Articles

Standardization of an LNA-based TaqMan assay qPCR analysis for Aspiculuris tetraptera DNA in mouse faeces

Aspiculuris tetraptera, as a parasitic pinworm, is most frequently detected in laboratory mice, and transmission is mediated by the eggs contained in the faeces of infected mice. A highly sensitive and quantitati...

Authors: Keishiro Isayama, Kenji Watanabe, Mariko Okamoto, Tomoaki Murata and Yoichi Mizukami

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks

Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating envir...

Authors: Qingshan Fan, Metha Wanapat, Tianhai Yan and Fujiang Hou

Role of aspartate ammonia-lyase in Pasteurella multocida

Pasteurella multocida is responsible for a highly infectious and contagious disease in birds, leading to heavy economic losses in the chicken industry. However, the pathogenesis of this disease is poorly understo...

Authors: Zui Wang, Li Li, Peng Liu, Chen Wang, Qin Lu, Lina Liu, Xiaozhong Wang, Qingping Luo and Huabin Shao

A comparative study on production of extracellular hydrolytic enzymes of Candida species isolated from patients with surgical site infection and from healthy individuals and their co-relation with antifungal drug resistance

Surgical site infection (SSI) is a crucial dilemma of surgery. Patients with SSIs not only face difficulty in treatment but also bear extra cost with high mortality rate. Resistant strains of Candida have emer...

Authors: Rakhshanda Erum, Farkhunda Samad, Adnan Khan and Shahana Urooj Kazmi

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae

Serotyping of Streptococcus pneumoniae is important for monitoring of vaccine impact. Unfortunately, conventional and molecular serotyping is expensive and technically demanding. This study aimed to determine the...

Authors: Sivkheng Kann, Sena Sao, Chanleakhena Phoeung, Youlet By, Juliet Bryant, Florence Komurian-Pradel, Vonthanak Saphonn, Monidarin Chou and Paul Turner

Antimicrobial resistance and metallo-beta-lactamase producing among commensal Escherichia coli isolates from healthy children of Khuzestan and Fars provinces; Iran

The emergence of metallo-β-lactamase (MBL)-producing isolates is alarming since they carry mobile genetic elements with great ability to spread; therefore, early detection of these isolates, particularly their...

Authors: Fahimeh Mahmoodi, Seyedeh Elham Rezatofighi and Mohammad Reza Akhoond

Repeated centrifuging and washing concentrates bacterial samples in peritoneal dialysis for optimal culture: an original article

Bacterial cultures allow the identification of infectious disease pathogens. However, obtaining the results of conventional culture methods is time-consuming, taking at least two days. A more efficient alterna...

Authors: Ni Tien, Bang-Jau You, Hsuan-Jen Lin, Chieh-Ying Chang, Che-Yi Chou, Hsiu-Shen Lin, Chiz-Tzung Chang, Charles C. N. Wang and Hung-Chih Chen

Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos

Ruminants burp massive amounts of methane into the atmosphere and significantly contribute to the deposition of greenhouse gases and the consequent global warming. It is therefore urgent to devise strategies t...

Authors: Sandra Bibiana Aguilar-Marin, Claudia Lorena Betancur-Murillo, Gustavo A. Isaza, Henry Mesa and Juan Jovel

Application of Bacillus thuringiensis strains with conjugal and mobilizing capability drives gene transmissibility within Bacillus cereus group populations in confined habitats

Bacillus thuringiensis bacteria share similar genetic, physiological, and biochemical characteristics with other members of the Bacillus cereus group. Their diversity and entomopathogenic origin are related to th...

Authors: Xiaomin Hu, Doudou Huang, Joseph Ogalo, Peiling Geng, Zhiming Yuan, Hairong Xiong, Xiaofu Wan and Jiahui Sun

The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection

Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. I...

Authors: Amalie Katrine Rendboe, Thor Bech Johannesen, Anna Cäcilia Ingham, Emeli Månsson, Søren Iversen, Sharmin Baig, Sofie Edslev, Jørgen Skov Jensen, Bo Söderquist, Paal Skytt Andersen and Marc Stegger

Sulfated vizantin causes detachment of biofilms composed mainly of the genus Streptococcus without affecting bacterial growth and viability

Sulfated vizantin, a recently developed immunostimulant, has also been found to exert antibiofilm properties. It acts not as a bactericide, but as a detachment-promoting agent by reducing the biofilm structura...

Authors: Taisuke Hasegawa, Shoji Takenaka, Masataka Oda, Hisanori Domon, Takumi Hiyoshi, Karin Sasagawa, Tatsuya Ohsumi, Naoki Hayashi, Yasuko Okamoto, Hirofumi Yamamoto, Hayato Ohshima, Yutaka Terao and Yuichiro Noiri

First isolation and whole-genome sequencing of a Shewanella algae strain from a swine farm in Brazil

Infections caused by Shewanella spp. have been increasingly reported worldwide. The advances in genomic sciences have enabled better understanding about the taxonomy and epidemiology of this agent. However, the s...

Authors: Vinicius Buiatte de Andrade Alves, Eneas Carvalho, Paloma Alonso Madureira, Elizangela Domenis Marino, Andreia Cristina Nakashima Vaz, Ana Maria Centola Vidal and Vera Letticie de Azevedo Ruiz

Young «oil site» of the Uzon Caldera as a habitat for unique microbial life

The Uzon Caldera is one of the places on our planet with unique geological, ecological, and microbiological characteristics. Uzon oil is the youngest on Earth. Uzon oil has unique composition, with low proport...

Authors: Sergey E. Peltek, Alla V. Bryanskaya, Yuliya E. Uvarova, Aleksey S. Rozanov, Timofey V. Ivanisenko, Vladimir A. Ivanisenko, Elena V. Lazareva, Olga V. Saik, Vadim M. Efimov, Sergey M. Zhmodik, Oxana P. Taran, Nikolay M. Slynko, Sergey V. Shekhovtsov, Valentin N. Parmon, Nikolay L. Dobretsov and Nikolay A. Kolchanov

Microbiology research at the systems biology and bioinformatics - 2019 (SBB-2019) school

Authors: Yuriy L. Orlov, Alexander N. Ignatov, Elvira R. Galieva and Oxana B. Dobrovolskaya

Virulent secondary metabolites of entomopathogenic bacteria genera, Xenorhabdus and Photorhabdus, inhibit phospholipase A₂ to suppress host insect immunity

Xenorhabdus and Photorhabdus are entomopathogenic bacteria that cause septicemia and toxemia in insects. They produce secondary metabolites to induce host immunosuppression. Their metabolite compositions vary amo...

Authors: Md. Mahi Imam Mollah and Yonggyun Kim

Rhamnolipids and surfactin inhibit the growth or formation of oral bacterial biofilm

Bacteria survive in various environments by forming biofilms. Bacterial biofilms often cause significant problems to medical instruments and industrial processes. Techniques to inhibit biofilm formation are es...

Authors: Ryota Yamasaki, Aki Kawano, Yoshie Yoshioka and Wataru Ariyoshi

Indole-3-lactic acid associated with Bifidobacterium-dominated microbiota significantly decreases inflammation in intestinal epithelial cells

Bifidobacterium longum subsp. infantis (B. infantis) is a commensal bacterium that colonizes the gastrointestinal tract of breast-fed infants. B. infantis can efficiently utilize the abundant supply of oligosacch...

Authors: Amy M. Ehrlich, Alline R. Pacheco, Bethany M. Henrick, Diana Taft, Gege Xu, M. Nazmul Huda, Darya Mishchuk, Michael L. Goodson, Carolyn Slupsky, Daniela Barile, Carlito B. Lebrilla, Charles B. Stephensen, David A. Mills and Helen E. Raybould

Influence of microbiota and metabolites on the quality of tobacco during fermentation

To explore the optimum fermentation conditions for tobacco leaves and also screen the microbiota and metabolites that are beneficial for fermentation.

Authors: Jingjing Li, Yuanyuan Zhao, Yanqing Qin and Hongzhi Shi

The attachment process and physiological properties of Escherichia coli O157:H7 on quartz

Manure application and sewage irrigation release many intestinal pathogens into the soil. After being introduced into the soil matrix, pathogens are commonly found to attach to soil minerals. Although the surv...

Authors: Liliang Wang, Yichao Wu, Peng Cai and Qiaoyun Huang

A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska

Root and stem rot caused by Rhizoctonia solani is a serious fungal disease of sugar beet and dry bean production in Nebraska. Rhizoctonia root rot and crown rot in sugar beet and dry bean have reduced the yield s...

Authors: Saurav Das, T. Plyler-Harveson, Dipak K. Santra, Bijesh Maharjan, Kathy A. Nielson and Robert M. Harveson

Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota

In the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive litera...

Authors: Nesreen H. Aljahdali, Yasser M. Sanad, Jing Han and Steven L. Foley

Utilization of different MurNAc sources by the oral pathogen Tannerella forsythia and role of the inner membrane transporter AmpG

The Gram-negative oral pathogen Tannerella forsythia strictly depends on the external supply of the essential bacterial cell wall sugar N-acetylmuramic acid (MurNAc) for survival because of the lack of the common...

Authors: Valentina M. T. Mayer, Markus B. Tomek, Rudolf Figl, Marina Borisova, Isabel Hottmann, Markus Blaukopf, Friedrich Altmann, Christoph Mayer and Christina Schäffer

Transcriptional response of Bacillus megaterium FDU301 to PEG200-mediated arid stress

For microorganisms on a paper surface, the lack of water is one of the most important stress factors. A strain of Bacillus megaterium FDU301 was isolated from plaques on a paper surface using culture medium with ...

Authors: Lei Zhao, Yanjun Zhou, Jianbei Li, Yucheng Xia, Weiyun Wang, Xiuqi Luo, Juan Yin and Jiang Zhong

Antimicrobial activity of omadacycline in vitro against bacteria isolated from 2014 to 2017 in China, a multi-center study

Omadacycline (ZL-2401) is a semi-synthetic derivative of minocycline. It has a broadspectrum activity against Gram-positive and Gram-negative bacteria, and atypical pathogens. The objective of this study was t...

Authors: Meng Xiao, Jing-jing Huang, Ge Zhang, Wen-hang Yang, Fanrong Kong, Timothy Kudinha and Ying-chun Xu

Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing

Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, afford...

Authors: S. Garcia-Garcia, A. Perez-Arguello, D. Henares, N. Timoneda and C. Muñoz-Almagro

Quantitative microbial risk assessment for waterborne pathogens in a wastewater treatment plant and its receiving surface water body

Access to safe water for drinking and domestic activities remains a challenge in emerging economies like South Africa, forcing resource-limited communities to use microbiologically polluted river water for per...

Authors: Joshua Mbanga, Akebe Luther King Abia, Daniel Gyamfi Amoako and Sabiha. Y. Essack

Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases

Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) ...

Authors: Adriana Piza-Buitrago, Verónica Rincón, John Donato, Sandra Yamile Saavedra, Carolina Duarte, Jaime Morero, Laurent Falquet, María Teresa Reguero and Emiliano Barreto-Hernández

The stability of the coiled-coil structure near to N-terminus influence the heat resistance of harpin proteins from Xanthomonas

Heat resistance is a common characteristic of harpins, a class of proteins found in Gram-negative bacteria, which may be related to the stability of coiled-coil (CC) structure. The CC structure is a ubiquitous...

Authors: Yue Liu, Xiaoyun Zhou, Wenbo Liu and Weiguo Miao

Screening of antibiofilm and anti-quorum sensing activty of Actinomycetes isolates extracts against aquaculture pathogenic bacteria

Indonesia is the third largest producer of fish and other aquaculture products in the world, making this industry a major contributor in the economy of Indonesia. However, this industry continually overcome ch...

Authors: Gloria Raissa, Diana Elizabeth Waturangi and Dinamella Wahjuningrum

Identifying candidate Aspergillus pathogenicity factors by annotation frequency

Members of the genus Aspergillus display a variety of lifestyles, ranging from saprobic to pathogenic on plants and/or animals. Increased genome sequencing of economically important members of the genus permits e...

Authors: Kayla K. Pennerman, Guohua Yin, Anthony E. Glenn and Joan W. Bennett

Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis

Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recen...

Authors: Zheng Zhang, Yong-xiang Yu, Yin-geng Wang, Xiao Liu, Li-fang Wang, Hao Zhang, Mei-jie Liao and Bin Li

Comparison of different modes of antibiotic delivery on gut microbiota depletion efficiency and body composition in mouse

The use of animal models with depleted intestinal microbiota has recently increased thanks to the huge interest in the potential role of these micro-organisms in human health. In particular, depletion of gut b...

Authors: Pauline Tirelle, Jonathan Breton, Gaëtan Riou, Pierre Déchelotte, Moïse Coëffier and David Ribet

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid

Microbiome and metagenomic studies have given rise to a new understanding of microbial colonization of various human tissues and their ability to impact our health. One human microbiome growing in notoriety, t...

Authors: Katelyn Brandt and Rodolphe Barrangou

Membrane and lipid metabolism plays an important role in desiccation resistance in the yeast Saccharomyces cerevisiae

Anhydrobiotes, such as the yeast Saccharomyces cerevisiae, are capable of surviving almost total loss of water. Desiccation tolerance requires an interplay of multiple events, including preserving the protein fun...

Authors: Qun Ren, Rebecca Brenner, Thomas C. Boothby and Zhaojie Zhang

Stool microbiome, pH and short/branched chain fatty acids in infants receiving extensively hydrolyzed formula, amino acid formula, or human milk through two months of age

Early infant feeding with intact or extensively hydrolyzed (EH) proteins or free amino acids (AA) may differentially affect intestinal microbiota composition and immune reactivity. This multicenter, double-bli...

Authors: Car Reen Kok, Bradford Brabec, Maciej Chichlowski, Cheryl L. Harris, Nancy Moore, Jennifer L. Wampler, Jon Vanderhoof, Devin Rose and Robert Hutkins

The pelvis urinary microbiome in patients with kidney stones and clinical associations

The long-held notion that, without urinary tract or circulatory infection, bladder urine and blood are sterile biofluids has been disproven. There have been no previous reports on the kidney pelvis urinary mic...

Authors: Fengping Liu, Nan Zhang, Yunhong Wu, Peng Jiang, Tingting Jiang, Yang Wang, Yuwei Zhang, Qixiao Zhai, Yeqing Zou and Ninghan Feng

High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis

Ferula sinkiangensis is an increasingly endangered medicinal plant. Arbuscular mycorrhiza fungi (AMF) are symbiotic microorganisms that live in the soil wherein they enhance nutrient uptake, stress resistance, an...

Authors: Yunfeng Luo, Zhongke Wang, Yaling He, Guifang Li, Xinhua Lv and Li Zhuang

Gut microbiota: effect of pubertal status

The make-up of gut microbiota at different puberty stages has not been reported. This cross-sectional study analyzed the bio-diversity of gut microbiota at different puberty stages.

Authors: Xin Yuan, Ruimin Chen, Ying Zhang, Xiangquan Lin and Xiaohong Yang

Comparison of three neutralizing broths for environmental sampling of low levels of Listeria monocytogenes desiccated on stainless steel surfaces and exposed to quaternary ammonium compounds

An effective environmental sampling method involves the use of a transport/neutralizing broth with the ability to neutralize sanitizer residues that are collected during sampling and to maintain viability of s...

Authors: Fengmin Li, Zhihan Xian, Hee Jin Kwon, Jiyoon Yoo, Laurel Burall, Stuart J. Chirtel, Thomas S. Hammack and Yi Chen

The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota

Microencapsulated organic acids and botanicals have the potential to develop into important tools for the poultry industry. A blend of organic acids and botanicals (AviPlus®P) has previously shown to reduce Salmo...

Authors: Kristina M. Feye, Christina L. Swaggerty, Michael H. Kogut, Steven C. Ricke, Andrea Piva and Ester Grilli

Uncovering fungal community composition in natural habitat of Ophiocordyceps sinensis using high-throughput sequencing and culture-dependent approaches

The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repe...

Authors: Chuan-Bo Zhang, Chao-Hui Ren, Yan-Li Wang, Qi-Qi Wang, Yun-Sheng Wang and Qing-Bei Weng

Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition

Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environmen...

Authors: O. H. Oduaran, F. B. Tamburini, V. Sahibdeen, R. Brewster, F. X. Gómez-Olivé, K. Kahn, S. A. Norris, S. M. Tollman, R. Twine, A. N. Wade, R. G. Wagner, Z. Lombard, A. S. Bhatt and S. Hazelhurst

Short chain fatty acids induced the type 1 and type 2 fimbrillin-dependent and fimbrillin-independent initial attachment and colonization of Actinomyces oris monoculture but not coculture with streptococci

Actinomyces oris is an early colonizer and has two types of fimbriae on its cell surface, type 1 fimbriae (FimP and FimQ) and type 2 fimbriae (FimA and FimB), which contribute to the attachment and coaggregation ...

Authors: Itaru Suzuki, Takehiko Shimizu and Hidenobu Senpuku

Phenotypic and proteomic approaches of the response to iron-limited condition in Staphylococcus lugdunensis

Staphylococcus lugdunensis is a coagulase-negative Staphylococcus part of the commensal skin flora but emerge as an important opportunistic pathogen. Because iron limitation is a crucial stress during infectious ...

Authors: Marion Aubourg, Anne Dhalluin, François Gravey, Marine Pottier, Nicolas Thomy, Benoit Bernay, Didier Goux, Matthieu Martineau and Jean-Christophe Giard

Rsp activates expression of the Cnt system in Staphylococcus aureus

The Cnt system is crucial for the optimal import of essential metals in metal-limiting conditions and contributes to virulence in S. aureus. In a screen for regulators of efflux pumps in a phage-based ultra-high-...

Authors: Laura Vinué and David C. Hooper

Experimental determination of evolutionary barriers to horizontal gene transfer

Horizontal gene transfer, the acquisition of genes across species boundaries, is a major source of novel phenotypes that enables microbes to rapidly adapt to new environments. How the transferred gene alters t...

Authors: Hande Acar Kirit, Mato Lagator and Jonathan P. Bollback

Diversity of mucoid to non-mucoid switch among carbapenemase-producing Klebsiella pneumoniae

Klebsiella pneumoniae is a leading cause of intractable hospital-acquired multidrug-resistant infections and carbapenemase-producing K. pneumoniae (CPKp) are particularly feared. Most of the clinical isolates pro...

Authors: Adriana Chiarelli, Nicolas Cabanel, Isabelle Rosinski-Chupin, Pengdbamba Dieudonné Zongo, Thierry Naas, Rémy A. Bonnin and Philippe Glaser

The role of the msaABCR operon in implant-associated chronic osteomyelitis in Staphylococcus aureus USA300 LAC

The msaABCR operon regulates several staphylococcal phenotypes such as biofilm formation, capsule production, protease production, pigmentation, antibiotic resistance, and persister cells formation. The msaABCR o...

Authors: Gyan S. Sahukhal, Michelle Tucci, Hamed Benghuzzi, Gerri Wilson and Mohamed O. Elasri

Methanosarcina acetivorans contains a functional ISC system for iron-sulfur cluster biogenesis

The production of methane by methanogens is dependent on numerous iron-sulfur (Fe-S) cluster proteins; yet, the machinery involved in Fe-S cluster biogenesis in methanogens remains largely unknown. Methanogen ...

Authors: Thomas M. Deere, Divya Prakash, Faith H. Lessner, Evert C. Duin and Daniel J. Lessner

High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus

Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs)...

Authors: Rim El Jeni, Kais Ghedira, Monia El Bour, Sonia Abdelhak, Alia Benkahla and Balkiss Bouhaouala-Zahar