Name: Dr Niyaz Ahmed, PhD

My Area of Interest: Pathogen Genomics and Evolution

My Favourite Quote: Invention is the talent of youth, and judgment of age

I am a: Staff Scientist and Group Leader at CDFD, Hyderabad

Short Profile:

I obtained a Graduate Degree in Veterinary Medicine in 1995 (Nagpur) with Post Graduate Degrees in Animal Biotechnology (MS) (NDRI, Karnal) and Molecular Medicine (PhD) (CDFD/Manipal University). My doctoral research was conducted under the supervision of Prof Seyed E. Hasnain, presently Vice-Chancellor of the University of Hyderabad. I joined CDFD in 1998 as a Staff Scientist and was promoted as an independent Group Leader in 2003. Having a research experience of 10 years in microbial biology and genomics, I have authored 75 research papers and reviews in high impact national and international journals. I am currently leading the Pathogen Evolution Lab at the CDFD (a premier institute of enquiry and learning in modern biology, funded by the Federal Government of India), Hyderabad. Research in my laboratory is aimed at understanding molecular genetic mechanisms underlying evolution of fitness and virulence in pathogenic bacteria such as Helicobacters, Mycobacteria and Spirochetes. I have been working on several important research projects funded by national and international agencies such as the DBT, ICMR, WHO-TDR, ISID, INSERM, Research Council of Norway (GLOBVAC) etc.
In my professional pursuits while I was fortunate to be elected as the General Secretary of the International Society for Genomic and Evolutionary Microbiology (http://www.isogem.org), an International learned body, currently headquartered at Sassari, Italy, I was also elected as member of the National Academy of Sciences of India and Corresponding Fellow of the European Helicobcter Study Group (EHSG) (http://www.helicobacter.org). I have been involved with the shaping of PLoS ONE, the flagship journal of the Public Library of Science, USA (http://www.plosone.org) and currently serve as its Section Editor (Microbiology and Genomics). Besides, I am also the Associate Editor of i) Annals of Clinical Microbiology and Antimicrobials ii) Infectious Agents and Cancer and iii) Acta Veterinaria Scandinavica.
I am an ardent supporter of post publication review and thus serve as the Member of the Faculty of 1000 Biology (http://www.f1000biology.com), the next-generation literature evaluation and awareness service for biology/medicine run by the world’s most distinguished faculty of over 2400 biomedical leaders (Medicine Reports Ltd.).
Also, in my free time I am involved with ‘Open Access’ advocacy and I have a related blog at http://niyazahmed.blogspot.com
My website is at http://www.isogem.org/niyaz.html

Question and Answers :

What are your future goals? Where do you see your research going?:
In my decade long (1998-2008) study of bacterial genome fluidity, many interesting questions have popped up and we intend to address these in the near future, including: 1) how is bacterial genome fluidity regulated; 2) what environmental stimuli are responsible for this fluidity; 3) what is the in vivo relevance of bacterial genome fluidity; and 4) how can bacterial genome fluidity be exploited for the generation and selection of optimally adapted microorganisms? Answering these questions will not only increase our knowledge of the mechanisms that are involved in the evolution and adaptation of bacterial pathogens, but will also have an impact on the development of accurate diagnostics and timely therapeutic interventions against infectious diseases. As the magnitude of bacterial genome fluidity becomes clear, the key research goals are evident: first, the exploitation of these data to design, improve and adapt appropriate diagnostics; second, the expansion of our knowledge of the underlying biology of each pathogen; and, finally, the exploitation of bacterial genome dynamics to develop new approaches to combat infectious diseases.
Nonetheless, the essence of the story until now is that we are heading fast to achieve a unified model of pathogen adaptation and spread that integrates three important factors, namely, 1) the evolution of bacterial virulence apparatuses, 2) environmental forces that shape bacterial population structure and the 3) host genetic background.
Such a unified approach to understand bacterial pathogenesis is a must to timely gauge emergence of pathogens, geographical patterns of pathogen prevalence and dissemination dynamics. Accordingly, metrics for ‘epidemic forecasting’ can be developed for planning control strategies.

Technologies seem to changing faster than ever, how do you adapt to that? What are the current technologies you are using?:
We believe that ‘technological leaps immediately benefit the prepared mind’. This is what has happened in our case. Our research on pathogen biology traditionally involved a lot of bacterial strain typing that began initially from PCR based identification (Ahmed et al., 1998. J Clin Microbiol. 36: 3094-309) to RAPDs (Prouzet-Mauleon et al., 2005. J Clin Microbiol 43:4237-4241) and to FAFLP ((Ahmed N et al., 2003. Infection Genet Evolution 2:193-199; Cousins DV et al., 2004. Int J Syst Evol Microbiol. 53: 1305-1314); it further metamorphosed to high throughput FAFLP (Ahmed N et al., 2004. J Clin Microbiol. 42:3240-3247) also in combination with spoligotyping and fluorescent VNTR analyses (Gutierrez et al., 2006. Emerging Infectious Dis 12: 367-374). Genome sequence based population structure decipherment in our laboratory evolved through MLST (Ahmed N et al., 2008. Nature Rev Microbiol. 6:387-94; Devi SM et al., 2006. BMC Genomics 7:191; Devi SM et al., 2007. BMC Genomics 8:184) and pan island sequencing (Alvi et al., 2007. J Clin Microbiol. 45:4039-4043) to whole genome Microarrays (Alvi et al., 2008 unpublished). Finally, we have recently completed whole genome sequencing of Mycobacterium indicus pranii (formerly, Mycobacterium w) (Ahmed N et al., 2007. PLoS ONE 2: e968; Saini et al., 2008 unpublished) up to 10X and are looking forward to harnessing the power of metagenomics and systems biology in the context of 1) environmental and pathogenic mycobacteria and 2) human and animal gut microflora and their role in health and disease.
So, ultimately, as experience with multi-scale integrative techniques grows, we hope to identify generic techniques that lead to novel and efficient means of controlling the global diseases such as tuberculosis and enteric infections.

In the broader picture, where do you see the application for your cutting-edge research?:
We foresee direct application of our efforts in the healthcare arena - from bench to the clinics! (Ahmed N et al., 2008. Nature Rev Microbiol. 6:387-94).
The increasing availability of DNA-sequence information for multiple pathogenic and non-pathogenic variants of individual bacterial species has indicated that both DNA acquisition and genome reduction have important roles in genome evolution. Such genomic fluidity, which is found in human pathogens such as Escherichia coli, Helicobacter pylori and Mycobacterium tuberculosis, has important consequences for the clinical management of the diseases that are caused by these pathogens and for the development of diagnostics and new molecular epidemiological methods.
For example, timely diagnosis is a must in case of Leptospirosis; symptoms resemble to those of common cold and patient dies due to multi-organ failure within four days! So the time for complacency is very short. Our comparative genomics (Victoria et al., PLoS ONE 3(7):e2752 and Ahmed et al., Annals Clinical Microbiol Antimicrobials 5:28) in such a scenario holds tremendous field implications, particularly towards diagnostic development and epidemiology.
Several new diagnostic targets for tuberculosis, both molecular and antigens, from our research efforts are already being commercialized. Our new findings based on Type 1 diabetes caused by intracellular mycobacteria (Sechi et al., 2008. Clin Infect Dis 46:148-149; Sechi et al., 2008. Clin Vaccine Immunol. 15:320-326) hold huge clinical application in diabetes treatment and control besides bolstering the knowhow on microbial triggers in diabetes.
Our efforts on understanding H. pylori virulence (Rizwan et al., J Bacteriology 190:1146-1151) and chronological evolution (Devi SM et al.,2006. BMC Genomics 7:191; Devi SM et al., 2007. BMC Genomics 8:184) are likely to unravel mechanistic insights into the role of this pathogen in gastric carcinoma. There is an unprecedented opportunity towards clinical application of this research (Hussain et al., PLoS ONE 3:e1481).

Fast forward to 2020. What’s your vision of Genomics in 2020?:
My vision for genomics in 2020 is optimistic - complete transformation of human and microbial genomics into metagenomics at the supra-organismal level in parallel with molecular biology’s traversal to molecular systems biology and supra-organismal metabolomics! This sounds mammoth, but it is imminent.
At that level of biological knowledge explosion, ten years from now, I will expect as a pathobiologist to have in hand the integrative tools for determining molecular basis of persistence of most pathogens, for which the scientists have struggled for decades.
In disease control arena, both biological experiments and modelling efforts have been successful at deciphering the properties of a disease at any particular level, but a full understanding requires the integration of ALL scales. This is a major challenge for genomics and systems biology as they stand today. In about a decade from now, this challenge will be likely overcome by novel, biologically inspired, computing architectures and paradigms (”building blocks of next century of computing”). This will likely precede the development of Abstract Machines / codification concepts and tool evolution to enable predictive modelling from molecular to population biology levels (e.g. metagenomics, species biodiversity, epidemiological level) including non-local interactions with climate and intervention data. If achieved, such an excellence in genomics besides revolutionizing human disease control will also be hugely impacting the cause of understanding complex biological systems, from cells and organisms to ecosystems.