Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano

Abstract

Bats are highly diverse and ecologically valuable mammals. They serve as host to bacteria, viruses and fungi that are either beneficial or harmful to its colony as well as to other groups of cave organisms. The bacterial diversity of two bat guano samples, C1 and C2, from Cabalyorisa Cave, Mabini, Pangasinan, Philippines were investigated using 16S rRNA gene amplicon sequencing. V3-V4 hypervariable regions were amplified and then sequenced using Illumina MiSeq 250 PE system. Reads were processed using Mothur and QIIME pipelines and assigned 12,345 OTUs for C1 and 5,408 OTUs for C2. The most dominant OTUs in C1 belong to the Proteobacteria (61.7%), Actinobacteria (19.4%), Bacteroidetes (4.2%), Firmicutes (2.7%), Chloroflexi (2.5%), candidate phylum TM7 (2.3%) and Planctomycetes (1.9%) while Proteobacteria (61.7%) and Actinobacteria (34.9%) dominated C2. Large proportion of sequence reads mainly associated with unclassified bacteria indicated possible occurrence of novel bacteria in both samples. XRF spectrophotometric analyses of C1 and C2 guano revealed significant differences in the composition of both major and trace elements. C1 guano recorded high levels of Si, Fe, Mg, Al, Mn, Ti and Cu while C2 samples registered high concentrations of Ca, P, S, Zn and Cr. Community structure of the samples were compared with other published community profiling studies from Finland (SRR868695), Meghalaya, Northeast India (SRR1793374) and Maharashtra State, India (CGS). Core microbiome among samples were determined for comparison. Variations were observed among previously studied guano samples and the Cabalyorisa Cave samples were attributed to either bat sources or age of the guano. This is the first study on bacterial diversity of guano in the Philippines through high-throughput sequencing.

Special Features of Bat Microbiota Differ From Those of Terrestrial Mammals

“…Although partial 16S rRNA genes were not able to assign sequences down to species level, the result is still meaningful as a guidance to targeted identification of pathogens. Since each pathogen carries unique DNA or RNA signatures that differentiate it from other organisms, if the database of these signatures can be curated, future metagenomic or transcriptomic studies will provide more detailed and conclusive results about bacterial pathogens (Leon et al, 2018). As an example, the identification of Bartonella mayotimonensis from metagenomic research proved the feasibility of this approach (Veikkolainen et al, 2014).…”

The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance

“…DNA (1 μg per sample) was used for library construction. Sequencing libraries were generated using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (New England BioLabs, Inc., USA) following the manufacturer’s instructions [ 68 ], and index codes were added to uniquely identify each sample. The DNA was then fragmented to a size of 350 bp through sonication, and fragments were end-polished, A-tailed, and ligated with a full-length adaptor for Illumina sequencing and further PCR amplification.…”

Using Environmental Sampling to Enable Zoonotic Pandemic Preparedness

“…Comparison studies (on the basis of partial sequences of the pol gene) highlights a greater genetic variety among bat AdVs affecting same and different bat species, illustrating the genetical diverse variety of DNA virus within bats. Considering these factors and the close proximity between humans and bats, further research needs to be conducted to understand the potential spillover of these viruses into human and animal populations and pathogenic potentials in spillover hosts Fecal sample from bats Targeted PCR of DNA dependent DNA Polymerase gene and Sanger sequencing Banskar et al 78 Frugivorous bat species Rousettus leschenaultii from Robbert cave India showed the presence of pathogenic Escherichia coli Guano pellets Culture-based approach using different microbiological media and 16 S rRNA (V3–V4 region) gene sequencing Leon et al 79 Two bat guano samples from Cabalyorisa cave, Philippines were analyzed. Abundance of Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes was seen in bat guano collected from one cave and the guano collected from the second cave location showed the abundance of Proteobacteria and Actinobacteria Guano pellets 16S rRNA gene amplicon sequencing.…”