ORIGINAL RESEARCH article
Front. Water
Sec. Environmental Water Quality
Volume 7 - 2025 | doi: 10.3389/frwa.2025.1589330
This article is part of the Research TopicMicrobial Source Tracking (MST) tools to identify the origins of fecal pollution in environmental water resources and the impact of microbial contaminants on human healthView all 3 articles
Application of 16S rDNA metagenomic library for source-tracking of fecal pollution in selected stations and tributaries of Manila Bay, Philippines
Provisionally accepted
Laurice Beatrice Raphaelle O. dela Pena
Diana Rose D. Mamawal
Mae Ashley G. Nacario
Mark Raymond A. Vejano
Windell L. Rivera*- University of the Philippines Diliman, Quezon City, Philippines
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Fecal contamination of important water resources poses a significant public health concern. To protect the public's health, the dominant sources and various factors that contribute to pathogenesis and fecal contamination must be assessed. This study aimed to assess the effectiveness of 16S rRNA gene amplicon sequencing in detecting pathogens and tracking their sources in Manila Bay, Philippines. We sequenced the 16S V3-V4 region from DNA extracts of fecal samples (n = 37) of chickens, ducks, pigs, cows, goats, dogs, and sewage; and environmental water sources (n = 55) from Manila Bay tributary rivers, coastal stations, and offshore sites, which represented the "source" and "sink" samples, respectively. We used SourceTracker2 to estimate the percent contribution of these sources to the microbial community in Manila Bay. Among the detected bacteria were human and animal pathogens, including Clostridiales, Alteromonadales, Campylobacterales, Pseudomonadales, and Aeromonadales. Phosphates, fecal coliform, and dissolved oxygen were the major drivers of the top bacterial groups. Microbial community signatures clustered according to their corresponding sample types based on the beta diversity distances, suggesting the potential application of source libraries for analyzing the sink samples. Validation of the fecal source library shows that SourceTracker2 correctly predicted the contribution of the six fecal sources, but had a lower distinction for bovine sources. Sewage accounted for 93% of the contamination in Manila Bay, followed by ducks (5.6%), indicating human waste as the primary source. This study demonstrates the utility of microbial source tracking in targeted water quality management strategies.
Keywords: Manila Bay, Metagenomics, pathogen, 16S rDNA, SourceTracker
Received: 07 Mar 2025; Accepted: 02 Jun 2025.
Copyright: © 2025 dela Pena, Mamawal, Nacario, Vejano and Rivera. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Windell L. Rivera, University of the Philippines Diliman, Quezon City, Philippines
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