DOI: 10.5281/zenodo.15282166
title: Human intestinal Bacteria Collection (HiBC):  Isolates and genomes metadata

description: The Human intestinal Bacteria Collection (HiBC) is a collection of bacterial strains, isolated from the human gut for which 16S rRNA gene sequences, genome sequences and culture conditions are made available to the research community. In addition to previously described bacteria, we include strains that represent novel species which have been taxonomically described and validly named, or will be in the future. This collection will be updated regularly.

This dataset includes the taxonomy of the isolates, as well as metadata regarding their cultivation and isolation. We also provide metadata regarding the sequencing, genome assembly process and the biological sequences.

UPDATE v7: INSDC accession for Segatella sinensis CLA-AA-H117 was a missing value and is now the correct value of GCA_040324585.2.

UPDATE v6: The growth atmosphere is now indicated by anaerobic or aerobic instead of "Anaerobe/Aerobe" that was a misleading term. The risk group of these two isolates went from 1 to 2:



CLA-AA-H205: Anaerostipes caccae 

CLA-AA-H83: Bacteroides fragilis


The risk group of the following isolates has been updated (usually from unknown to 1, or from 2 to 1):



CLA-SR-H026: Aedoeadaptatus acetigenes

CLA-KB-H139: Bacteroides xylanisolvens

CLA-SR-H015: Bacteroides xylanisolvens

CLA-AA-H187: Blautia fusiformis

CLA-AA-H274: Brotaphodocola catenula

CLA-AA-H286: Butyricimonas faecihominis

CLA-AA-H278: Clostridium fessum

CLA-AA-H147: Dorea ammoniilytica

CLA-SR-H027: Dorea formicigenerans

CLA-KB-H89: Dorea longicatena

CLA-KB-H94: Dorea longicatena

CLA-SR-H022: Enterococcus lactis

CLA-AA-H250: Hominenteromicrobium mulieris

CLA-AA-H232: Hominilimicola fabiformis

CLA-AA-H246: Hominisplanchenecus faecis

CLA-AA-H276: Hominiventricola filiformis

CLA-AA-H213: Oliverpabstia intestinalis

CLA-AA-H241: Oliverpabstia intestinalis

CLA-AA-H58: Pilosibacter fragilis

CLA-KB-H110: Ruthenibacterium lactatiformans

CLA-AA-H174: Segatella sinensis

CLA-AA-H2: Veillonella parvula

CLA-AA-H273: Waltera acetigignens


Typos in media list have been fixed. 

UPDATE v5: The accessions number for the genomes on INSDC databases are added under the column Accession. Plus two typos in the risk group column have been corrected as follow:



CLA-AA-H173: from Risk Group 4 (!) to 2 like the other strain of Sutterella wadsworthensis

CLA-AA-H198: from Risk Group 4 (!) to 1 like the other Bifidobacterium species.


UPDATE v4: Only the taxonomy of a couple of isolates has been changed, as follow:



CLA-ER-H4: Collinsella sp900547855 instead of Collinsella sp900544645

CLA-AA-H142: Pilosibacter fragilis (f__Clostridiaceae) instead of Sakamotonia hominis gen. nov. (f__Lachnospiraceae)

CLA-AA-H58: Pilosibacter fragilis (f__Clostridiaceae) instead of Sakamotonia hominis gen. nov. (f__Lachnospiraceae)

CLA-AA-H89B: Lachnospira intestinalis sp. nov. instead of Lachnospira hominis sp. nov.

CLA-JM-H10: Lachnospira hominis sp. nov. instead of Lachnospira intestinalis sp. nov.

CLA-JM-H7B: Faecalibacterium taiwanense instead of Faecalibacterium faecis sp. nov.

CLA-JM-H45: Merdimmobilis hominis instead of Hominicola intestinalis gen. nov.


UPDATE v3: The genome of one of our isolate had been unfortunately swapped. This mistake has been now corrected on Zenodo and Coscine. The genome of Segatella sinensis CLA-AA-H117 should be considered correct with 103 contigs and 3 671 232 nt. Please note that the genome available at the NCBI is the correct one (GCA_040324585.2). Two typos regarding taxonomy have been corrected as well: Maccoya intestinihominis has been corrected to Maccoyia intestinihominis and Faecousia faecis to Faecousia intestinalis.