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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162468
mra00555-24
10.1128/mra.00555-24
mra.00555-24
Genome Sequences
genomics-and-proteomicsGenomics and ProteomicsGenome sequence of Lactobacillus johnsonii XZ17, isolated from a C57BL/6J mouse lung
https://orcid.org/0000-0001-7393-0936
Ravi Keerthikka 1
Oh Gina J. 2
Moore Bethany B. 2 3
https://orcid.org/0000-0002-4505-9642
Huffnagle Gary B. 1 4 ghuff@umich.edu

https://orcid.org/0000-0003-3096-409X
Zhou Xiaofeng 2 3 xiazhou@med.umich.edu

1 Department of Molecular, Cellular, and Developmental Biology, University of Michigan , Ann Arbor, Michigan, USA
2 Department of Microbiology and Immunology, University of Michigan , Ann Arbor, Michigan, USA
3 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan , Ann Arbor, Michigan, USA
4 Mary H. Weiser Food Allergy Center, University of Michigan , Ann Arbor, Michigan, USA
Editor Klepac-Ceraj Vanja Department of Biological Sciences, Wellesley College , Wellesley, Massachusetts, USA

Address correspondence to Xiaofeng Zhou, xiazhou@med.umich.edu
Address correspondence to Gary B. Huffnagle, ghuff@umich.edu
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00555-2423 5 2024
24 7 2024
Copyright © 2024 Ravi et al.
2024
Ravi et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

Lactobacillus johnsonii XZ17 was isolated from the lung homogenate of a healthy C57BL/6J mouse. XZ17 is diminished in the lungs of syngeneic bone marrow-transplanted recipient mice. Long-read sequencing of XZ17 yielded a single genome of 1,948,140 bp, with a GC content of 34.64%.

KEYWORDS

lactic acid bacteria
lung microbiome
immunomodulation
BMT mice
HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI) 153028 Zhou Xiaofeng HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R01AI138348 Huffnagle Gary B. HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI) R35HL144481 Moore Bethany B. cover-dateSeptember 2024
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pmcANNOUNCEMENT

Lactobacillus johnsonii is a lactic acid bacterium associated with the healthy gut of many vertebrate hosts (1, 2). As a probiotic, this species has several health-promoting effects, like inhibition and exclusion of pathogens (3–5) and host immunomodulation (6, 7). Here, we present the genome sequence of L. johnsonii strain XZ17 isolated from the mouse lung. Notably, L. johnsonii XZ17 abundance decreases in mouse lungs following bone marrow transplantation (8, 9).

A healthy C57BL/6J mouse, housed in a specific pathogen-free animal research facility at the University of Michigan, was euthanized by CO2. The mouse lung was aseptically isolated, homogenized, and cultured on de Man, Rogosa, and Sharpe (MRS) agar for 24 hours at 37°C under aerobic conditions. Several pure cultures were established by re-streaking and subsequently maintained as frozen stocks. Sequencing the 16S rRNA revealed that all isolates were identical and exhibited 100% homology with the known 16S rRNA sequence of L. johnsonii (GeneBank CP091981.1). One isolate, XZ17, was selected for comprehensive genomic sequencing. For isolating high molecular weight (HMW) DNA, an overnight bacterial culture of XZ17 in MRS broth was grown aerobically at 37°C (16–18 hours of incubation), and Nanobind HMW DNA extraction kit (Circulomics) with RNase treatment was used for DNA isolation.

Sequencing libraries were prepared using the ligation sequencing kit (SQK-LSK109) and selecting DNA fragments of all sizes with the short fragment buffer (SFB), according to the Oxford Nanopore Technologies library preparation protocol. The libraries were sequenced on an R9.4.1 ﬂow cell for 3 hours using a MinION sequencer (Oxford Nanopore Technologies). Guppy v6.0.7, in high-accuracy mode, was used for base calling. A total of 24 Mb was obtained after base calling, distributed across 7,712 reads, with a maximum length of a read at 62,782 bp and an N50 value of 8,282 bp. The genome sequences were assembled de novo as previously described (10). De novo assembly was performed using Flye v2.9 (11) with default parameters. The assembly was further polished through two rounds of Racon v1.5.0 (12) using the default parameters for all except score for matching and mismatching bases (--match 8 --mismatch -6). A final round of polish was carried out using Medaka v1.2.3 (13), using default parameters. XZ17 (genome coverage, 35×) was finally assembled into one contig of length 1.9 Mb. CheckM analysis (v1.2.2) (14), using taxonomic workflow for L. johnsonii species, reported a completeness of 93.65% and a contamination rate of 0.83%. The XZ17 genome is 1,948,140 bp and has a GC content of 34.64%. The genome of L. johnsonii is characterized by low GC content, with an average of 34.47% observed across 89 strains (15).

Sequence annotation for the strain was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (v6.7) (16). The annotation predicted 1,879 genes, 1,780 coding sequences, 68 pseudogenes, 78 tRNAs, 6 rRNAs (5S, 16S, and 23S), and 3 noncoding RNAs.

ACKNOWLEDGMENTS

This work was supported in part by funding provided by NIH grants NHLBI R01HL153028 (X.Z.), NIAID R01AI138348 (G.B.H.), NHLBI R35HL144481 (B.B.M.), the Mary H. Weiser Food Allergy Center (MHWFAC) (G.B.H.), the Nina and Jerry D. Luptak Endowment of the MHWFAC (G.B.H.), the University of Michigan Rackham Graduate School Research grant (K.R.), and the MCDB Graduate Program of the University of Michigan (K.R.).

DATA AVAILABILITY

All data are available under BioProject accession number PRJNA1095000 and BioSample accession number SAMN40710645. The genome was deposited in GenBank (CP151183.1), and the nanopore base-called data were submitted to SRA (SRR28520834).
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