Articles

Role of biliary stent and neoadjuvant chemotherapy in the pancreatic tumor microbiome

Intra-tumor microbiota have been implicated in pancreatic ductal adenocarcinoma (PDAC) development, treatment response and post-treatment survivorship. Moreover, therapeutic interventions targeting microbiota ...

Authors: Harika Nalluri, Eric Jensen and Christopher Staley

Selection strategy of dextran sulfate sodium-induced acute or chronic colitis mouse models based on gut microbial profile

Dextran sulfate sodium (DSS) replicates ulcerative colitis (UC)-like colitis in murine models. However, the microbial characteristics of DSS-triggered colitis require further clarification. To analyze the chan...

Authors: Hao-Ming Xu, Hong-Li Huang, Yan-Di Liu, Jia-Qi Zhu, You-Lian Zhou, Hui-Ting Chen, Jing Xu, Hai-Lan Zhao, Xue Guo, Wei Shi, Yu-Qiang Nie and Yong-Jian Zhou

Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota

Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exist...

Authors: Elizabeth Fleming, Victor Pabst, Zoe Scholar, Ruoyun Xiong, Anita Y. Voigt, Wei Zhou, Amelia Hoyt, Rachel Hardy, Anna Peterson, Ryan Beach, Yvette Ondouah-Nzutchi, Jinhong Dong, Lucinda Bateman, Suzanne D. Vernon and Julia Oh

Beware of pharyngeal Fusobacterium nucleatum in COVID-19

Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker ...

Authors: Lirong Bao, Cheng Zhang, Jinglu Lyu, Caixia Yan, Ranran Cao, Ming Pan and Yan Li

Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans

Compared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ...

Authors: Louise B. Thingholm, Corinna Bang, Malte C. Rühlemann, Annika Starke, Florian Sicks, Verena Kaspari, Anabell Jandowsky, Kai Frölich, Gabriele Ismer, Andreas Bernhard, Claudia Bombis, Barbara Struve, Philipp Rausch and Andre Franke

Stool preparation under anaerobic conditions contributes to retention of obligate anaerobes: potential improvement for fecal microbiota transplantation

Fecal microbiota transplantation (FMT) in patients with ulcerative colitis has shown variable efficacy depending on the protocol used. A previous randomized controlled trial reported that anaerobic preparation...

Authors: Hirotaka Shimizu, Katsuhiro Arai, Takashi Asahara, Takuya Takahashi, Hirokazu Tsuji, Satoshi Matsumoto, Ichiro Takeuchi, Reiko Kyodo and Yuichiro Yamashiro

Detection of viable and total fungal community in zaopei of Chinese strong-flavor baijiu using PMA combined with qPCR and HTS based on ITS2 region

Chinese strong-flavor baijiu (CSFB), one of the three major baijiu types, is the most popular baijiu type among consumers in China. A variety of microbes are involved in metabolizing raw materials to produce e...

Authors: Huanming Liu, Guangxun Tan, Qitong Chen, Weiwei Dong, Ping Chen, Kaiyun Cai, Yuanliang Hu, Weiyan Zhang, Nan Peng, Yunxiang Liang and Shumiao Zhao

Enhanced reduction of polymicrobial biofilms on the orthodontic brackets and enamel surface remineralization using zeolite-zinc oxide nanoparticles-based antimicrobial photodynamic therapy

The aim of this study was to evaluate the anti-biofilm and anti-metabolic activities of zeolite-zinc oxide nanoparticles (Zeo/ZnONPs)-based antimicrobial photodynamic therapy (aPDT) against pre-formed polymicr...

Authors: Maryam Pourhajibagher and Abbas Bahador

Antibiotic resistance in the pathogenic foodborne bacteria isolated from raw kebab and hamburger: phenotypic and genotypic study

In recent years, interest in the consumption of ready-to-eat (RTE) food products has been increased in many countries. However, RTE products particularly those prepared by meat may be potential vehicles of ant...

Authors: Maryam Rajaei, Mir-Hassan Moosavy, Sahar Nouri Gharajalar and Seyed Amin Khatibi

Effect of drops containing Lactobacillus reuteri (DSM 17938 and ATCC PTA 5289) on plaque acidogenicity and other caries-related variables in orthodontic patients

The purpose of the study was to investigate the effect of probiotics on biofilm acidogenicity and on the number of salivary Streptococcus mutans and lactobacilli in orthodontic patients.

Authors: Sahal Alforaidi, Andrea Bresin, Naif Almosa, Anna Lehrkinder and Peter Lingström

Rickettsia burneti and Brucella melitensis co-infection: a case report and literature review

Rickettsia is the pathogen of Q fever, Brucella ovis is the pathogen of brucellosis, and both of them are Gram-negative bacteria which are parasitic in cells. The mixed infection of rickettsia and Brucella ovis ...

Authors: Jiangqin Song, Xiaorong Hu, Xiaolong Li, Youping Chen, Xiangyuan Yan, Weifang Zhu, Yan Ding and Junyang Zhou

Characteristics of and risk factors for biliary pathogen infection in patients with acute pancreatitis

Infection in patients with acute pancreatitis, especially severe acute pancreatitis patients, is a common and important phenomenon, and the distributions and drug resistance profiles of bacteria causing biliar...

Authors: Shayan Chen, Jiyu Shi, Minghui Chen, Jun Ma, Zhaowei Zeng, Rui Wang, Yunfeng Cui and Xue Gao

Bistable auto-aggregation phenotype in Lactiplantibacillus plantarum emerges after cultivation in in vitro colonic microbiota

Auto-aggregation is a desired property for probiotic strains because it is suggested to promote colonization of the human intestine, to prevent pathogen infections and to modulate the colonic mucosa. We recent...

Authors: Julia Isenring, Annelies Geirnaert, Christophe Lacroix and Marc J. A. Stevens

Two target genes based multiple cross displacement amplification combined with a lateral flow biosensor for the detection of Mycobacterium tuberculosis complex

Tuberculosis (TB) is a serious chronic infectious disease caused by Mycobacterium tuberculosis complex (MTBC). Hence, the development of a novel, simple, rapid and sensitive method to detect MTBC is of great sign...

Authors: Junfei Huang, Ziyu Xiao, Xinggui Yang, Xu Chen, Xiaojuan Wang, Yijiang Chen, Wenlin Zheng, Wei Chen, Huijuan Chen and Shijun Li

The effect of ArcA on the growth, motility, biofilm formation, and virulence of Plesiomonas shigelloides

The anoxic redox control binary system plays an important role in the response to oxygen as a signal in the environment. In particular, phosphorylated ArcA, as a global transcription factor, binds to the promo...

Authors: Junxiang Yan, Yuehua Li, Xueqian Guo, Xiaochen Wang, Fenxia Liu, Ang Li and Boyang Cao

Gut microbiota changes in preeclampsia, abnormal placental growth and healthy pregnant women

Preeclampsia (PE) is a condition of high blood pressure that is usually concurrent with proteinuria in pregnancy. PE complicates the management of both maternal and fetal health and contributes to most adverse...

Authors: Lihui Huang, Min Cai, Li Li, Xin Zhang, Yang Xu, Jianhua Xiao, Qian Huang, Guijuan Luo, Zhaoyang Zeng, Cuiyuan Jin, Yuanxiang Jin, Jun He and Weitao Yang

Comparison of virulence-related determinants between the ST59-t437 and ST239-t030 genotypes of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen for human infection. Hospital-acquired (HA) and community-acquired (CA) MRSA infections are serious clinical problems worldwide. In this...

Authors: Feng Liao, Wenpeng Gu, Xiaoqing Fu, Bin Yuan and Yunhui Zhang

MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

Microbiome big data from population-scale cohorts holds the key to unleash the power of microbiomes to overcome critical challenges in disease control, treatment and precision medicine. However, variations int...

Authors: Li Shao, Jie Liao, Jingyang Qian, Wenbin Chen and Xiaohui Fan

Prevalence of methicillin resistance and superantigenic toxins in Staphylococcus aureus strains isolated from patients with cancer

This study aimed to determine the frequency of methicillin-resistant Staphylococcus aureus (MRSA), antibiotic resistance patterns, superantigenic toxins profile, and clonality of this pathogen in patients with ca...

Authors: Effat Abbasi Montazeri, Azar Dokht Khosravi, Saeedeh Khazaei and Ali Sabbagh

Synergistic effects of silver ions and metformin against enterococcus faecalis under high-glucose conditions in vitro

This study aimed to evaluate the synergistic antibacterial activities of silver ions (Ag⁺) and metformin hydrochloride (Met) against Enterococcus faecalis (E. faecalis) under normal or high-glucose conditions.

Authors: Xuying Wu, Wei Fan and Bing Fan

Application of a multiplex immunochromatographic assay for rapid identification of carbapenemases in a clinical microbiology laboratory: performance and turn-around-time evaluation of NG-test Carba 5

Prompt and accurate identification of carbapenemase production is essential for appropriate treatment and infection control. NG-Test Carba 5 (termed herein “Carba 5”; NG Biotech, Guipry, France) is a multiplex...

Authors: Jung Yoon, Chang Hyun Kim, Soo-Young Yoon, Chae Seung Lim and Chang Kyu Lee

Oral iron supplementation after antibiotic exposure induces a deleterious recovery of the gut microbiota

Oral iron supplementation is commonly prescribed for anemia and may play an important role in the gut microbiota recovery of anemic individuals who received antibiotic treatment. This study aims to investigate...

Authors: Thibault Cuisiniere, Annie Calvé, Gabriela Fragoso, Manon Oliero, Roy Hajjar, Emmanuel Gonzalez and Manuela M. Santos

Interplay and cooperation of Helicobacter pylori and gut microbiota in gastric carcinogenesis

Chronic Helicobacter pylori infection is a critical risk factor for gastric cancer (GC). However, only 1–3 % of people with H. pylori develop GC. In gastric carcinogenesis, non-H. pylori bacteria in the stomach m...

Authors: Seyedeh Zahra Bakhti and Saeid Latifi-Navid

Genetic and antimicrobial resistance profiles of non-O157 Shiga toxin-producing Escherichia coli from different sources in Egypt

The Shiga toxin-producing Escherichia coli (STEC) represented a great risk to public health. In this study, 60 STEC strains recovered from broiler and duck fecal samples, cow’s milk, cattle beef, human urine, and...

Authors: Mohamed Sabry Abd Elraheam Elsayed, Samah Mahmoud Eldsouky, Tamer Roshdy, Abeer Mohamed Ahmed Bayoume, Ghada M. Nasr, Ali S. A. Salama, Behiry A. Akl, Al Shaimaa Hasan, Amany Kasem Shahat, Rana Atef Khashaba, Walid Abdellatif Abdelhalim, Hend E. Nasr, Lina Abdelhady Mohammed and Ahmed Salah

Skin dysbiosis in the microbiome in atopic dermatitis is site-specific and involves bacteria, fungus and virus

Microbial dysbiosis with increased Staphylococcus aureus (S. aureus) colonization on the skin is a hallmark of atopic dermatitis (AD), however most microbiome studies focus on bacteria in the flexures and the mic...

Authors: Rie Dybboe Bjerre, Jacob Bak Holm, Albert Palleja, Julie Sølberg, Lone Skov and Jeanne Duus Johansen

Carbon starvation of Pseudomonas aeruginosa biofilms selects for dispersal insensitive mutants

Biofilms disperse in response to specific environmental cues, such as reduced oxygen concentration, changes in nutrient concentration and exposure to nitric oxide. Interestingly, biofilms do not completely dis...

Authors: Harikrishnan A. S. Nair, Sujatha Subramoni, Wee Han Poh, Nabilah Taqiah Binte Hasnuddin, Martin Tay, Michael Givskov, Tim Tolker-Nielsen, Staffan Kjelleberg, Diane McDougald and Scott A. Rice

Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea

Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gu...

Authors: Siham Fatani, Yoshimoto Saito, Mohammed Alarawi, Takashi Gojobori and Katsuhiko Mineta

Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair’s large freshwater ecosystems

Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spat...

Authors: Abdolrazagh Hashemi Shahraki, Subba Rao Chaganti and Daniel Heath

Reproductive tract microbiota of women in childbearing age shifts upon gynecological infections and menstrual cycle

This study was undertaken to discover whether the vaginal microbe of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respec...

Authors: Lijuan Cheng, Yan Gao, Qing Xia, Hui Wang, Xiuzhen Xie, Yurong Liu, Heying Shang and Yutao Diao

Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

To understand inter-individual variability of fecal microbe transplantation (FMT) to enhance anti-PD-1 immunotherapy (IT) for melanoma, we analyzed the data sets from two recent publications with a microbial s...

Authors: Hyunmin Koo and Casey D. Morrow

Effects of mulberry leaf silage on antioxidant and immunomodulatory activity and rumen bacterial community of lambs

Rumen is a natural fermentation system and the microorganisms inside can effectively utilize plant bioresource and interact with host metabolism. Here, analysis of rumen microbiome, together with animal perfor...

Authors: Bing Wang and Hailing Luo

Lacticaseibacillus rhamnosus TR08 alleviated intestinal injury and modulated microbiota dysbiosis in septic mice

Probiotics are widely used in intestinal microbiota imbalance caused by sepsis, however, the protective mechanism is still unclear. This study aimed to explore protective effect of Lacticaseibacillus rhamnosus TR...

Authors: Jiangtao Yin, Wen Sun, Xianqiang Yu, Xiaojia Xiao, Baiqiang Li, Zhihui Tong, Lu Ke, Wenjian Mao and Weiqin Li

Genetic characterization of Carbapenem-Resistant Escherichia coli from China, 2015–2017

The molecular characteristics of carbapenem-resistant Escherichia coli (CREco) remain unclear.

Authors: Fengtian Li, Kun Ye, Xin Li, Liyan Ye, Ling Guo, Lifeng Wang and Jiyong Yang

Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences

Infants with cystic fibrosis (CF) suffer from gastrointestinal (GI) complications, including pancreatic insufficiency and intestinal inflammation, which have been associated with impaired nutrition and growth....

Authors: Alexander Eng, Hillary S. Hayden, Christopher E. Pope, Mitchell J. Brittnacher, Anh T. Vo, Eli J. Weiss, Kyle R. Hager, Daniel H. Leung, Sonya L. Heltshe, Daniel Raftery, Samuel I. Miller, Lucas R. Hoffman and Elhanan Borenstein

Saline and alkaline stresses alter soil properties and composition and structure of gene-based nitrifier and denitrifier communities in a calcareous desert soil

Saline and alkaline stresses damages the health of soil systems. Meanwhile, little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the re...

Authors: Jiaxin Guo, Yongxue Zhou, Huijuan Guo and Wei Min

The Mesorhizobium huakuii transcriptional regulator AbiEi plays a critical role in nodulation and is important for bacterial stress response

Bacterial abortive infection (Abi) systems are type IV toxin–antitoxin (TA) system, which could elicit programmed cell death and constitute a native survival strategy of pathogenic bacteria under various stres...

Authors: Xiaohong Chen, Aiqi Hu, Qian Zou, Sha Luo, Hetao Wu, Chunlan Yan, Tao Liu, Donglan He, Xiaohua Li and Guojun Cheng

Elucidating bacterial adhesion to mucosal surface by an original AFM approach

Fish skin represents an ancient vertebrate mucosal surface, sharing characteristics with other mucosal surfaces including those of the intestine. The skin mucosa is continuously exposed to microbes in the surr...

Authors: Karen Dunker, Sol Gomez de la Torre Canny, Catherine Taylor Nordgård, Etienne Dague, Cécile Formosa-Dague, Ingrid Bakke and Marit Sletmoen

Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina

Understanding the specificity and flexibility of the algal symbiosis-host association is fundamental for predicting how species occupy a diverse range of habitats. Here we assessed the algal symbiosis diversit...

Authors: Martina Prazeres, T. Edward Roberts, Shadrina Fildzah Ramadhani, Steve S. Doo, Christiane Schmidt, Marleen Stuhr and Willem Renema

An optimised protocol for detection of SARS-CoV-2 in stool

SARS-CoV-2 has been detected in stool samples of COVID-19 patients, with potential implications for faecal-oral transmission. Compared to nasopharyngeal swab samples, the complexity of the stool matrix poses a...

Authors: Tianqi Li, Enriqueta Garcia-Gutierrez, Daniel A. Yara, Jacob Scadden, Jade Davies, Chloe Hutchins, Alp Aydin, Justin O’Grady, Arjan Narbad, Stefano Romano and Lizbeth Sayavedra

Correction to: Prevalence and mechanisms of antibiotic resistance in Escherichia coli isolated from mastitic dairy cattle in Canada

Authors: Satwik Majumder, Dongyun Jung, Jennifer Ronholm and Saji George

Investigating the effect of an identified mutation within a critical site of PAS domain of WalK protein in a vancomycin-intermediate resistant Staphylococcus aureus by computational approaches

Vancomycin-intermediate resistant Staphylococcus aureus (VISA) is becoming a common cause of nosocomial infections worldwide. VISA isolates are developed by unclear molecular mechanisms via mutations in several g...

Authors: Neda Baseri, Shahin Najar-Peerayeh and Bita Bakhshi

Genetic fingerprinting and aflatoxin production of Aspergillus section Flavi associated with groundnut in eastern Ethiopia

Aspergillus species cause aflatoxin contamination in groundnut kernels, being a health threat in agricultural products and leading to commodity rejection by domestic and international markets. Presence of Aspergi...

Authors: Abdi Mohammed, Paola C. Faustinelli, Alemayehu Chala, Mashilla Dejene, Chemeda Fininsa, Amare Ayalew, Chris O. Ojiewo, David A. Hoisington, Victor S. Sobolev, Jaime Martínez-Castillo and Renee S. Arias

Associations between the gut microbiome and metabolome in early life

The infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic ...

Authors: Quang P. Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Wimal W. Pathmasiri, Susan McRitche, Susan J. Sumner, H. Robert Frost and Anne G. Hoen

Emerging MDR-Mycobacterium avium subsp. avium in house-reared domestic birds as the first report in Egypt

Avian tuberculosis is a chronic and zoonotic disease that affects a wide variety of birds, mammals, and humans. This study aimed to estimate the frequency of Mycobacterium avium subsp. avium in some domestic bird...

Authors: Abdelazeem M. Algammal, Hany R. Hashem, Amenah S. Al-otaibi, Khyreyah J. Alfifi, Esraa M. El-dawody, Eman Mahrous, Helal F. Hetta, Ali W. El-Kholy, Hazem Ramadan and Reham M. El-Tarabili

Evaluation of the Genmark ePlex® and QIAstat-Dx® respiratory pathogen panels in detecting bacterial targets in lower respiratory tract specimens

The ePlex® and QIAstat-Dx® respiratory pathogen panels detect multiple respiratory pathogens, mainly viruses but also Legionella pneumophila, Mycoplasma pneumoniae and Bordetella pertussis. The assays have been m...

Authors: Suzanne A. V. van Asten, Stefan A. Boers, Jolanda D. F. de Groot, R. Schuurman and Eric C. J. Claas

Mother-to-infant transmission of the carcinogenic colibactin-producing bacteria

The Escherichia coli strain that is known to produce the genotoxic secondary metabolite colibactin is linked to colorectal oncogenesis. Therefore, understanding the properties of such colibactin-positive E. coli ...

Authors: Yuta Tsunematsu, Koji Hosomi, Jun Kunisawa, Michio Sato, Noriko Shibuya, Emiko Saito, Haruka Murakami, Yuko Yoshikawa, Yuji Iwashita, Noriyuki Miyoshi, Michihiro Mutoh, Hideki Ishikawa, Haruhiko Sugimura, Motohiko Miyachi, Keiji Wakabayashi and Kenji Watanabe

Inhibition of Streptococcus mutans biofilms with bacterial-derived outer membrane vesicles

Biofilms are microbial communities surrounded by a self-produced extracellular matrix which protects them from environmental stress. Bacteria within biofilms are 10- to 1000-fold more resistant to antibiotics,...

Authors: Yihui Wang, Joseph P. Hoffmann, Sarah M. Baker, Kerstin Höner zu Bentrup, William C. Wimley, Joseph A. Fuselier, Jacob P. Bitoun and Lisa A. Morici

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

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

Induction of amylase and protease as antibiofilm agents by starch, casein, and yeast extract in Arthrobacter sp. CW01

In unfavourable environment, such as nutrient limitation, some bacteria encased themselves into a three dimensional polymer matrix called biofilm. The majority of microbial infections in human are biofilm rela...

Authors: Jeffrine Solihin, Diana Elizabeth Waturangi and Tresnawati Purwadaria

Skin microbiota dynamics following B. subtilis formulation challenge: an in vivo study in mice

Modulating the microbiota is a leading-edge strategy for the restoration and maintenance of a healthy, balanced environment. The use of health-promoting bacteria has demonstrated some potential benefits as an ...

Authors: Veronica Moskovicz, Rina Ben-El, Guy Horev and Boaz Mizrahi