chemical compositions and microbial communities of salt-tolerant alfalfa silage. Salt-tolerant alfalfa was ensiled with no additive control, and cellulase for 30...

Authors: Duo Wen Sa, Qiang Lu, Zhen Wang, Gentu Ge, Lin Sun and Yushan Jia

Effectiveness of antibacterial agents against cell-invading bacteria such as Streptococcus pyogenes and Haemophilus influenzae

Recurrent tonsillitis is one of the most common otolaryngological disorders caused by cell-invading bacteria, such as Streptococcus pyogenes (S. pyogenes) and Haemophilus influenzae. The aim of this study was to ...

Authors: Hiroyuki Iuchi, Junichiro Ohori, Satoshi Kiyama, Naoko Imuta, Junichiro Nishi, Yuichi Kurono and Masaru Yamashita

Association of gestational diabetes mellitus with changes in gut microbiota composition at the species level

Gestational diabetes mellitus (GDM), a common endocrine disorder with rising prevalence in pregnancy, has been reported to be associated with alteration of gut microbiota in recent years. However, the role of ...

Authors: Fang Chen, Yu Gan, Yingtao Li, Wenzhi He, Weizhen Wu, Kejian Wang and Qing Li

Lactobacillus rhamnosus HDB1258 modulates gut microbiota-mediated immune response in mice with or without lipopolysaccharide-induced systemic inflammation

Gut microbiota closely communicate in the immune system to maintain a balanced immune homeostasis in the gastrointestinal tract of the host. Oral administration of probiotics modulates gut microbiota compositi...

Authors: Sang-Kap Han, Yeon-Jeong Shin, Dong-Yeon Lee, Kyung Min Kim, Seo-Jin Yang, Du Seong Kim, Ji-Whi Choi, Seunghun Lee and Dong-Hyun Kim

Phenotypic changes in group B streptococci grown in the presence of the polyols, erythritol, sorbitol and mannitol

Group B streptococci (GBS) are important neonatal bacterial pathogens that can cause severe invasive disease in the newborn. It is thought that in many cases of invasive neonatal GBS disease, the bacteria asce...

Authors: Maram Hulbah, Matthew A. Croxen and Gregory J. Tyrrell

Diagnostic utility of GeneXpert MTB/RIF assay versus conventional methods for diagnosis of pulmonary and extra-pulmonary tuberculosis

Tuberculosis (T.B) is one of the major infectious diseases in the developing countries. The diagnosis of extrapulmonary T.B (EPTB) remains problematic and emergence of resistant strains poses a significant thr...

Authors: Asmaa Mohammed Elbrolosy, Rana H. El Helbawy, Osama M. Mansour and Reda Abdel Latif

Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca

Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed tha...

Authors: Hongfei Wang, Manik Prabhu Narsing Rao, Yanli Gao, Xinyang Li, Rui Gao, Yuanguo Xie, Qiuli Li and Wenjun Li

Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats

Chinese soft-shell turtle (Pelodiscus sinensis) is an important commercial species for their high nutritional value and unique taste, but it has been a vulnerable species due to habitat loss. In this study, homol...

Authors: Benli Wu, Long Huang, Jing Chen, Ye Zhang, Jun Wang and Jixiang He

Changes of gut microbiome composition and metabolites associated with hypertensive heart failure rats

The potential role of the gut microbiome (GM) in heart failure (HF) had recently been revealed. However, the underlying mechanisms of the GM and fecal metabolome in HF have not been characterized. The Dahl sal...

Authors: Lin Li, Sen-jie Zhong, Si-yuan Hu, Bin Cheng, Hong Qiu and Zhi-xi Hu

Deviations in the gut microbiota of neonates affected by maternal group B Streptococcus colonization

Group B Streptococcus (GBS) infection is the leading cause of septicemia, meningitis, and pneumonia in neonates. Aberrant gut colonization in early life may predispose children to various diseases in adulthood...

Authors: Yue-feng Li, Xue-lei Gong, Su-xiang Chen, Kejian Wang and Yan-hua Jiang

Prevalence, population structure, distribution of serotypes, pilus islands and resistance genes among erythromycin-resistant colonizing and invasive Streptococcus agalactiae isolates recovered from pregnant and non-pregnant women in Isfahan, Iran

The information on antibiotic resistance and molecular features of Group B Streptococcus (GBS) are essential for epidemiological purposes as well as vaccine development. Therefore, we aimed to assess the antimicr...

Authors: Tahereh Motallebirad, Hossein Fazeli, Ataollah Ghahiri, Dariush Shokri, Saba Jalalifar, Sharareh Moghim and Bahram Nasr Esfahani

Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC)

Ulcerative colitis (UC) is one of the primary types of inflammatory bowel disease (IBD), the occurrence of which has been increasing worldwide. Although IBD is an intensively studied human microbiome-associate...

Authors: Wendy Li, Yang Sun, Lin Dai, Hongju Chen, Bin Yi, Junkun Niu, Lan Wang, Fengrui Zhang, Juan Luo, Kunhua Wang, Rui Guo, Lianwei Li, Quan Zou, Zhanshan (Sam) Ma and Yinglei Miao

Tauroursodeoxycholic acid prevents Burkholderia pseudomallei-induced endoplasmic reticulum stress and is protective during melioidosis in mice

Burkholderia pseudomallei, a facultative intracellular bacterium, is the aetiological agent of melioidosis that is responsible for up to 40% sepsis-related mortality in epidemic areas. However, no effective vacci...

Authors: Siqi Yuan, Yao Fang, Mengling Tang, Zhiqiang Hu, Chenglong Rao, Jiangao Chen, Yupei Xia, Meijuan Zhang, Jingmin Yan, Bin Tang, Xiaoyi He, Jianping Xie, Xuhu Mao and Qian Li

Detection and characterization of carbapenem resistant Gram‐negative bacilli isolates recovered from hospitalized patients at Soba University Hospital, Sudan

Antimicrobial resistance (AMR) poses a complex threat to global health security and universal health coverage. Recently, nosocomial infections with carbapenemase-producing Gram-negative bacilli (GNB) is increa...

Authors: Hana S. Elbadawi, Kamal M. Elhag, Elsheikh Mahgoub, Hisham N. Altayb, Francine Ntoumi, Linzy Elton, Timothy D. McHugh, John Tembo, Giuseppe Ippolito, Abdinasir Yusuf Osman, Alimuddin Zumla and Muzamil M. Abdel Hamid

Prevalence and antibiotics susceptibility profiles of Streptococcus pyogenes among pediatric patients with acute pharyngitis at Felege Hiwot Comprehensive Specialized Hospital, Northwest Ethiopia

Streptococcus pyogenes (S. pyogenes) is a Gram positive bacterium which is a leading cause of pharyngitis, skin and soft tissue infection and post streptococcal syndromes. Due to lack of β-lactamase enzyme produc...

Authors: Destaw Kebede, Alemale Admas and Daniel Mekonnen

Analysis of culturable airborne fungi in outdoor environments in Tianjin, China

Fungal spores dispersed in the atmosphere may become cause of different pathological conditions and allergies for human beings. A number of studies have been performed to analyze the diversity of airborne fung...

Authors: Yumna Nageen, Michael Dare Asemoloye, Sergei Põlme, Xiao Wang, Shihan Xu, Pramod W. Ramteke and Lorenzo Pecoraro

Comparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms

The prevalence of clinical multidrug-resistant (MDR) Pseudomonas aeruginosa has been increasing rapidly worldwide over the years and responsible for a wide range of acute and chronic infections with high mortalit...

Authors: Mingju Hao, Wanshan Ma, Xiutao Dong, Xiaofeng Li, Fang Cheng and Yujiao Wang

Sewage and sewage-contaminated environments are the most prominent sources to isolate phages against Pseudomonas aeruginosa

P. aeruginosa is the primary source of hospital-acquired infections. Unfortunately, antibiotic resistance is growing to precariously high levels, making the infections by this pathogen life-threatening and hard t...

Authors: Bahareh Lashtoo Aghaee, Mohammadali Khan Mirzaei, Mohammad Yousef Alikhani and Ali Mojtahedi

Sex differences in the phylum‐level human gut microbiota composition

Evidence was previously provided for sex-related differences in the human gut microbiota composition, and sex-specific discrepancy in hormonal profiles was proposed as a main determinant of these differences. ...

Authors: Alexander Koliada, Vladislav Moseiko, Mariana Romanenko, Oleh Lushchak, Nadiia Kryzhanovska, Vitaly Guryanov and Alexander Vaiserman

Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium

The coral microbiome plays a key role in host health by being involved in energy metabolism, nutrient cycling, and immune system formation. Inoculating coral with beneficial bacterial consortia may enhance the...

Authors: Ying Zhang, Qingsong Yang, Juan Ling, Lijuan Long, Hui Huang, Jianping Yin, Meilin Wu, Xiaoyu Tang, Xiancheng Lin, Yanying Zhang and Junde Dong

Correction to: Aging progression of human gut microbiota

Authors: Congmin Xu, Huaiqiu Zhu and Peng Qiu

Characteristics and variation of fecal bacterial communities and functions in isolated systolic and diastolic hypertensive patients

Hypertension (HTN) is one of the major cardiovascular risk factors, which contributes to increasing target organ damages and cardiovascular morbidity and mortality worldwide. Isolated systolic HTN (ISH) and is...

Authors: Pan Wang, Ying Dong, Kun Zuo, Chunming Han, Jie Jiao, Xinchun Yang and Jing Li

A buffered media system for yeast batch culture growth

Fungi are premier hosts for the high-yield secretion of proteins for biomedical and industrial applications. The stability and activity of these secreted proteins is often dependent on the culture pH. As yeast...

Authors: Rianne C. Prins and Sonja Billerbeck

Decreased abundance of Akkermansia after adrenocorticotropic hormone therapy in patients with West syndrome

Infants suffer from a severe epileptic encephalopathy known as West syndrome (WS). Treatment with adrenocorticotropic hormone (ACTH) indicates the involvement of the gut-brain axis in WS. Several pieces of evi...

Authors: Lu Xu, Dandan Chen, Congying Zhao, Lihua Jiang, Shanshan Mao, Chao Song and Feng Gao

Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs

Members of the Erysipelotrichaceae family have a high abundance in the intestinal tract of mammals, and have been reported to be associated with host metabolic disorders and inflammatory diseases. In our previ...

Authors: Jinyuan Wu, Min Liu, Mengqing Zhou, Lin Wu, Hui Yang, Lusheng Huang and Congying Chen

Metallo-β-lactamase and AmpC genes in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates from abattoir and poultry origin in Nigeria

Gram-negative bacteria (GNB) including Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae represent the most relevant reservoir of resistance genes such as metallo-β-lactamase (MBL) and AmpC gene...

Authors: Chika Ejikeugwu, Okoro Nworie, Morteza Saki, Hussein O. M. Al-Dahmoshi, Noor S. K. Al-Khafaji, Chika Ezeador, Emmanuel Nwakaeze, Peter Eze, Eniola Oni, Chidiebere Obi, Ifeanyichukwu Iroha, Charles Esimone and Michael U. Adikwu

Genetic variability in multidrug-resistant Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in North India

Information on the genetic variability of drug resistant isolates of Mycobacterium tuberculosis is of paramount importance to understand transmission dynamics of disease and to improve TB control strategies. Desp...

Authors: Ajay Vir Singh, Suman Singh, Anjali Yadav, Shweta Kushwah, Rajbala Yadav, Davuluri Kushma Sai and Devendra Singh Chauhan

Correction to: Effects of continuous cropping of sweet potatoes on the bacterial community structure in rhizospheric soil

An amendment to this paper has been published and can be accessed via the original article.

Authors: Zhiyuan Gao, Yaya Hu, Meikun Han, Junjie Xu, Xue Wang, Lanfu Liu, Zhonghou Tang, Weijing Jiao, Rong Jin, Ming Liu, Zhengjun Guan and Zhimin Ma