Manuscripts / Journal Articles
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Anthropogenic disturbance selectively influences the rhizosphere archaeal communities of Sundarban mangroves, India : 2025
Dhruba Bhattacharya , Shayantan Mukherji , Anish Bhattacharyya, Suparna Mitra , Abhrajyoti Ghosh
PMID: 41105276 DOI: 10.1007/s11274-025-04613-2 -
Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts : 2025
Magdalena Kujawska , David Seki , Lisa Chalklen , Jennifer Malsom , Raymond Kiu , Sara Goatcher , Ioulios Christoforou , Suparna Mitra , Lucy Crouch , Lindsay J Hall
PMID: 40934885 DOI: 10.1016/j.chom.2025.08.008 -
Systematic Review: The Relationship Between the Faecal Microbiome and Colorectal Neoplasia in Shotgun Metagenomic Studies : 2025
Sarah Manning , Eleanor Hackney , Yashvee Dunneram , Mark A Hull , Suparna Mitra , Christopher J Stewart , Panayiotis Louca , Nick Meader , Linda Sharp , Colin Rees
Affiliations Expand PMID:
40793873 PMCID: PMC12395896 DOI: 10.1111/apt.7025 -
How Have Massively Parallel Sequencing Technologies Furthered Our Understanding of Oncogenesis and Cancer Progression? : 2025
Diogo Ann Onuselogu , Saskia Benz , Suparna Mitra
Affiliations Expand
PMID: 39546208 DOI: 10.1007/978-1-0716-4192-7_15 -
Long-term stability of the faecal microbiome profile in faecal immunochemical test (FIT) samples : 2024
Suparna Mitra, Christopher J Stewart , Andrew Nelson, James S Hampto, Andrea C Masi, Sarah Manning , Linda Sharp , Mark A Hull , Colin J Rees
Affiliations Expand PMID: 38902030 DOI: 10.1136/gutjnl-2024-332584 -
Gastro Hep Advances. 2023.
Christian Zenner, Lisa Chalklen, Helena Adjei, Matthew J Dalby, Suparna Mitra, Emma Cornwell, Alex Shaw, Kathleen Sim, Simon J. Kroll, Lindsay J. Hall. Faecal cytokine levels of preterm infants coupled with microbiome profiles represent a potential non-invasive method to predict severity of necrotizing enterocolitis. Gastro Hep Advances. 2023. (submitted) -
Gut letter. 2023.
Suparna Mitra∗, Christopher J Stewart, Andrew Nelson, James S Hampton, Andrea C Masi, Sara
Manning, Christopher A Lamb, Linda Sharp, Mark A Hull, Colin J Rees. Long-term stability of
the faecal microbiome profile in immunochemical test (FIT) samples. Gut letter. 2023.
(submitted) -
Colorectal Dis. 2022
James S Hampton, Sara Koo, Christina Dobson, Christopher J Stewart, Laura J Neilson, Kyle
Montague, Suparna Mitra, John Whelpton, Caroline Addison, Phil Kelly, Stephen Rushton, Mark
A Hull, Linda Sharp, Colin J Rees. The COLO-COHORT (Colorectal Cancer Cohort)
study: Protocol for a multi-centre, observational research study and development of
a consent-for-contact research platform. Colorectal Dis. 2022. https://doi.org/10.1111/
codi.16160 -
Cell. Infect. Microbiol. 2021.
Anthony Buckley, Ines B. Moura, Norie Arai, William Spittal, Emma Clark, Yoshihiro Nishida,
Hannah C. Harris, Karen Bentley, Georgina Davis, Dapeng Wang, Suparna Mitra, Takanobu
Higashiyama, Mark H. Wilcox. Trehalose-Induced Remodelling of the Human Microbiota
Affects Clostridioides difficile Infection Outcome in an In Vitro Colonic Model: A Pilot
Study Front. Cell. Infect. Microbiol. 2021. https://doi.org/10.3389/fcimb.2021.670935 -
Journal of Nutrition 2021
Gael Nana, Suparna Mitra, Henry Watson, Caroline Young, Henry M Wood, Sarah L Perry, Amanda
DRace, Philip Quirke, Giles J Toogood, Paul M Loadman, Mark A Hull Luminal Bioavailability of
Orally Administered Ω-3 PUFAs in the Distal Small Intestine, and Associated Changes
to the Ileal Microbiome, in Humans with a Temporary Ileostomy 2021 (Under review). The
Journal of Nutrition 2021. https://doi.org/10.1093/jn/nxab113 -
Rheumatology (Oxford) 2020.
Christopher Rooney, Kulveer Mankia, Suparna Mitra, Ines Moura, Paul Emery, Mark Wilcox,
Perturbations of the gut microbiome in anti-CCP positive individuals at risk of
developing rheumatoid arthritis. Rheumatology (Oxford) 2020. https://doi.org/10.1093/
rheumatology/keaa792 -
Ecotoxicol Environ Saf. 2020.
Shayantan Mukherji, Anandita Ghosh, Chandrima Bhattacharyya, Ivy Mallick, Anish Bhattacharyya,
Suparna Mitra and Abhrajyoti Ghosh. Molecular and culture-based surveys of metabolically
active hydrocarbon-degrading archaeal communities in Sundarban mangrove sediments.
Ecotoxicol Environ Saf. 2020. https://doi.org/10.1016/j.ecoenv.2020.110481 -
Rep Med. 2020.
Cristina Alcon-Giner, Matthew J Dalby, Shabhonam Caim, Jennifer Ketskemety, Alex Shaw, Kathleen
Sim, Melissa A E Lawson, Raymond Kiu, Charlotte Leclaire, Lisa Chalklen, Magdalena Kujawska,
Suparna Mitra, Fahmina Fardus-Reid, Gustav Belteki, Katherine McColl, Jonathan R Swann, J
Simon Kroll, Paul Clarke , Lindsay J Hall. Microbiota supplementation with Bifidobacterium
and Lactobacillus modifies the preterm infant gut microbiota and metabolome: an
observational study Cell Rep Med. 2020. https://doi.org/10.1016/j.xcrm.2020.100077 -
mSystems. 2018,
Gourvendu Saxena§, Suparna Mitra§, Ezequiel Marzinelli, Xie Chao, Toh Jun Wei, Peter D. Steinberg,
Rohan Williams, Staffan Kjelleberg, Federico Lauro and Sanjay Swarup. Metagenomics Reveals
the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway. mSystems. 2018, 5;3(3). pii: e00136-17. https://doi.org/10.1128/mSystems.
00136-17 -
Gut. 2017
Henry Watson§, Suparna Mitra§, Fiona C. Croden, Morag Taylor, Henry M. Wood, Sarah L. Perry,
Jade Spencer, Philip Quirke, Giles J Toogood, Clare L Lawton, Louise Dye, Paul M Loadman, Mark A
Hull. A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements
on the human intestinal microbiota. Gut. 2017, 67(11). https://gut.bmj.com/content/67/
11/1974. -
BMC Genomics. 2017
Cristina Alcon-Giner, Shabhonam Caim, Suparna Mitra, Jennifer Ketskemety, Udo Wegmann, John
Wain, Gusztav Belteki, Paul Clarke, Lindsay J. Hall. Optimisation of 16s rRNA gut microbiota
profiling of extremely low birth weight infants. BMC Genomics. 2017, 18(1):841. https:
//doi.org/10.1186/s12864-017-4229-x. -
Open Forum Infectious Diseases. 2017
Suparna Mitra, Caroline Chilton, Jane Freeman, Henry Wood, Phillip Quirke, Morag Taylor, Richard
J. Vickers, Mark H. Wilcox. Preservation of Gut Microbiome Following Ridinilazole vs.
Fidaxomicin Treatment of Clostridium difficile Infection. Abstract: Open Forum Infectious
Diseases. 2017 :4 (Suppl1). (presented in ID Week Oct’17) -
MyD88-dependent manner. 2017
Kevin R. Hughes, Lukas C. Harnisch, Cristina Alcon-Giner, Suparna Mitra, Christopher J.
Wright, Jennifer Ketskemety, Douwe van Sinderen, Andrew J. M. Watson, Lindsay J. Hall.
Bifidobacterium breve reduces apoptotic epithelial cell shedding in an exopolysaccharide
and MyD88-dependent manner. 2017, https://doi.org/10.1098/rsob.160155. -
Obstet Gynecol Int. 2017
Antonios Anagnostopoulos, Suparna Mitra Bridget Decruze, Robert Macdonald and John Kirwan.
Safety and Cost Considerations during the Introduction Period of Laparoscopic Radical
Hysterectomy. Obstet Gynecol Int. 2017, 2103763 https://doi.org/10.1155/2017/2103763. -
J. Biotechnol 2017
Daniel H Huson, Mike Steel, Mohamed El Hadidi, Suparna Mitra, Silke Peter and Matthias Willmann.
A statistical test for detecting taxonomic or functional inhomogeneity using replicated
metagenomic samples. J. Biotechnol 2017, 250: 45-50. https://doi.org/10.1016/j.jbiotec.
2016.10.020 -
PLoS Comput. Biol. 2016,
Daniel H. Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra,
Hans-Joachim Ruscheweyh, Rewati Tappu. MEGAN Community Edition- Interactive
Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput.
Biol. 2016, 1004957. http://dx.doi.org/10.1371/journal.pcbi.1004957. -
Microbiome. 2015
Suparna Mitra∗, Daniela I. Drauz, Morten Alhede, Liu Yang, Rikki W. Purbojati, Yap Z. Hwee,
Kavita K. Kushwaha, Gorm M. Hansen, Henrik Sillesen, Peter R. Hansen, Liang Yang, Tim
Tolker-Nielsen, Stephan C. Schuster, Michael Givskov. In-silico analyses of atherosclerotic
plaque metagenomic samples from human patients. Microbiome. 2015, 3:38. http:
//www.microbiomejournal.com/content/3/1/38. -
Sundarbans. Archaea. 2015
Anish Bhattacharyya, Niladri S. Majumder, Pijush Basak, Shayantan Mukherji, Debojyoti Roy,
Sudip Nag, Anwesha Haldar, Dhrubajyoti Chattopadhyay, Suparna Mitra∗, Maitree Bhattacharyya
and Abhrajyoti Ghosh. Diversity and distribution of archaea in the mangrove sediment
of Sundarbans. Archaea. 2015, 968582. http://www.hindawi.com/journals/archaea/2015/
968582/ -
Environ. Sci. Technol. 2015
Gourvendu Saxena, Ezequiel M. Marzinelli, Nyi N. Naing, Zhili He, Yuting Liang, Lauren Tom,
Suparna Mitra, Han Ping, Umid M. Joshi, Sheela Reuben, Kalyan C. Mynampati, Shailendra
Mishra, Shivshankar Umashankar, Jizhong Zhou, Gary Andersen, Staffan Kjelleberg and Sanjay
Swarup. Ecogenomics reveals metals and land-use pressures on microbial communities
in the waterways of a megacity. Environ. Sci. Technol. 2015, 49(3), pp:1462-1471. http:
//pubs.acs.org/doi/abs/10.1021/es504531s. -
BioMed Research International. 2014
Antje Damms-Machado, Suparna Mitra, Asja Friedrich, Klaus M. Kramer, Tobias Meile, Alfred
Königsrainer, Daniel H. Huson, Stephan C. Bischoff. Effect of laparoscopic sleeve gastrectomy
versus very low calorie diet on gut microbiota composition and nutrient absorption: a
longitudinal metagenomic and metabolomic study. Translational and Clinical Research in
Surgery, BioMed Research International. 2014, 2015:806248. http://www.hindawi.com/journals/
bmri/2015/806248/ -
Bioresource Technology. 2013
Ravi P. More§, Suparna Mitra§, Sajan C. Raju, Atya Kapley, Hemant J. Purohit. Mining and
assessment of catabolic pathways in the metagenome of a common effluent treatment
plant. Bioresource Technology. 2013, 153:137-146. http://www.sciencedirect.com/science/
article/pii/S0960852413017914 -
BMC Genomics 2013
Suparna Mitra∗,§, Karin Förster-Fromme§, Antje Damms-Machado, Tim Scheurenbrand, Saskia
Biskup, Daniel H. Huson and Stephan C. Bischoff. Analysis of the intestinal microbiota
using SOLiD 16SrRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics
2013,14(Suppl 5):S16. http://www.biomedcentral.com/1471-2164/14/S5/S16 -
Environmental Microbiology Reports 2012
Reema Singh, Vinay Narayan, Patricia McLenachan, Richard C. Winkworth, Suparna Mitra, Peter
J. Lockhart, Lorraine Berry, Abdulla M. Hatha, William Aalbersberg and Dhana Rao. Detection
and diversity of pathogenic Vibrio from Fiji. Environmental Microbiology Reports 2012, 4
(4):403-411. http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2012.00344.x/full. -
BMC Genomics 2011
Suparna Mitra∗, Mario Stärk and Daniel H. Huson. Analysis of 16S rRNA environmental
sequences using MEGAN. BMC Genomics 2011,12(Suppl 3):S17.
http://www.biomedcentral.com/1471-2164/12/S3/S17. -
MEGAN4 Genome Research 2011.
Daniel H. Huson, Suparna Mitra, Hans-Joachim Ruscheweyh, Nico Weber and Stephan C. Schuster.
Integrative analysis of environmental sequences using MEGAN4 Genome Research 2011.
http://genome.cshlp.org/content/21/9/1552.full. -
BMC Bioinformatics 2011
Suparna Mitra∗, Paul Rupek, Daniel C. Richter, Tim Urich, Jack A. Gilbert, Folker Meyer, Andreas
Wilke and Daniel H. Huson. Functional analysis of metagenomes and metatranscriptomes
using SEED and KEGG. BMC Bioinformatics 2011, 12(Suppl 1):S21.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044276/. -
ISME J 2010
Suparna Mitra∗, Jack A. Gilbert, Dawn Field and Daniel H. Huson. Comparison of multiple
metagenomes using phylogenetic networks based on ecological indices. ISME J 2010,
4:1236-1242. http://www.nature.com/ismej/journal/v4/n10/abs/ismej201051a.html. -
BMC Bioinformatics 2010
Suparna Mitra∗, Max Schubach and Daniel H. Huson. Short clones or long clones? A simulation
study on the use of paired reads in metagenomics. BMC Bioinformatics 2010, 11(Suppl 1):S12.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009484/. -
Bioinformatics 2009
Suparna Mitra∗, Bernhard Klar and Daniel H. Huson. Visual and statistical comparison of
metagenomes. Bioinformatics 2009, volume 25 (15):1849-55.
http://bioinformatics.oxfordjournals.org/content/25/15/1849.full. -
BMC Bioinformatics 2009
Daniel H. Huson, Daniel C. Richter, Suparna Mitra, Alexander F. Auch and Stephan C. Schuster.
Methods for comparative metagenomics. BMC Bioinformatics 2009, volume 10 (Suppl 1):S12.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648729/.
