Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate

Umer Zeeshan Ijaz* (Corresponding Author), Ozan Gundogdu, Ciara Keating, Miriam van Eekert, Walter Gibson, Julian Parkhill, Faraji Abilahi, Benard Liseki, Viet-Anh Nguyen, Steven Sugden, Christopher Quince, Jeroen H J Ensink, Belen Torondel, Alan Walker

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Pit latrines are used by billions of people globally, often in developing countries where they provide a low-tech and low-cost sanitation method. However, health and social problems can arise from a lack of emptying or maintenance of these facilities. A better understanding of the biological and environmental parameters within pit latrines could inform attempts to enhance material decomposition rates, and therefore slow fill-up rate. In this study, we have performed a spatial analysis of 35 Tanzanian pit latrines to identify bacteria and environmental factors that are associated with faster or slower pit latrine fill-up rates. Using
ordination of microbial community data, we observed a linear gradient in terms of beta diversity with increasing pit latrine sample depth, corresponding to a shift in microbial community structure from gut-associated families in the top layer to environmental- and wastewater-associated taxa at greater depths. We also investigated the bacteria and environmental parameters associated with fill-up rates, and identified pH, volatile solids, and volatile fatty acids as features strongly positively correlated with pit latrine fill-up rates, whereas phosphate was strongly negatively correlated with fill-up rate. A number of pit latrine microbiota taxa were also correlated with fill-up rates. Using a multivariate regression, we identified the Lactobacillaceae and Incertae_Sedis_XIII taxa as particularly strongly positively and negatively correlated with fill-up rate, respectively. This study therefore increases knowledge of the microbiota within pit latrines, and identifies potentially important bacteria and environmental variables associated with fill-up rates. These new insights may be useful for future studies investigating the decomposition process within pit latrines.
Original languageEnglish
Article number960747
JournalFrontiers in Microbiology
Publication statusPublished - 23 Sept 2022

Bibliographical note

Funding statement
This research received financial support from the Bill and Melinda Gates Foundation (grant number OPP52641 to the London School of Hygiene and Tropical Medicine). AWW and JP were supported by the Wellcome Trust [grant number 098051]. AWW and the Rowett Institute, University of Aberdeen, receive core funding support from the Scottish Government Rural and Environmental Science and In review Analysis Service (RESAS). UZI is funded by NERC Independent Research Fellowship (NE/L011956/1) and further supported by EPSRC (EP/P029329/1 and EP/V030515/1). CQ is funded through an MRC fellowship (MR/M50161X/1) as part of the MRC Cloud Infrastructure for Microbial Bioinformatics consortium (MR/L015080/1).

In review Pit latrine microbiota associated with depth and fill-up rate. We would like to thank all the field and laboratory teams and to all the pit latrine owners who participated in this study. We also thank Paul Scott, Richard Rance and members of the Wellcome Sanger Institute's sequencing team for generating 16S rRNA gene data.


  • sanitation3
  • microbiota4
  • 16S rRNA gene sequencing5
  • Pit latrines
  • decomposition


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