Authors need to be prudent when assigning names to microbial isolates

Stackebrandt, Erko; Mondotte, Juan A.; Fazio, Luigi Lembo; Jetten, Mike S. M.

doi:10.1007/s10482-021-01675-8

Cited by 5 publications

(3 citation statements)

References 30 publications

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“…61 A cut-off value of 98.7% was used as a first layer of delineation between known and novel species. 62…”

Section: Methodsmentioning

confidence: 99%

“…61 A cut-off value of 98.7% was used as a first layer of delineation between known and novel species. 62 For phage infection assays, E. coli strains were incubated in BHI medium overnight at 37 °C and 100 µl of biomass was plated onto LB agar plates. After drying, 2.5 µl of phage lysate dilution series (in BHI medium down to 10 -7 ) were pipetted onto the plate, each dilution in triplicate.…”

Section: Bacterial Isolation and Characterizationmentioning

confidence: 99%

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Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

Afrizal

Jennings

Hitch

et al. 2022

Preprint

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Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. Fundamental and clinical research is in need of comprehensive and well-curated repositories of cultured bacteria from the intestine of mammalian hosts. In this work, we expanded the mouse intestinal bacterial collection (www.dsmz.de/miBC) to 212 strains, all publicly available and taxonomically described. This includes the study of strain-level diversity, small-sized bacteria, and the isolation and characterization of the first cultured members of one novel family, 10 novel genera, and 39 novel species. We demonstrate the value of this collection by performing two studies. First, metagenome-educated design of synthetic communities (SYNs) allowed establishing custom strain consortia that reflect different susceptibilities to DSS-induced colitis. Second, nine phylogenetically and functionally diverse species were used to amend the Oligo-Mouse Microbiota (OMM)12 model [Brugiroux et al. 2016 Nat Microbiol]. These strains compensated for differences observed between gnotobiotic OMM12 and specific-pathogen free (SPF) mice at multiple levels, including body composition and immune cell populations (e.g., induction of T-cell subtypes) in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks from this work are available to the community for use in future studies. In conclusion, this work improves our knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates.

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“…61 A cut-off value of 98.7% was used as a first layer of delineation between known and novel species. 62…”

Section: Methodsmentioning

confidence: 99%

Section: Bacterial Isolation and Characterizationmentioning

confidence: 99%

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

Afrizal

Jennings

Hitch

et al. 2022

Preprint

View full text Add to dashboard Cite

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“…Nowadays, conventional and high throughput sequencers can amplify all the nine variable regions of the 16S rRNA gene. Although, many 16S rRNA-based bacterial identification studies lack a complete set of variable regions (Stackebrandt et al 2021). The classical and high throughput sequencing technologies produce a large volume of whole-genome data.…”

Section: Introductionmentioning

confidence: 99%

Concatenated 16S rRNA Sequence Analysis Improve Bacterial Taxonomy

Paul

2022

Preprint

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Microscopic, biochemical, molecular, and computer-based approaches are extensively used to identify and classify bacterial populations. Further, advances in DNA sequencing and bioinformatics workflows facilitated sophisticated genome-based methods for microbial taxonomy. Although sequencing of 16S rRNA gene is widely employed to identify and classify the bacterial community as a cost-effective and single-gene approach. However, the accuracy of the 16S rRNA sequence-based species identification is limited by multiple copies of the gene and their higher sequence identity between closely related species. Availability of a large volume of bacterial whole-genome data provided an opportunity to develop comprehensive species-specific 16S rRNA reference libraries. With defined rules, we have concatenated four 16S rRNA gene copy variants to develop a species-specific reference library. Using this approach, species-specific 16S rRNA gene libraries were developed for four closely related Streptococcus species (S. gordonii, S. mitis, S. oralis, and S. pneumoniae). Sequence similarity and phylogenetic analysis of concatenated 16S rRNA copies yielded better resolution than single gene copy approaches. The approach is very effective to classify genetically related species, and it may reduce misclassification of bacterial species and genome assemblies.

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