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Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species

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Abstract

The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.

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Acknowledgements

We would like to thank Dr. Archana Pant for critical reading of our article and constructive suggestions. Authors acknowledge Ms. Sonali Porey and Dr. Shakti Kumar for technical assistance. We thank all the staff of GARBH-Ini cohort including research physicians, study nurses, clinical and laboratory technicians, field workers, internal quality improvement team, project team, and the data management team. We are grateful to Prof. M.K. Bhan, Prof. H.P.S. Sachdev, Prof. R.M. Pandey, and other members of the Steering Committee for their scientific and technical inputs. We specifically thank S. Sinha and Dr. A. Gambhir from the Department of Biotechnology, Government of India, for their generous support. We acknowledge the supports of administrative staff of all participating institutes, particularly V. Krishnamoorthy (Grants Manager, THSTI) and M. Juyal (Technical Officer, Data Management). We wish to extend our thank to the two hospitals (Gurugram Civil Hospital and Safdarjung Hospital) and their staff and the team of expert radiologists (Dr. C. Singh, Dr. G. Sahi, Dr. S.B. Chaudhary, Dr. R. Mishra) for facilitating the study. The work was funded by the Department of Biotechnology, Govt. of India (No.BT/PR9983/MED/97/194/2013) and, for some components of the biorepository, by the Grand Challenges India–All Children Thriving Program, Biotechnology Industry Research Assistance Council (grant BIRAC/GCI/0114/03/14-ACT). Funding agency has no role in study designing, sample collection, analysis, and interpretation of data and writing the manuscript.

MEMBERS OF GARBH-Ini: Translational Health Science and Technology Institute, NCR Biotech Cluster, Faridabad, Delhi NCR, India (Shinjini Bhatnagar, Bhabatosh Das, Nitya Wadhwa, Pallavi S. Kshetrapal, Balakrish G. Balakrish Nair, Uma Chandra Mouli Natchu, Satyajit Rath, Kanika Sachdeva, Shailaja Sopory, Sumit Misra, Amanpreet Singh, Dharmendra Sharma, Ramachandran Thiruvengadam,); National Institute of Biomedical Genomics, Kalyani, West Bengal, India (Arindam Maitra, Partha P. Majumder); Regional Centre for Biotechnology, NCR Biotech Cluster, Faridabad, Delhi NCR, India (Tushar K. Maiti, Dinakar M. Salunke); Clinical Development Services Agency, Translational Health Science and Technology Institute, NCR Biotech Cluster, Faridabad, Delhi NCR, India (Monika Bahl); Gurugram Civil Hospital, Haryana, India (Sunita Sharma, Umesh Mehta, Brahmdeep Sindhu); Safdarjung Hospital, New Delhi, India (Sugandha Arya, Rekha Bharti, Harish Chellani, Pratima Mittal); Maulana Azad Medical College, New Delhi, India (Siddarth Ramji, Reva Tripathi, Anju Garg); The Ultrasound Lab, Defense Colony, New Delhi, India (Ashok Khurana); Hamdard Institute of Medical Sciences and Research, Jamia Hamdard University, New Delhi, India (Reva Tripathi); All India Institute of Medical Sciences, New Delhi, India (Smriti Hari, Yashdeep Gupta, Nikhil Tandon); Government of Haryana, India (Rakesh Gupta); International Centre for Genetic Engineering and Biotechnology, New Delhi, India (Dinakar M. Salunke); and Indian Institute of Science Education and Research, Pune, Maharashtra, India (Vineeta Bal).

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Author notes

  1. Tarini Shankar Ghosh

    Present address: APC Microbiome Ireland, University College Cork, Cork, Ireland

  2. Ojasvi Mehta and Tarini Shankar Ghosh contributed equally to this work.

Authors and Affiliations

  1. Molecular Genetics Laboratory, Translational Health Science and Technology Institute|, NCR Biotech Science Cluster, 3rd Milestone, Faridabad – Gurgaon Expressway, PO box #04, Faridabad, Haryana, 121001, India

    Ojasvi Mehta, Tarini Shankar Ghosh, Akansha Kothidar, M. Rama Gowtham, Ridhima Mitra, G. Balakrish Nair & Bhabatosh Das

  2. Pediatric Biology Center, Translational Health Science and Technology institute, NCR Biotech Science Cluster, Faridabad, India

    Pallavi Kshetrapal, Nitya Wadhwa, Ramachandran Thiruvengadam & Shinjini Bhatnagar

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  1. Ojasvi Mehta
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Consortia

GARBH-Ini study group

  • Shinjini Bhatnagar
  • , Bhabatosh Das
  • , Nitya Wadhwa
  • , Pallavi S. Kshetrapal
  • , Balakrish G. Balakrish Nair
  • , Uma Chandra Mouli Natchu
  • , Satyajit Rath
  • , Kanika Sachdeva
  • , Shailaja Sopory
  • , Sumit Misra
  • , Amanpreet Singh
  • , Dharmendra Sharma
  • , Ramachandran Thiruvengadam
  • , Arindam Maitra
  • , Partha P. Majumder
  • , Tushar K. Maiti
  • , Dinakar M. Salunke
  • , Monika Bahl
  • , Sunita Sharma
  • , Umesh Mehta
  • , Brahmdeep Sindhu
  • , Sugandha Arya
  • , Rekha Bharti
  • , Harish Chellani
  • , Pratima Mittal
  • , Siddarth Ramji
  • , Reva Tripathi
  • , Anju Garg
  • , Ashok Khurana
  • , Smriti Hari
  • , Yashdeep Gupta
  • , Nikhil Tandon
  • , Rakesh Gupta
  •  & Vineeta Bal

Contributions

BD, SB, and GBN conceived the idea and designed the experiments. Members of GARBH-Ini cohort collected HVS samples. OM, TSG, RG, RM, and AK performed experiments. BD, SB, PK, RT, and NW contributed reagents. BD, TSG, OM, and SB did data analysis. BD wrote the manuscript. All authors have read and approved the manuscript.

Corresponding author

Correspondence to Bhabatosh Das.

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All authors declare that they have no competing interests.

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Mehta, O., Ghosh, T.S., Kothidar, A. et al. Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species. Microb Ecol 80, 487–499 (2020). https://doi.org/10.1007/s00248-020-01501-0

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