Teachers’ day group photo with our Masters batches of 2015 and 2016

September 8, 2016 Leave a comment

img_20160906_174050

Categories: Dr Niyaz Ahmed

Two new publications from our lab

September 8, 2016 Leave a comment

Sit back, relax and read them. Do send us your suggestions and comments  🙂

1) Molecular epidemiology and genome dynamics of New Delhi metallo-beta-lactamase (NDM) producing extraintestinal pathogenic E. coli (ExPEC) strains from India.

Ranjan A, Shaik S, Mondal A, Nandanwar N, Hussain A, Semmler T, Kumar N, Tiwari S, Jadhav S, Wieler LH, Ahmed N.

Antimicrob Agents Chemother. 2016 Sep 6. pii: AAC.01345-16. [Epub ahead of print]

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2) Multipronged regulatory functions of a novel endonuclease (TieA) from Helicobacter pylori.

Devi S, Ansari SA, Tenguria S, Kumar N, Ahmed N.

Nucleic Acids Res. 2016 Aug 22. pii: gkw730. [Epub ahead of print]

Categories: Dr Niyaz Ahmed

New articles added to PLOS Prokaryotic Genome Collection

July 5, 2016 Leave a comment
The PLOS Prokaryotic Genome Collection (http://collections.plos.org/prokaryotic-genome) has been updated with the addition of the following articles.  We hope to also bring out a hard bound, updated edition of the collection very soon.

 

Research Articles

 

Complete Genomes of <i>Bacillus coagulans</i> S-lac and <i>Bacillus subtilis</i> TO-A JPC, Two Phylogenetically Distinct Probiotics

Credit:10.1371/journal.pone.0001358
Indu Khatri, Shailza Sharma, T. N. C. Ramya, Srikrishna Subramanian
PLOS ONE   03 Jun 2016
Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology

Credit:10.1371/journal.pone.0155459
Sabiha Shaik, Narender Kumar, Aditya K. Lankapalli, Sumeet K. Tiwari, Ramani Baddam, Niyaz Ahmed
PLOS ONE  01 Jun 2016
TGS-TB: Total Genotyping Solution for <i>Mycobacterium tuberculosis</i> Using Short-Read Whole-Genome Sequencing

Credit:10.1371/journal.pone.0142951
Tsuyoshi Sekizuka, Akifumi Yamashita, Yoshiro Murase, Tomotada Iwamoto, Satoshi Mitarai, Seiya Kato, Makoto K…
PLOS ONE  13 Nov 2015
Genomic Pathogen Typing Using Solid-State Nanopores

Credit:10.1371/journal.pone.0142944
Allison H. Squires, Evrim Atas, Amit Meller
PLOS ONE  12 Nov 2015
Comparative Analysis of Super-Shedder Strains of <i>Escherichia coli</i> O157:H7 Reveals Distinctive Genomic Features and a Strongly Aggregative Adherent Phenotype on Bovine Rectoanal Junction Squamous Epithelial Cells

Credit:10.1371/journal.pone.0116743
Rebecca Cote, Robab Katani, Matthew R. Moreau, Indira T. Kudva, Terrance M. Arthur, Chitrita DebRoy, Michael M. Mw…
PLOS ONE  09 Feb 2015
The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

Credit:10.1371/journal.pone.0097279
Laurens Kraal, Sahar Abubucker, Karthik Kota, Michael A. Fischbach, Makedonka Mitreva
PLOS ONE  14 May 2014
<i>Helicobacter pylori</i> Genomic Microevolution during Naturally Occurring Transmission between Adults

Credit:10.1371/journal.pone.0082187
Bodo Linz, Helen M. Windsor, John P. Gajewski, Caylie M. Hake, Daniela I. Drautz, Stephan C. Schuster, Barry J. Mar…
PLOS ONE  10 Dec 2013
Categories: Dr Niyaz Ahmed

Gut Pathogens has a new enhanced IF of 2.816!

June 21, 2016 Leave a comment

Gut Pathogens’ new IF  (2.816 in 2016) is now well ahead of other BMC journals such as BMC Infectious Diseases, BMC Microbiology, BMC Public Health, BMC Gastroenterology and BMC Cancer to name a few. Lets see how it helps us in getting more high quality submissions.

Articles published by Gut Pathogens in 2015

January 1, 2016 Leave a comment

 

Lactobacilli with probiotic potential in the prairie vole (Microtus ochrogaster)

Senait Assefa, Kathleen Ahles, Simone Bigelow, J. Thomas Curtis and Gerwald A. Köhler

Gut Pathogens 2015 7:35   (Published on: 30 December 2015)

Comparison of a novel chemiluminescent based algorithm to three algorithmic approaches for the laboratory diagnosis of Clostridium difficile infection

Goret, J. Blanchi, C. Eckert, S. Lacome, A. Petit, F. Barbut, C. Bébéar and Francis Mégraud

Gut Pathogens 2015 7:33     (Published on: 23 December 2015)

Non-Typhoidal Salmonella in poultry meat and diarrhoeic patients: prevalence, antibiogram, virulotyping, molecular detection and sequencing of class I integrons in multidrug resistant strains

Rasha M. Gharieb, Yasmine H. Tartor and Mariam H. E. Khedr

Gut Pathogens 2015 7:34      (Published on: 23 December 2015)

Development of gut inflammation in mice colonized with mucosa-associated bacteria from patients with ulcerative colitis

Zhengyu Du, Tomas Hudcovic, Jakub Mrazek, Hana Kozakova, Dagmar Srutkova, Martin Schwarzer, Helena Tlaskalova-Hogenova, Martin Kostovcik and Miloslav Kverka

Gut Pathogens 2015 7:32       (Published on: 21 December 2015)

Core 2 mucin-type O-glycan inhibits EPEC or EHEC O157:H7 invasion into HT-29 epithelial cells

Jun Ye, Qiong Pan, Yangyang Shang, Xiaolong Wei, Zhihong Peng, Wensheng Chen, Lei Chen and Rongquan Wang

Gut Pathogens 2015 7:31            (Published on: 15 December 2015)

Description of Campylobacter jejuni Bf, an atypical aero-tolerant strain

Ramila Cristiane Rodrigues, Anne-Lise Pocheron, Mathieu Hernould, Nabila Haddad, Odile Tresse and Jean-Michel Cappelier

Gut Pathogens 2015 7:30        (Published on: 19 November 2015)

Animal models to study acute and chronic intestinal inflammation in mammals

Janelle A. Jiminez, Trina C. Uwiera, G. Douglas Inglis and Richard R. E. Uwiera

Gut Pathogens 2015 7:29          (Published on: 10 November 2015)

Survey of small intestinal and systemic immune responses following murineArcobacter butzleri infection

Markus M. Heimesaat, Gül Karadas, Marie Alutis, André Fischer, Anja A. Kühl, Angele Breithaupt, Ulf B. Göbel, Thomas Alter, Stefan Bereswill and Greta Gölz

Gut Pathogens 2015 7:28       Published on: 19 October 2015

Streptococcus bovis infectious endocarditis and occult gastrointestinal neoplasia: experience with 25 consecutive patients treated surgically

Anthony Alozie, Kerstin Köller, Lumi Pose, Maximilian Raftis, Gustav Steinhoff, Bernd Westphal, Georg Lamprecht and Andreas Podbielski

Gut Pathogens 2015 7:27        (Published on: 15 October 2015)

Helicobacter pylori virulence genes in the five largest islands of Indonesia

Muhammad Miftahussurur, Ari Fahrial Syam, Dadang Makmun, Iswan Abbas Nusi, Lukman Hakim Zein, Zulkhairi, Fardah Akil, Willi Brodus Uswan, David Simanjuntak, Tomohisa Uchida, Pangestu Adi, Amanda Pitarini Utari, Yudith Annisa Ayu Rezkitha, Phawinee Subsomwong, Nasronudin and Yoshio Yamaoka

Gut Pathogens 2015 7:26         (Published on: 5 October 2015)

Specific detection of OCT4 isoforms in inflammatory bowel disease

Maria Maragkoudaki, Anna Vaiopoulou, George E. Theodoropoulos, Evangelia Legaki, Leonardo A. Sechi, George Karamanolis, George Zografos and Maria Gazouli

Gut Pathogens 2015 7:25          (Published on: 1 October 2015)

The O-antigen negative ∆wbaV mutant of Salmonella enterica serovar Enteritidis shows adaptive resistance to antimicrobial peptides and elicits colitis in streptomycin pretreated mouse model

Sangeeta Jaiswal, Niladri Bhusan Pati, Manupriyam Dubey, Chandrashekhar Padhi, Prakash Kumar Sahoo, Shilpa Ray, Aryashree Arunima, Nirmal Kumar Mohakud and Mrutyunjay Suar

Gut Pathogens 2015 7:24          (Published on: 3 September 2015)

High dietary zinc supplementation increases the occurrence of tetracycline and sulfonamide resistance genes in the intestine of weaned pigs

Wilfried Vahjen, Dominika Pietruszyńska, Ingo C. Starke and Jürgen Zentek

Gut Pathogens 2015 7:23            (Published on: 26 August 2015)

Interaction of caffeine with the SOS response pathway in Escherichia coli

Alyssa K Whitney and Tiffany L Weir

Gut Pathogens 2015 7:21               (Published on: 18 August 2015)

Genome architecture of Lactobacillus plantarum PS128, a probiotic strain with potential immunomodulatory activity

Wei-Hsien Liu, Chih-Hsien Yang, Ching-Ting Lin, Shiao-Wen Li, Wei-Shen Cheng, Yi-Ping Jiang, Chien-Chen Wu, Chuan-Hsiung Chang and Ying-Chieh Tsai

Gut Pathogens 2015 7:22

Characterization of the cytolethal distending toxin (typhoid toxin) in non-typhoidal Salmonella serovars

Lorraine D Rodriguez-Rivera, Barbara M Bowen, Henk C den Bakker, Gerald E Duhamel and Martin Wiedmann

Gut Pathogens 2015 7:19    (Published on: 24 July 2015)

Virulence characteristics of hcp + Campylobacter jejuni and Campylobacter coliisolates from retail chicken

Nicolae Corcionivoschi, Ozan Gundogdu, Lynn Moran, Carmel Kelly, Pam Scates, Lavinia Stef, Ada Cean, Brendan Wren, Nick Dorrell and Robert H Madden

Gut Pathogens 2015 7:20    (Published on: 24 July 2015)

Presumable role of outer membrane proteins of Salmonella containing sialylated lipopolysaccharides serovar Ngozi, sv. Isaszeg and subspeciesarizonae in determining susceptibility to human serum

Bożena Futoma-Kołoch, Urszula Godlewska, Katarzyna Guz-Regner, Agata Dorotkiewicz-Jach, Elżbieta Klausa, Jacek Rybka and Gabriela Bugla-Płoskońska

Gut Pathogens 2015 7:18    (Published on: 16 July 2015)

Pathotypes and probiotics: response to a commentary on the detection of a Shiga toxin producing Escherichia coli in a Crohn’s disease patient

Josias Rodrigues

Gut Pathogens 2015 7:17      (Published on: 11 July 2015)

First description of plasmid-mediated quinolone resistance determinants and β-lactamase encoding genes in non-typhoidal Salmonella isolated from humans, one companion animal and food in Romania

Liora Colobatiu, Alexandra Tabaran, Mirela Flonta, Ovidiu Oniga, Simona Mirel and Marian Mihaiu

Gut Pathogens 2015 7:16     (Published on: 26 June 2015)

The prediction of virulence based on presence of virulence genes in E. coli may not always be accurate

Trudy M Wassenaar and Florian Gunzer

Gut Pathogens 2015 7:15     (Published on: 19 June 2015)

Draft genomes of Shigella strains used by the STOPENTERICS consortium

Omar Rossi, Kate S Baker, Armelle Phalipon, François-Xavier Weill, Francesco Citiulo, Philippe Sansonetti, Christiane Gerke and Nicholas R Thomson

Gut Pathogens 2015 7:14    (Published on: 4 June 2015)

Genome sequences of the Shiga-like toxin-producing Escherichia coliNCCP15655 and NCCP15656

Min-Jung Kwak, Soon-Kyeong Kwon, Seung-Hak Cho and Jihyun F Kim

Gut Pathogens 2015 7:13    (Published on: 12 May 2015)

Presence and significance of Helicobacter spp. in the gastric mucosa of Portuguese dogs

Irina Amorim, Annemieke Smet, Odete Alves, Silvia Teixeira, Ana Laura Saraiva, Marian Taulescu, Celso Reis, Freddy Haesebrouck and Fátima Gärtner

Gut Pathogens 2015 7:12    (Published on: 16 April 2015)

Oxygen limitation induces acid tolerance and impacts simulated gastro-intestinal transit in Listeria monocytogenes J0161

Danny Sewell, Stuart CH Allen and Carol A Phillips

Gut Pathogens 2015 7:11     (Published on: 10 April 2015)

Draft genomes of four enterotoxigenic Escherichia coli (ETEC) clinical isolates from China and Bangladesh

Fei Liu, Xi Yang, Zhiyun Wang, Matilda Nicklasson, Firdausi Qadri, Yong Yi, Yuying Zhu, Na Lv, Jing Li, Ruifen Zhang, Huijuan Guo, Baoli Zhu, Åsa Sjöling and Yongfei Hu

Gut Pathogens 2015 7:10     (Published on: 8 April 2015)

Association of Intact dupA (dupA1) rather than dupA1 cluster with duodenal ulcer in Indian population

Jawed Alam, Prachetash Ghosh, Mou Ganguly, Avijit Sarkar, Ronita De and Asish K Mukhopadhyay

Gut Pathogens 2015 7:9   (Published on: 28 March 2015)

Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces

SangJoon Mo, Bong-Soo Kim, Sung-Jo Yun, Jung-Ju Lee, Suk-Hyun Yoon and Chung-Hun Oh

Gut Pathogens 2015 7:8    (Published on: 27 March 2015)

The neurotoxic effects of ampicillin-associated gut bacterial imbalances compared to those of orally administered propionic acid in the etiology of persistent autistic features in rat pups: effects of various dietary regimens

Afaf El-Ansary, Ramesa Shafi Bhat, Sooad Al-Daihan and Abeer M Al Dbass

Gut Pathogens 2015 7:7   (Published on: 22 March 2015)

RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response toVibrio parahaemolyticus infection

Rama Rao, Ya Bing Zhu, Tahereh Alinejad, Suma Tiruvayipati, Kwai Lin Thong, Jun Wang and Subha Bhassu

Gut Pathogens 2015 7:6  (Published on: 14 March 2015)

Cocktails of probiotics pre-adapted to multiple stress factors are more robust under simulated gastrointestinal conditions than their parental counterparts and exhibit enhanced antagonistic capabilities against Escherichia coli andStaphylococcus aureus

Moloko Gloria Mathipa and Mapitsi Silvester Thantsha

Gut Pathogens 2015 7:5    (Published on: 26 February 2015)

Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses

Mohd Asrore Mohd Shaufi, Chin Chin Sieo, Chun Wie Chong, Han Ming Gan and Yin Wan Ho

Gut Pathogens 2015 7:4 (Published on: 26 February 2015)

Genotyping and clinical factors in pediatric diarrhea caused by rotaviruses: one-year surveillance in Surabaya, Indonesia

Subijanto Marto Sudarmo, Katsumi Shigemura, Alpha Fardah Athiyyah, Kayo Osawa, Oktavian Prasetia Wardana, Andy Darma, Reza Ranuh, Dadik Raharjo, Soichi Arakawa, Masato Fujisawa and Toshiro Shirakawa

Gut Pathogens 2015 7:3     (Published on: 8 February 2015)

The vesicle-associated function of NOD2 as a link between Crohn’s disease and mycobacterial infection

Alexey A Nabatov

Gut Pathogens 2015 7:1 (Published on: 29 January 2015)

Escherichia coli from Crohn’s disease patient displays virulence features of enteroinvasive (EIEC), enterohemorragic (EHEC), and enteroaggregative (EAEC) pathotypes

Ana Carolina da Silva Santos, Fernando Gomes Romeiro, Ligia Yukie Sassaki and Josias Rodrigues

Gut Pathogens 2015 7:2    (Published on: 29 January 2015)

New publication from Lab: Devi S et al., Scientific Reports 2015; 5:15049 | DOI: 10.1038/srep15049

October 16, 2015 Leave a comment

SREP

Categories: Dr Niyaz Ahmed

Birthday of Yan Berghofer 

September 21, 2015 Leave a comment

We celebrated birthday of our German intern, Mr Jan Berghoefer ….

Categories: Dr Niyaz Ahmed