Sandeep Kumar
Research Associate in the Rumen Microbiology Group of Professor
Devki Nandan Kamra at the Indian Veterinary Research Institute in
Bareilly
Sandeep was in New Zealand on a 6-month LEARN work trainee award from
September 2011 to March 2012.
Sandeep worked alongside Dr Peter Janssen and Dr Gemma Henderson;
Animal Nutrition and Health at AgResearch, Grasslands.
Sandeep’s research at the Indian Veterinary Research Institute considers the
effects of feed additives on ruminant methane emissions and rumen
microbial diversity of domesticated and wild ruminants. The overall goal of his
research is to gain a better understanding of livestock methane emissions
and so be able to mitigate these whilst simultaneously improving livestock
productivity.
The aim of the LEARN project was to test the development of a sequence
analysis pipeline. Sandeep defined ground rules to help establish and
underpin nomenclatural schemes that are suitable for rumen bacteria. He
then tested these rules on pyrosequencing datasets.
Results:
16S rRNA sequences in two test groups of bacteria were checked for chimera
and realigned. A 97% percent sequence similarity cut-off was confirmed as a
ground rule to classify sequences into “species” operational taxonomic units
(or OTUs). A 93% percent sequence similarity cut-off was confirmed as a
ground rule to classify sequences into “genus” OTUs.
Sandeep analysed a number of pyrosequencing datasets using this revised
and more detailed clustering. It worked very well in that phylogenetic
assignment was much improved, i.e. instead of sequencing data previously
only being classified at the genus level, sequences could be assigned to the
species level.
Benefits of improved next generation sequencing pipeline:
Identification of dominant OTU’s in rumen samples has helped other projects
in the rumen microbiology team. For example, Butyrivibrio species that are of
greater importance in the rumen ecological system have been selected for
further study to better understand their roles in fibre degradation. The means
of improving taxonomic resolution that Sandeep has tested can now be
applied to the recently funded Global Research Alliance taxonomy project
and will contribute to the general understanding of rumen microbiology and
therefore also to understanding issues such as methane mitigation
General comments:
Sandeep’s research has been very valuable for all parties involved. We
gained an extra set of hands to add value to our work on methane
mitigation. Sandeep learned many new techniques that he can apply in
future. He also attended the New Zealand Microbiological Society
Conference and presented a poster.
Outputs:
Sandeep Kumar, Neeta Agarwal, Deepak Kumar, L.C. Chaudhary & D.N.
Kamra. 2011. Methanogen archaeal diversity in chinkara (Gazella gazella)
feces. 56th Annual Meeting of the New Zealand Microbiological Society, 23rd –
25th November, Palmerston North, New Zealand – poster. Conference
attendance sponsored by LEARN Award.
Sandeep Kumar. 2012. IMPROVED SEQUENCE ANALYSIS PIPELINE FOR
BUTYRIVIBRIO AND LESSONS FOR OTHER BACTERIAL GROUPS. Presentation
given at the Rumen Microbiology Team Seminar, 8th February 2012.