Faecal pollution has always been a major problem and detection of traditional indicator species such as Escherichia coli or species of the genus Enterococci results in closure of coastal beaches to public. As these easily culturable bacteria are present in both animals and humans, even if they are found in water samples, their presence cannot tell us anything about source of faecal pollution. This is a limitation of using E. coli like traditional indicators because we need to efficiently use our finite resources for reducing human health risks; that requires data about the specific sources of faecal pollution. Finding human-specific indicators is important also because human faeces is a major reservoir for human pathogens.
As previous studies have found specific gut microbiota of specific host, which is also dependant on factors like diet; characterization of these host-specific microbes may identify bacteria that can be used as host-specific indicators of faecal pollution. Molecular techniques like terminal restriction fragment length polymorphism, family-specific cloning and sequencing of nearly full-length 16S rRNA gene have been used in many previous studies to identify host-specific phylotypes within the order Bacteroidales for humans, cows, pigs, dogs etc. Similarly, subtractive hybridization and genomic enrichment of the metagenome have been previously used for identifying alternative host-specific indicator microbes including a human-specific species from Bacteroides spp. Apart from Bacteroidales, other taxonomic groups from which alternative host-specific indicator bacterial species have been described include, Bifidobacteriaceae and Lachnospiraceae. Human microbiom project revealed staggering variety and complexity of microbes from the human gut. Though, Bacteroidales and Clostridiales have been reported as among the most abundant faecal anaerobes; there is lot of interrelated variation among these. Thus, identification of the most common and abundant human-specific bacterial indicator species has turned out to be difficult.
The authors of this study examined 38 sewage samples collected over a 4 year period from the city of Milwaukee, Wisconsin USA and 11 other samples collected from different geographic locations of USA to characterize microbial community structure specific to humans. Mainly, a taxonomic group from Clostridiales which is very specific to humans was on focus. Sewage sampling ideally represents a random, composite sampling of several individuals and hence there is no issue of individual variability in indentifying most common human-specific microbes. To understand distribution of Clostridiales species, previously published data sets for human, cattle and chicken, were used.
Majority of Clostridiales from sewage samples and human faecal samples were identified as Lachnospiraceae which were rarely found in the samples of both cattle and chicken. Network analysis revealed that Lachnospiraceae family shared most pyrotags among human faecal and sewage samples which means, members of Lachnospiraceae were mostly originating from humans. Among Lachnospiraceae, the two most abundant species were Roseburia sp and Blautia wexlerae.
Thus, members of Lachnospiraceae can be seen as potential alternative indicators, which could give information about human-specific source of faecal pollution. The criteria for host-specific indicators include their abundance in the host of interest so that sensitivity for their detection is maximised, their almost nonexistence in other hosts making them specific to host of interest and their robustness over a large geographic region. Lachnospiraceae is estimated to make 19% to 50% human faecal microbiota and previous investigation on Lachnospiraceae support the notion of this study that they can be used as alternative indicators. The authors conducted even further molecular analysis and provided evidence of chronic human faecal pollution of surface waters by targeting a gene (Lachno2) from one of the most abundant members of Lachnospiraceae.
The authors have suggested that sewage sampling could be used as a measure of microbial community patterns in the human population linked with age, health and dietary habits. Being high in diversity and abundance, functional roles of members of Lachnospiraceae in human gut have been discussed. In conclusion, they are the most promising candidates of human-specific indicators among Clostridiales. It is unlikely that single host-specific single species would be the most ideal indicator with the necessary sensitivity for quick detection methods. This study proposes effective alternative indicators using highly advanced molecular technologies. The question remains is that how cost-effective these molecular methods would be for practical routine use? This question becomes even more important for developing countries like Bangladesh where problem of faecal pollution would be a big challenge, I guess.
McLellan, S. L., Newton, R. J., Vandewalle, J. L., Shanks, O. C., Huse, S. M., Eren, A. M., & Sogin, M. L. (2013). Sewage reflects the distribution of human faecal Lachnospiraceae. Environmental microbiology, 15(8), 2213-2227.