Ecological and evolutionary microbiology

Antibiotics influence the toxicity of the delta endotoxins of Bacillus thuringiensis towards the cotton bollworm, Helicoverpa armigera

The cotton bollworm, Helicoverpa armigera is one of the most important crop pests worldwide. It has developed high levels of resistance to synthetic insecticides, and hence, Bacillus thuringiensis (Bt) formulatio...

Authors: Inakarla Paramasiva, Hari C Sharma and Pulipaka Venkata Krishnayya

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process

Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently...

Authors: Daniela Bulgari, Paola Casati, Fabio Quaglino and Piero A Bianco

Characterization of bacteriophage communities and CRISPR profiles from dental plaque

Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human sub...

Authors: Mayuri Naidu, Refugio Robles-Sikisaka, Shira R Abeles, Tobias K Boehm and David T Pride

Genome sequence and phenotypic analysis of a first German Francisella sp. isolate (W12-1067) not belonging to the species Francisella tularensis

Francisella isolates from patients suffering from tularemia in Germany are generally strains of the species F. tularensis subsp. holarctica. To our knowledge, no other Francisella species are known for Germany. ...

Authors: Kerstin Rydzewski, Tino Schulz, Elzbieta Brzuszkiewicz, Gudrun Holland, Christian Lück, Jens Fleischer, Roland Grunow and Klaus Heuner

Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers

Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas a...

Authors: César A Trujillo, Nathalia Arias-Rojas, Lucie Poulin, César A Medina, Anibal Tapiero, Silvia Restrepo, Ralf Koebnik and Adriana J Bernal

Differential efficiency in exogenous DNA acquisition among closely related Salmonella strains: implications in bacterial speciation

Acquisition of exogenous genetic material is a key event in bacterial speciation. It seems reasonable to assume that recombination of the incoming DNA into genome would be more efficient with higher levels of ...

Authors: Hong-Xia Bao, Le Tang, Lu Yu, Xu-Yao Wang, Yang Li, Xia Deng, Yong-Guo Li, Ang Li, Da-Ling Zhu, Randal N Johnston, Gui-Rong Liu, Ye Feng and Shu-Lin Liu

A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia

Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, tr...

Authors: Tong Dan, Wenjun Liu, Zhihong Sun, Qiang Lv, Haiyan Xu, Yuqin Song and Heping Zhang

The genetic diversity of cereulide biosynthesis gene cluster indicates a composite transposon Tnces in emetic Bacillus weihenstephanensis

Cereulide is a cyclic dodecadepsipeptide ionophore, produced via non-ribosomal peptide synthetases (NRPS), which in rare cases can lead to human death. Early studies had shown that emetic toxin formation belon...

Authors: Xiaofen Mei, Kai Xu, Lingling Yang, Zhiming Yuan, Jacques Mahillon and Xiaomin Hu

Conservation of streptococcal CRISPRs on human skin and saliva

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are utilized by bacteria to resist encounters with their viruses. Human body surfaces have numerous bacteria that harbor CRISPRs, and their c...

Authors: Refugio Robles-Sikisaka, Mayuri Naidu, Melissa Ly, Julia Salzman, Shira R Abeles, Tobias K Boehm and David T Pride

Polymicrobial airway bacterial communities in adult bronchiectasis patients

Chronic airway infection contributes to the underlying pathogenesis of non-cystic fibrosis bronchiectasis (NCFBr). In contrast to other chronic airway infections, associated with COPD and CF bronchiectasis, wh...

Authors: Paul Purcell, Hannah Jary, Audrey Perry, John D Perry, Christopher J Stewart, Andrew Nelson, Clare Lanyon, Darren L Smith, Stephen P Cummings and Anthony De Soyza

Real-time PCR assays for genotyping of Cryptococcus gattii in North America

Cryptococcus gattii has been the cause of an ongoing outbreak starting in 1999 on Vancouver Island, British Columbia and spreading to mainland Canada and the US Pacific Northwest. In the course of the outbreak,

Authors: Erin J Kelley, Elizabeth M Driebe, Kizee Etienne, Mary E Brandt, James M Schupp, John D Gillece, Jesse S Trujillo, Shawn R Lockhart, Eszter Deak, Paul S Keim and David M Engelthaler

Erratum to: Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance

Authors: Ana Maldonado-Contreras, Shrinivasrao P Mane, Xue-Song Zhang, Luis Pericchi, Teresa Alarcón, Monica Contreras, Bodo Linz, Martin J Blaser and María Gloria Domínguez-Bello

The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations

Bacterial habitats, such as soil and the gut, are structured at the micrometer scale. Important aspects of microbial life in such spatial ecosystems are migration and colonization. Here we explore the coloniza...

Authors: Simon van Vliet, Felix JH Hol, Tim Weenink, Peter Galajda and Juan E Keymer

Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a s...

Authors: Aurélie Chambouvet, Cédric Berney, Sarah Romac, Stéphane Audic, Finlay Maguire, Colomban De Vargas and Thomas A Richards

Discovery of a novel rumen methanogen in the anaerobic fungal culture and its distribution in the rumen as revealed by real-time PCR

The novel archaea belonging to Rumen Cluster C (RCC), which may play an important role in methane production in the rumen have received increased attention. However, the present information on RCC in the rumen...

Authors: Wei Jin, Yan Fen Cheng, Sheng Yong Mao and Wei Yun Zhu

Molecular characterization of cytolethal distending toxin gene-positive Escherichia coli from healthy cattle and swine in Nara, Japan

Cytolethal distending toxin (CDT)-producing Escherichia coli (CTEC) has been isolated from patients with gastrointestinal or urinary tract infection, and sepsis. However, the source of human infection remains unk...

Authors: Atsushi Hinenoya, Kensuke Shima, Masahiro Asakura, Kazuhiko Nishimura, Teizo Tsukamoto, Tadasuke Ooka, Tetsuya Hayashi, Thandavarayan Ramamurthy, Shah M Faruque and Shinji Yamasaki

Zearalenone lactonohydrolase activity in Hypocreales and its evolutionary relationships within the epoxide hydrolase subset of a/b-hydrolases

Zearalenone is a mycotoxin produced by several species of Fusarium genus, most notably Fusarium graminearum and Fusarium culmorum. This resorcylic acid lactone is one of the most important toxins causing serious ...

Authors: Delfina Popiel, Grzegorz Koczyk, Adam Dawidziuk, Karolina Gromadzka, Lidia Blaszczyk and Jerzy Chelkowski

The IncI1 plasmid carrying the bla _CTX-M-1 gene persists in in vitro culture of a Escherichia coli strain from broilers

Commensal bacteria are a reservoir for antimicrobial-resistance genes. In the Netherlands, bacteria producing Extended Spectrum Beta-Lactamases (ESBL) are found on chicken-meat and in the gut of broilers at a ...

Authors: Egil AJ Fischer, Cindy M Dierikx, Alieda van Essen-Zandbergen, Herman JW van Roermund, Dik J Mevius, Arjan Stegeman and Don Klinkenberg

Survival of taylorellae in the environmental amoeba Acanthamoeba castellanii

Taylorella equigenitalis is the causative agent of contagious equine metritis, a sexually-transmitted infection of Equidae characterised in infected mares by abundant mucopurulent vaginal discharge and a variabl...

Authors: Julie Allombert, Anne Vianney, Claire Laugier, Sandrine Petry and Laurent Hébert

Starvation can diversify the population structure and virulence strategies of an environmentally transmitting fish pathogen

Generalist bacterial pathogens, with the ability for environmental survival and growth, often face variable conditions during their outside-host period. Abiotic factors (such as nutrient deprivation) act as se...

Authors: Lotta-Riina Sundberg, Heidi M T Kunttu and E Tellervo Valtonen

Drug-resistant and hospital-associated Enterococcus faecium from wastewater, riverine estuary and anthropogenically impacted marine catchment basin

Enterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). It is believed that the recent evolution of two clinically relev...

Authors: Ewa Sadowy and Aneta Luczkiewicz

Cigarette smoke condensate increases C. albicans adhesion, growth, biofilm formation, and EAP1, HWP1 and SAP2 gene expression

Smokers are more prone to oral infections than are non-smokers. Cigarette smoke reaches the host cells but also microorganisms present in the oral cavity. The contact between cigarette smoke and oral bacteria ...

Authors: Abdelhabib Semlali, Kerstin Killer, Humidah Alanazi, Witold Chmielewski and Mahmoud Rouabhia

Population analysis of Vibrio parahaemolyticus originating from different geographical regions demonstrates a high genetic diversity

Vibrio parahaemolyticus is frequently isolated from environmental and seafood samples and associated with gastroenteritis outbreakes in American, European, Asian and African countries. To distinguish between dif...

Authors: Sara Urmersbach, Thomas Alter, Madura Sanjeevani Gonsal Koralage, Lisa Sperling, Gunnar Gerdts, Ute Messelhäusser and Stephan Huehn

Development and antimicrobial susceptibility studies of in vitro monomicrobial and polymicrobial biofilm models with Aspergillus fumigatus and Pseudomonas aeruginosa

Mixed microbial infections of the respiratory tracts with P. aeruginosa and A. fumigatus capable of producing biofilms are commonly found in cystic fibrosis patients. The primary objective of this study was to de...

Authors: Elias K Manavathu, Dora L Vager and Jose A Vazquez

Reliable differentiation of Meyerozyma guilliermondii from Meyerozyma caribbica by internal transcribed spacer restriction fingerprinting

Meyerozyma guilliermondii (anamorph Candida guilliermondii) and Meyerozyma caribbica (anamorph Candida fermentati) are closely related species of the genetically heterogenous M. guilliermondii complex. Conventio...

Authors: Wahengbam Romi, Santosh Keisam, Giasuddin Ahmed and Kumaraswamy Jeyaram

Phylogenetic analysis of faecal microbiota from captive cheetahs reveals underrepresentation of Bacteroidetes and Bifidobacteriaceae

Imbalanced feeding regimes may initiate gastrointestinal and metabolic diseases in endangered felids kept in captivity such as cheetahs. Given the crucial role of the host’s intestinal microbiota in feed ferme...

Authors: Anne AMJ Becker, Myriam Hesta, Joke Hollants, Geert PJ Janssens and Geert Huys

High prevalence and two dominant host-specific genotypes of Coxiella burnetii in U.S. milk

Coxiella burnetii causes Q fever in humans and Coxiellosis in animals; symptoms range from general malaise to fever, pneumonia, endocarditis and death. Livestock are a significant source of human infection as th...

Authors: Talima Pearson, Heidie M Hornstra, Remy Hilsabeck, Lauren T Gates, Sonora M Olivas, Dawn M Birdsell, Carina M Hall, Sabrina German, James M Cook, Meagan L Seymour, Rachael A Priestley, Ashley V Kondas, Christine L Clark Friedman, Erin P Price, James M Schupp, Cindy M Liu…

A degenerate PCR-based strategy as a means of identifying homologues of aminoglycoside and β-lactam resistance genes in the gut microbiota

The potential for the human gut microbiota to serve as a reservoir for antibiotic resistance genes has been the subject of recent discussion. However, this has yet to be investigated using a rapid PCR-based ap...

Authors: Fiona Fouhy, R Paul Ross, Gerald F Fitzgerald, Catherine Stanton and Paul D Cotter

Histoplasma capsulatum and Pneumocystis spp. co-infection in wild bats from Argentina, French Guyana, and Mexico

Histoplasma capsulatum and Pneumocystis organisms cause host infections primarily affecting the lung tissue. H. capsulatum is endemic in the United States of America and Latin American countries. In special envi...

Authors: Antonio E González-González, Cécile M Aliouat-Denis, José A Ramírez-Bárcenas, Christine Demanche, Muriel Pottier, Laura E Carreto-Binaghi, Haroon Akbar, Sandra Derouiche, Magalie Chabé, El Moukhtar Aliouat, Eduardo Dei-Cas and Maria Lucia Taylor

Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance

A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutation...

Authors: Sean Michael Carroll, Katherine S Xue and Christopher J Marx

The murine lung microbiome in relation to the intestinal and vaginal bacterial communities

This work provides the first description of the bacterial population of the lung microbiota in mice. The aim of this study was to examine the lung microbiome in mice, the most used animal model for inflammator...

Authors: Kenneth Klingenberg Barfod, Michael Roggenbuck, Lars Hestbjerg Hansen, Susanne Schjørring, Søren Thor Larsen, Søren Johannes Sørensen and Karen Angeliki Krogfelt

Pinewood nematode-associated bacteria contribute to oxidative stress resistance of Bursaphelenchus xylophilus

Pine wilt disease (PWD) caused by the pinewood nematode Bursaphelenchus xylophilus is one of the most serious forest diseases in the world. The role of B. xylophilus-associated bacteria in PWD and their interacti...

Authors: Cláudia S L Vicente, Yoriko Ikuyo, Manuel Mota and Koichi Hasegawa

Conjugative transfer of an IncA/C plasmid-borne bla_CMY-2gene through genetic re-arrangements with an IncX1 plasmid

Our observation that in the Mexican Salmonella Typhimurium population none of the ST19 and ST213 strains harbored both the Salmonella virulence plasmid (pSTV) and the prevalent IncA/C plasmid (pA/C) led us to hyp...

Authors: Magdalena Wiesner, Marcos Fernández-Mora, Miguel A Cevallos, Crispín Zavala-Alvarado, Mussaret B Zaidi, Edmundo Calva and Claudia Silva

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-orga...

Authors: Hannah M Doll, David W Armitage, Rebecca A Daly, Joanne B Emerson, Daniela S Aliaga Goltsman, Alexis P Yelton, Jennifer Kerekes, Mary K Firestone and Matthew D Potts

Prevalence and characterization of Salmonella enterica from the feces of cattle, poultry, swine and hedgehogs in Burkina Faso and their comparison to human Salmonellaisolates

Production and wild animals are major sources of human salmonellosis and animals raised for food also play an important role in transmission of antimicrobial resistant Salmonella strains to humans. Furthermore, i...

Authors: Assèta Kagambèga, Taru Lienemann, Laura Aulu, Alfred S Traoré, Nicolas Barro, Anja Siitonen and Kaisa Haukka

Disturbance induced decoupling between host genetics and composition of the associated microbiome

Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity how...

Authors: Karl Mathias Wegner, Nils Volkenborn, Hannes Peter and Alexander Eiler

Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location

The observation that specific members of the microbial intestinal community can be shared among vertebrate hosts has promoted the concept of a core microbiota whose composition is determined by host-specific s...

Authors: Bastiaan Star, Thomas HA Haverkamp, Sissel Jentoft and Kjetill S Jakobsen

Gene discovery, evolutionary affinity and molecular detection of Oxyspirura petrowi, an eye worm parasite of game birds

Oxyspirura petrowi appears to be emerging as a nematode parasite that could negatively impact Northern Bobwhite quail individuals and populations within Texas and other regions of the United States. Despite this ...

Authors: Lixin Xiang, Fengguang Guo, Haili Zhang, Lloyd LaCoste, Dale Rollins, Andrea Bruno, Alan M Fedynich and Guan Zhu

Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance

Helicobacter pylori has diverged in parallel to its human host, leading to distinct phylogeographic populations. Recent evidence suggests that in the current human mixing in Latin America, European H. pylori (hpE...

Authors: Ana Maldonado-Contreras, Shrinivasrao P Mane, Xue-Song Zhang, Luis Pericchi, Teresa Alarcón, Monica Contreras, Bodo Linz, Martin J Blaser and María Gloria Domínguez-Bello

Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons

Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with differ...

Authors: Yan He, Ben-Jie Zhou, Guan-Hua Deng, Xiao-Tao Jiang, Hai Zhang and Hong-Wei Zhou

Diversity of methanogens in the hindgut of captive white rhinoceroses, Ceratotherium simum

The white rhinoceros is on the verge of extinction with less than 20,200 animals remaining in the wild. In order to better protect these endangered animals, it is necessary to better understand their digestive...

Authors: Yu-heng Luo, André-Denis G Wright, You-long Li, Hua Li, Qi-hong Yang, Ling-juan Luo and Ming-xian Yang

Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity

Host plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil micro...

Authors: Florence Kurth, Katharina Zeitler, Lasse Feldhahn, Thomas R Neu, Tilmann Weber, Václav Krištůfek, Tesfaye Wubet, Sylvie Herrmann, François Buscot and Mika T Tarkka

The saliva microbiome of Pan and Homo

It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced...

Authors: Jing Li, Ivan Nasidze, Dominique Quinque, Mingkun Li, Hans-Peter Horz, Claudine André, Rosa M Garriga, Michel Halbwax, Anne Fischer and Mark Stoneking

Sub-inhibitory concentrations of some antibiotics can drive diversification of Pseudomonas aeruginosa populations in artificial sputum medium

Pseudomonas aeruginosa populations within the cystic fibrosis lung exhibit extensive phenotypic and genetic diversification. The resultant population diversity is thought to be crucial to the persistence of infec...

Authors: Elli A Wright, Joanne L Fothergill, Steve Paterson, Michael A Brockhurst and Craig Winstanley

Growth inhibition of an Araucaria angustifolia (Coniferopsida) fungal seed pathogen, Neofusicoccum parvum, by soil streptomycetes

Araucariaceae are important forest trees of the southern hemisphere. Life expectancy of their seedlings can largely be reduced by fungal infections. In this study we have isolated and characterized such a fung...

Authors: Fernando Rostirolla Dalmas, Leandro Astarita, Luigi DeFilippis, Elisabeth Magel, Hans-Peter Fiedler, Robert Bauer and Rüdiger Hampp

Conservation of the genes for HC-toxin biosynthesis in Alternaria jesenskae

HC-toxin, a cyclic tetrapeptide, is a virulence determinant for the plant pathogenic fungus Cochliobolus carbonum. It was recently discovered that another fungus, Alternaria jesenskae, also produces HC-toxin.

Authors: Wanessa D Wight, Roman Labuda and Jonathan D Walton

Widespread acquisition of antimicrobial resistance among Campylobacter isolates from UK retail poultry and evidence for clonal expansion of resistant lineages

Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimi...

Authors: Helen ML Wimalarathna, Judith F Richardson, Andy J Lawson, Richard Elson, Richard Meldrum, Christine L Little, Martin CJ Maiden, Noel D McCarthy and Samuel K Sheppard

Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China

Sika deer (Cervus nippon) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer have not been comprehensively studied, it i...

Authors: Zhi Peng Li, Han Lu Liu, Guang Yu Li, Kun Bao, Kai Ying Wang, Chao Xu, Yi Feng Yang, Fu He Yang and André-Denis G Wright

Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection

Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recr...

Authors: Alexandra Stock, Virginia Edgcomb, William Orsi, Sabine Filker, Hans-Werner Breiner, Michail M Yakimov and Thorsten Stoeck

Metaproteomic analysis of ratoon sugarcane rhizospheric soil

The current study was undertaken to elucidate the mechanism of yield decline in ratoon sugarcane using soil metaproteomics combined with community level physiological profiles (CLPP) analysis.

Authors: Wenxiong Lin, Linkun Wu, Sheng Lin, Aijia Zhang, Mingming Zhou, Rui Lin, Haibin Wang, Jun Chen, Zhixing Zhang and Ruiyu Lin