Lacrimispora defluvii PI-S10-B5A ^T sp. nov., an Obligate Anaerobe, Isolated from an Industrial Waste and Reclassification of Hungatella xylanolytica as Lacrimispora xylanolytica and Clostridium indicum as Lacrimispora indica Comb. nov.

Publisher: Springer International Country of Publication: United States NLM ID: 7808448 Publication Model: Electronic Cited Medium: Internet ISSN: 1432-0991 (Electronic) Linking ISSN: 03438651 NLM ISO Abbreviation: Curr Microbiol Subsets: MEDLINE

Original Publication: New York, Springer International.

Industrial Waste* ; Clostridium*; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Bacteria, Anaerobic/genetics ; Phospholipids/analysis ; Fatty Acids/analysis

A bacterial strain was isolated from the waste slurry of an industrial effluent treatment plant near Patancheru, Hyderabad, India, and designated as PI-S10-B5A ^T . It was an obligately anaerobic, spore-forming, rod-shaped, motile bacterium that stained Gram-positive. The strain revealed high 16S rRNA gene sequence identity with Hungatella xylanolytica DSM 3808 ^T (99.4%) followed by members of the genus Lacrimispora (98.8-93.3%). However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization of genome sequence exhibited similarity in the range of 94.3-68.7% and 57.4-18.8%, respectively, with all closely related strains. A multi-gene phylogenetic analysis of strain PI-S10-B5A ^T was performed to investigate the taxonomic affiliation, which revealed formation of a coherent cluster with the members of the genus Lacrimispora. The DNA G + C content was 41.8 mol%. Major polar lipids were glyco- and phospholipids. The fatty acids analysis showed C 16:0 to be the major fatty acid. The predominant respiratory quinone was menaquinone-7 (MK-7). Based on phenotypic, chemotaxonomic, and whole-genome phylogenetic analysis, strain PI-S10-B5A ^T is assigned as a novel species of the genus Lacrimispora, for which the name Lacrimispora defluvii is proposed. The type strain of the novel species is PI-S10-B5A ^T (= MTCC 12280 ^T ; = DSM 24980 ^T ) isolated from waste slurry of effluent treatment plant. The genomic analysis of type strains of C. indicum PI-S10-A1B ^T and H. xylanolytica DSM 3808 ^T showed ANI and AAI values consistent with members of the genus Lacrimispora. Therefore, these strains are ascertained to the genus Lacrimispora and reclassified as Lacrimispora indica and Lacrimispora xylanolytica comb. nov.
(© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Whitman WB, Oren A, Chuvochina M, da Costa MS, Garrity GM, Rainey FA et al (2018) Proposal of the suffix–ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the international code of nomenclature of prokaryotes.’ Int J Syst Evol Microbiol 68:967–969. (PMID: 29458499)
Parte AC (2018) LPSN—list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 68:1825–1829. (PMID: 29724269)
Rainey FA, Hollen BJ, Small AM (2015) Clostridium. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, DeVos P, Hedlund B, Dedysh S (eds) Bergeys manual of systematics of archaea and bacteria. Wiley, New Jersy, pp 1–112.
Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J et al (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44:812–826. (PMID: 7981107)
Yutin N, Galperin MY (2013) A genomic update on clostridial phylogeny: gram-negative spore formers and other misplaced clostridia. Environ Microbiol 15:2631–2641. (PMID: 238342454056668)
Prescott JF (2016) Taxonomic relationships among the clostridia. In: Uzal FA (ed) Clostridial diseases of animals. Wiley, Ames, pp 3–5.
Kaur S, Yawar M, Kumar PA, Suresh K (2014) Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov. Int J Syst Evol Microbiol 64:710–718. (PMID: 24186873)
Haas KN, Blanchard JL (2020) Reclassification of the Clostridium clostridioforme and Clostridiumsphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa. Int J Syst Evol Microbiol 70:23–34. (PMID: 31782700)
García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al (2019) Analysis of 1000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 10:2083. (PMID: 316080196767994)
Cruz-Morales P, Orellana CA, Moutafis G, Moonen G, Rincon G, Nielsen LK, Marcellin E (2019) Revisiting the evolution and taxonomy of clostridia, a phylogenomic update. Genom Biol Evol 11:2035–2044.
Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 64:316–324. (PMID: 24505069)
Sangal V, Goodfellow M, Jones AL, Schwalbe EC et al (2016) Next-generation systematics: an innovative approach to resolve the structure of complex prokaryotic taxa. Sci Rep 6:38392. (PMID: 279249125141411)
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68(461):466.
Shakya M, Ahmed SA, Davenport KW et al (2020) Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Sci Rep 10:1723. (PMID: 320153546997174)
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106:19126–19131. (PMID: 198550092776425)
Gundawar K, Kumari S, Sharma S, Grover V, Patil PB, Korpole S (2019) Clostridium indicum sp. nov., a novel anaerobic bacterium isolated from the sludge of an industrial effluent. Int J Syst Evol Microbiol 69:672–678. (PMID: 30676311)
Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. Cambridge University Press, London.
Lányi B (1988) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67.
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654.
Suresh K, Prakash D, Rastogi N, Jain RK (2007) Clostridium nitrophenolicum sp. nov., a novel anaerobic p-nitrophenol-degrading bacterium, isolated from a subsurface soil sample. Int J Syst Evol Microbiol 57:1886–1890. (PMID: 17684276)
Shetty N, Hill G, Ridgway GL (1998) The Vitek analyzer for routine bacterial identification and susceptibility testing: protocols, problems, and pitfalls. J Clin Pathol 51:316–323. (PMID: 9659247500679)
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Tech Note 101:1–6.
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241.
Tamaoka J (1986) Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 123:31–36.
Schumann P (2011) Peptidoglycan structure. Methods Microbiol 38:101–129.
Suresh K, Mayilraj S, Chakrabarti T (2006) Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family “Flexibacteraceae.” Int J Syst Evol Microbiol 56:1703–1707. (PMID: 16825654)
Thompson JD, Higgins DG, Gibson TJ, Clustal W (1994) Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680. (PMID: 7984417308517)
Kumar S, Stecher G, Tamura K (2016) Mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. (PMID: 270049048210823)
Yoon SH, Ha SM, Lim JM, Chun KSJ (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. (PMID: 28204908)
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75.
van Heel AJ, de Jong A, Song C, Viel JH, Kok J, Kuipers OP (2018) BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res 46:W278–W281. (PMID: 297882906030817)
Ankenbrand MJ, Keller A (2016) bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 59:783–791. (PMID: 27603265)
Eddy S (2010) HMMER3: a new generation of sequence homology search software. http://hmmer.janelia.org.
Edgar RC (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. (PMID: 15034147390337)
Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577. (PMID: 17654362)
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. (PMID: 244516233998144)
Letunic I, Bork P (2019) Interactive Tree of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47:W256–W259. (PMID: 309314756602468)
Chaudhari N, Gupta V, Dutta C (2016) BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 6:24373. (PMID: 270715274829868)
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069. (PMID: 24642063)
Zuo G, Hao B (2015) CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genom Proteom Bioinform 13:321–331.
Kobayashi H, Tanizawa Y, Sakamoto M, Ohkuma Tohno M (2021) Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999. Int J Syst Evol Microbiol 71(8):004951.
Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264. (PMID: 161597571236649)
Medlar AJ, Törönen P, Holm L (2018) AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acid Res 46:W479–W485. (PMID: 297627246030964)
Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME, Holmes B, Steigerwalt AG, Villarma A, Sheth M, Batra D, Rowe LA (2020) Division of the genus Chryseobacterium: observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 70:4432. (PMID: 327352087660247)
Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK (2022) Establishment of genome based criteria for classification of the family Desulfovibrionaceae and proposal of two novel genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front Microbiol 13:738205. (PMID: 356943089174804)
Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H (2021) Genome-based taxonomic rearrangement of the order geobacterales including the description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. Front Microbiol 12:737531. (PMID: 346591668516083)
Baindara P, Nayudu N, Korpole S (2020) Whole genome mining reveals a diverse repertoire of lanthionine synthetases and lanthipeptides among the genus Paenibacillus. J Appl Microbiol 128:473–490. (PMID: 31633851)
Scholten-Koerselman I, Houwaard F, Janssen P, Zehnder AJ (1986) Bacteroides xylanolyticus sp. nov., a xylanolytic bacterium from methane producing cattle manure. Antonie Van Leeuwenhoek 52:543–554. (PMID: 3813526)

MTCC Department of Biotechnology, Ministry of Science and Technology, India

0 (RNA, Ribosomal, 16S)
0 (Industrial Waste)
0 (DNA, Bacterial)
0 (Phospholipids)
0 (Fatty Acids)

Clostridium xylanolyticum; Bacteroides xylanolyticus

Date Created: 20221109 Date Completed: 20221111 Latest Revision: 20221111

20231215

10.1007/s00284-022-03096-w

36352237