ABSTRACT
We report the draft genome sequence of a putative probiotic strain, Lactobacillus fermentum ASBT-2, isolated from domestic sewage in Kerala, India. The strain showed probiotic properties (tolerance to low pH and bile salts, binding to host matrix) and reduced the coliform count by 90% in a biofilter used to treat wastewater.
ANNOUNCEMENT
We have developed a microbiome engineering tool to treat wastewater and food with potential probiotic strains and bacteriophages isolated from domestic sewage. Lactobacillus fermentum is recognized as a potential probiotic strain with antimicrobial, antioxidative, and cholesterol reduction properties (1–5). The organism was isolated from domestic sewage in Kerala, India, cultured in selective medium, De Man, Rogosa and Sharpe agar (MRS) (6), and confirmed with 16S rRNA gene ribotyping (7).
Genomic DNA was extracted using the phenol-chloroform method (8). The paired-end sequencing library was prepared using the TruSeq Nano DNA library prep kit with an average library size of 478 bp. The Illumina HiSeq platform was used for sequencing (9, 10) the paired-end library, with a read length of 2 × 150 bp. Both quantity and quality checks of the amplified library were performed in a Bioanalyzer 2100 instrument (Agilent Technologies) using a high-sensitivity DNA chip per the manufacturer’s instructions. High-quality (5.63 Gb) data, obtained after filtering the reads through Trimmomatic (v0.30) with a quality value (QV) of >20, were used for assembly. All the software settings used were under the default parameters unless otherwise mentioned. De novo assembly of paired-end reads was performed using Velvet v1.2.10. (11), and assembly was optimized with a kmer value of 121. The gaps of the assembled scaffold were filled using Gapcloser v1.12 (12). The total number of reads was 37,902,034, and the details of the assembled genome are listed in Table 1. tRNAscan-SE v1.3.1 was used for identification of probable tRNA genes (13). RNAmmer v1.2 was used for rRNA gene identification (14), which yielded a total of five 5S rRNAs and one 16S rRNA.
Summary of the sequencing details of ASBT-2
The 64 scaffolds obtained from de novo assembly were subjected to gene prediction using Prodigal v2.6.3 (15), which resulted in the identification of 2,019 coding sequences. The predicted proteins of genes were subjected to a similarity search against NCBI’s nonredundant (nr) database using the BLASTP algorithm. Out of 2,019 predicted proteins, 1,989 got a hit in the NCBI database; the remaining 30 were novel proteins. Simultaneously, all the 2,019 proteins were searched for similarity against the UniProt, COG, and Pfam databases using BLASTP with an E value threshold of 1e−5.
Data availability.This whole-genome shotgun project has been deposited at GenBank under BioProject number PRJNA639667, SRA accession number SRR12020697, and BioSample accession number SAMN15244744.
ACKNOWLEDGMENTS
This work was supported by the Reinvent the Toilet Challenge (RTTC) award (2014) funded by the Bill & Melinda Gates Foundation-BIRAC (Government of India) (grant numbers BIRAC/GCI/0067/02/13-RTTC and OPP1107707). We thank Amrita Vishwa Vidyapeetham, University Grant Commission (UGC), for providing funding to roll number 302092 (Pradeesh Babu) through beneficiary code BININ00345622U and the Council of Scientific and Industrial Research (CSIR) for funding provided to Amrita Salim (roll number 318345).
We declare no conflict of interest.
FOOTNOTES
- Received 18 June 2020.
- Accepted 29 June 2020.
- Published 16 July 2020.
- Copyright © 2020 Babu et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
