Posts Tagged ‘Open Access’

Naveen Kumar joins as new PhD student in our group

July 20, 2015 Leave a comment

N Naveen Kumar has joined our lab as a PhD student on July 1.  He has been previously at IISc Bangalore (group of S. Vijaya) and in Bhat Biotech company. Naveen comes with good research experience (a paper in PLOS Pathogens) in cellular microbiology and immunology. We welcome Naveen to the realm of PBL!

Categories: Lab Tags: , ,

New appointments

June 16, 2015 Leave a comment

Dr Ahmed has been recently invited to the following positions: 1) Editorial Board – Scientific Reports 2) Member, Board of Studies, School of Biotechnology, KIIT University, India

Categories: Lab Tags: ,

MGEN launched with Open Data policy

April 13, 2015 Leave a comment

An elaborate and extensive data sharing and archiving policy and a plausible partnership with Figshare is what makes MGEN a unique platform.  We at GutPathogens are also contemplating to form a similarly elaborate and explicit policy for the Genome Reports (formerly the ‘genome announcements’) being published by the latter. 

Thank you to our reviewers in 2013

January 2, 2014 Leave a comment

Gut Pathogens

The Gut Pathogens editorial team would like to thank all of the experts who reviewed manuscripts for the journal in 2013. We understand that this takes precious time, and we really appreciate all your time and efforts. Your support enables the journal to continue to be a success and publish high quality content. The journal has a very impressive average time from submission to a first decision of just 17 days for 2013, which is largely due to the timeliness of our reviewers. Thank you again to you all, and happy new year!

Extended scope for Gut Pathogens

December 19, 2013 Leave a comment

Gut Pathogens is pleased to announce an extended scope for the journal. This scope reflects a broad range of topics, including metagenomics, new genome sequences, microbiota profiling and systems biology, as well as the biological and clinical aspects of gut microbes.

Topical areas include, but are not limited to:

  • Microbial etiology of gut ailments
  • Gut invasion mechanisms
  • Microbial toxins and virulence factors in infections of the gut and associated glands – liver, pancreas
  • Bacterial adaptation to gut niches and evolution of pathogenicity
  • Biology and ecology of gut commensals and microbiota in health and disease
  • Biology and ecology of probiotic organisms
  • Host susceptibility or resistance to gut pathogens
  • Immune mechanisms of gut infections
  • Etiology of inflammatory bowel diseases
  • Molecular and serological diagnosis
  • Treatment and drug resistance mechanisms
  • Molecular epidemiology, transmission dynamics and evolutionary genetics
  • Vaccines for gut pathogens
  • Comparative and veterinary infectious diseases of the gut
  • Pathogenesis of bacterial, parasitic and viral infections of the gut
  • Genome sequencing, comparative genomics and systems biology
  • Microbiota analysis, metagenomics and gut microbiomes

Please visit the Gut Pathogens website to view the full journal scope.

We will be happy to answer any pre-submission enquiries at

Gut Pathogens

New thematic series in Gut Pathogens: Probiotics and Metagenomics of gut pathogens

December 13, 2013 Leave a comment

Gut Pathogens is delighted to introduce two new thematic series, highlighting articles published in the journal on the topics of Probiotics and Metagenomic analysis of gut pathogens. These new article collections are currently open for submissions on all aspects of probiotic research and metagenomic analysis of gut microbes.

Probiotic species Lactobacillus

Probiotic species Lactobacillus

Probiotics is a term used to describe any micro-organism which has a beneficial impact on another organism. There has been extensive research into probiotics and their health implications, and Gut Pathogens is excited to introduce a new article collection highlighting the latest research in this area. The series brings together a variety of original research and review articles discussing the topics of new trends and future prospects for probiotics, health implications, probiotic use for treating disease, and their effect on mental health.

The series includes a timely review of the approaches currently being used and developed to identify probiotic species of the genus Lactobacillus. Herbel et al., compare multiple tools and techniques, including Whole Genome Sequencing and real time PCR, used for identifying probiotic bacterial strains and give an informed prediction of future in this area. A recent piece of original research published in this series investigates the use of the probiotic Lactobacillus rhamnosus GG (LGG) in the treatment of Human rotavirus (HRV), the most common cause of severe diarrhoea in infants and young children. The authors discovered that LGG treatment induced cell death and partially prevented virus-induced tissue damage, providing a promising outlook for the probiotic treatment of HRV.

Digestive system

The human digestive system

Genomic analysis of gastrointestinal tract pathogens is key to understanding them and could potentially lead to the development of therapeutics, including probiotics, against them. To showcase the latest research in all aspects of metagenomics of gut pathogens and microbiota, a special series has been introduced.

A fascinating piece of original research by Monira et al., published in this series investigates the metagenomic profile of gut microbiota in children during cholera and recovery. This article gives an important insight into the possibility of post-cholera intervention to promote the restoration of the gut environment. Another interesting research article in this series explores the differences in gut microbiota composition between obese and lean children. This may lead to the development of new approaches to managing childhood obesity and associated disorders.

These new article collections are currently open for submissions on all aspects of probiotic research and metagenomic analysis of gut microbes. For more information on submitting to these article series, please visit the journal website or contact

Jennifer Franklin
Journal Development Editor

Prospective genomics in epidemics – lessons from the German E. coli outbreak

July 23, 2011 Leave a comment

The Open Access biomedical journal, PLoS ONE  recently published an article by Mellmann et al. entitled, Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. The following is an opinion piece by Dr. Niyaz Ahmed, who works as a section editor for PLoS ONE and the academic editor of this paper. He is an expert in the area of molecular epidemiology and genomics of bacterial pathogens at the University of Hyderabad, India. As the subject of this blog is also of significant interest to the audience of Gut Pathogens, we are reproducing Dr Ahmed’s blog post hereunder [with thanks to PLoS ONE community blog, EveryONE) where the blog was originally posted.

When a monstrously virulent strain of never-before-seen E. coli suddenly appeared in Germany last month, the rush to decode became an immediate focus. Several groups became engaged simultaneously to crack the genome of the underlying bug and then followed a huge crowd-sourcing effort on the internet as soon as the genome sequences were made available. Given that reasonable data were made available by these authors within 60 hours of the outbreak, not much of the evolutionary history of the organism had been dissected and a great deal of the interpretation remained vague. An informed, scientific treatise was needed to help health control authorities and policy makers launch a serious mitigation campaign; this work, in that sense, constitutes the first official report on the genomic footprint of the underlying E. coli strain. The authors report chronological (step-wise) recombination of the genome in the outbreak strains over a period of ten years. This reveals the extraordinary capability of certain pathogens to recombine so that a devastating phenotype finally emerges with a multi-dimensional fitness advantage. Further, the study of Mellmann et al. demonstrates the might of present-day sequencing technologies such as Ion Torrent in enabling genome-guided epidemiology, diagnostics, and interventions.

I have no hesitation to say that the study carried out by Mellmann et al. is truly a technical masterpiece, a first time proof-of-principle, whereby, next generation sequencing could be harnessed in real-time when certain ‘gold standards’ such as serotyping failed miserably. This report has an important bearing on the new proposed field of ‘epidemic forecasting’ in which the spread potentials of a pathogen could be predicted based on genomic fingerprints – in other words, predicting if the infection will assume pandemic proportions.  The finding that the E. coli strains analyzed were enteroaggregative (EAEC) could explain this. EAECs could persist in recovered or subclinical cases and that they could be carried by the latter on travel routes worldwide.

One of the possible shortcomings of the study could be that it is silent on the mechanistic details of ‘adornment’ of these bacteria with several layers of fitness – multiple antibiotic resistance, acid tolerance, enteroaggregative capacity and shigatoxin production all bundled up in one ‘naturally’ chimeric strain in just 10 years is extremely dramatic!  The pace of evolution of the German outbreak strains has surpassed even Helicobacter pylori, an organism notorious for its speed of recombination, recasting its entire genome every forty years. We recently had an opportunity to sequence and look at H. pylori genomes hierarchically obtained across ten years. We did not find major insertion, deletion and substitution events.

Technology helped with the dissection of the E. coli epidemic in hours and days, but the editorial process also was seamless and prompt enough to enable rapid dissemination of results. Open and early access is very important for the dissemination of findings during epidemic times because much of the control and mitigation measures need planning in the light of latest research findings.