# Complete genome sequence of two Christensenella minuta strains CIP 112228 and CIP 112229, isolated from human fecal samples

Christiane Bouchier, Gérald Touak, Damien Rei, D. Clermont

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Christiane Bouchier, Gérald Touak, Damien Rei, D. Clermont. Complete genome sequence of two Christensenella minuta strains CIP 112228 and CIP 112229, isolated from human fecal samples. Microbiology Resource Announcements, 2024, 13 (12), pp.e00766-24. 10.1128/mra.00766-24. pasteur-05095636

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# Complete genome sequence of two *Christensenella minuta* strains CIP 112228 and CIP 112229, isolated from human fecal samples

Christiane Bouchier,¹ Gérald Touak,¹ Damien Rei,² Dominique Clermont¹

**AUTHOR AFFILIATIONS** See affiliation list on p. 2.

**ABSTRACT** *Christensenella minuta* is one of the representative bacterial species of the human gut microbiome. We report the complete genome sequence of two strains, *Christensenella minuta* CIP 112228 and CIP 112229, isolated from two healthy volunteers.

**KEYWORDS** microbial genomics, human microbiome

In the microbiome-based therapy field, *Christensenella minuta* is reported as a potential probiotic for effective interventions on gut microbiomes and improvement of host health (1).

In order to increase the amount of genomic information on the species *C. minuta*, we report the complete genome sequence of two strains of *C. minuta* CIP 112228 and CIP 112229 from human feces belonging to the ancillary cohort “COSIMMGEN J” initiated for the study approved by the COMITE DE PROTECTION DES PERSONNES Ile de France 1 - DOSSIER : 2018-fév.-14819. These strains were isolated from two different healthy human stool samples, targeted by polyclonal antibodies against *Christensenella* spp. and sorted using flow cytometry under anaerobic conditions (2). They were grown in pre-reduced tryptone, peptone, glucose yeast extract medium (supplemented with 0.1% l-cysteine–HCl and vitamins) (3) at 37°C and under strict anaerobic conditions (5% H₂/5% CO₂/90% N₂).

Genomic DNA used for Illumina and Nanopore sequencing were extracted from an 8 mL overnight culture via a Nanobind CBB kit (Pacific Biosciences, USA) following the manufacturer's protocols. Illumina sequencing was performed by the Mutualized Platform for Microbiology (Institut Pasteur, Paris, France) following their standard workflow for library preparation (Nextera tagmentation kit, Illumina, USA) and an Illumina NextSeq 550 device using a 2 × 150 bp protocol. Paired-end reads were trimmed using `fqCleanER v23.12` workflow with a Phred quality score of 25 and read length ≥ 100 bases https://gitlab.pasteur.fr/GIPhy/fqCleanER. The same gDNA aliquots were also used for long-read sequencing using the ligation sequencing gDNA kit (SQK-NBD114.24, Oxford Nanopore Technologies, UK) and sequenced on a MinION Mk1C device for 48 h (Oxford Nanopore Technologies, UK) with R10.4 flow cell (FLO-MIN114, Oxford Nanopore Technologies, UK). The Dorado v0.3.0 tool was used to perform base calling. The ONT reads were processed using `Filtlong v0.2.0` (length >5,000 bp) https://github.com/rrwick/Filtlong. The ONT-filtered reads were assembled with Flye v2.9 which generated a circularized contig for each strain (4). Error correction and polishing were then done using the ONT-filtered reads and Illumina-trimmed paired-end reads using Medaka v1.4.4 (Oxford Nanopore Technologies, UK). A second round of polishing was done using Illumina-trimmed reads with PolyPolish v0.5.0 (5). Rotation of the polished genome to start at the *dnaA* gene was carried out using the fixstart command in circlator v1.5.5 (6).

**Editor** Vanja Klepac-Ceraj, Wellesley College
Department of Biological Sciences, Wellesley,
Massachusetts, USA

Address correspondence to Christiane Bouchier,
christiane.bouchier@pasteur.fr.

The authors declare no conflict of interest.

Received 24 July 2024

Accepted 11 October 2024

Published 29 October 2024

Copyright © 2024 Bouchier et al. This is an open-
access article distributed under the terms of the
Creative Commons Attribution 4.0 International
license.
<table><caption>TABLE 1 Genome features of the two *Christensenella minuta* strains</caption><thead><tr><th rowspan="2">Feature</th><th rowspan="2"></th><th colspan="2">Data for strain</th></tr><tr><th>CIP112228</th><th>CIP112229</th></tr></thead><tbody><tr><td rowspan="7">Long read</td><td>Number of reads</td><td>16 370</td><td>12 231</td></tr><tr><td>Total bases</td><td>200 632 862</td><td>171 834 363</td></tr><tr><td>Mean read length (bp)</td><td>13 811</td><td>14 049</td></tr><tr><td>Mean read quality</td><td>17.6</td><td>17.6</td></tr><tr><td>Median read length (bp)</td><td>10 220</td><td>10 296</td></tr><tr><td>Median read quality</td><td>18.4</td><td>18.4</td></tr><tr><td>N50 read length (bp)</td><td>15 802</td><td>16 535</td></tr><tr><td rowspan="2">Short read</td><td>Number of paired-end reads</td><td>2 142 245</td><td>6 160 111</td></tr><tr><td>Read length (bp)</td><td>151</td><td>151</td></tr><tr><td rowspan="4">Assembly</td><td>Genome size (bp)</td><td>2 770 534</td><td>2 770 539</td></tr><tr><td>Long-read coverage (×)</td><td>71</td><td>61</td></tr><tr><td>Short-read coverage (×)</td><td>216</td><td>634</td></tr><tr><td>GC content (%)</td><td>52</td><td>52</td></tr><tr><td rowspan="4">Annotation</td><td>Predicted number of coding sequences</td><td>2 539</td><td>2 539</td></tr><tr><td>Number of rRNAs</td><td>6</td><td>6</td></tr><tr><td>Number of tRNAs</td><td>51</td><td>51</td></tr><tr><td>GenBank accession number</td><td>CP149434</td><td>CP149433</td></tr></tbody></table>

The completed genome of the strain CIP 112228 consists of one circular chromosome (2,770,534 bp, 51.87% GC) with an overall sequencing coverage of 71 × (ONT reads). The strain CIP 11229 has a circular genome size of 2,770,539 bp with a GC% of 51.87 and a genome coverage of 61 × (ONT reads).

The annotation of the genomes was performed using the NCBI Prokaryotic Genome Annotation Pipeline (version 6.7, March 2024) (Table 1).

## ACKNOWLEDGMENTS

The authors acknowledge Samuel Bellais of BIOASTER (Paris) for the targeted cell sorting under anaerobic conditions and Rémy Artus of ICAREb-biobank (Institut Pasteur, Paris) for his help in obtaining fecal samples.

## AUTHOR AFFILIATIONS

## AUTHOR ORCIDs

Christiane Bouchier http://orcid.org/0000-0003-3549-1543

## AUTHOR CONTRIBUTIONS

Christiane Bouchier, Formal analysis, Methodology, Writing – original draft | Gérald Touak, Formal analysis, Methodology, Visualization | Damien Rei, Conceptualization, Supervision, Visualization | Dominique Clermont, Conceptualization, Funding acquisition, Supervision, Writing – review and editing

## DATA AVAILABILITY

The collection of volunteer's samples has been reviewed by the COMITE DE PROTEC-TION DES PERSONNES Ile de France 1 - N°IRB / IORG # : IORG0009918 - N° ID-RCB : 0-A01353-36.

The genome sequences were deposited at GenBank under the accession numbers CP149433 and CP149434.

<footnote n="1">¹CIP, CRBIP, C2RT, Microbiology Department, Institut Pasteur, Paris, France</footnote>

<footnote n="2">²NBX Biosciences, SAS, Centre ADVISOR, Montpellier, France</footnote>
The Illumina paired-end reads can be found at SRA accession numbers SRR29733043 and SRR29733044. The ONT-filtered reads from the MinION MK1C run can be found at SRA accession numbers SRR29734392 and SRR29734393.

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