- Email: [email protected]
Description of ‘Gorbachella massiliensis’ gen. nov., sp. nov., ‘Fenollaria timonensis’ sp. nov., ‘Intestinimonas timonensis’ sp. nov. and ‘Collinsella ihuae’ sp. nov. isolated from healthy fresh stools with culturomics
Accepted Manuscript Description of “Gorbachella massiliensis” gen. nov., sp. nov., “Fenollaria timonensis” sp. nov., “Intestinimonas timonensis” sp. nov., “Collinsella ihuae” sp. nov. isolated from healthy fresh stools with culturomics G.A. Durand, F. Cadoret, J.C. Lagier, P.E. Fournier, D. Raoult PII:
S2052-2975(17)30005-7
DOI:
10.1016/j.nmni.2017.01.005
Reference:
NMNI 293
To appear in:
New Microbes and New Infections
Received Date: 9 December 2016 Revised Date:
5 January 2017
Accepted Date: 9 January 2017
Please cite this article as: Durand GA, Cadoret F, Lagier JC, Fournier PE, Raoult D, Description of “Gorbachella massiliensis” gen. nov., sp. nov., “Fenollaria timonensis” sp. nov., “Intestinimonas timonensis” sp. nov., “Collinsella ihuae” sp. nov. isolated from healthy fresh stools with culturomics, New Microbes and New Infections (2017), doi: 10.1016/j.nmni.2017.01.005. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
ACCEPTED MANUSCRIPT Description of “Gorbachella massiliensis” gen. nov., sp. nov., “Fenollaria timonensis” sp. nov., “Intestinimonas timonensis” sp. nov., “Collinsella ihuae” sp. nov. isolated from healthy fresh stools with culturomics
RI PT
G.A. Durand, F. Cadoret, J.C. Lagier, P.E. Fournier and D. Raoult*
Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 27 Boulevard Jean
SC
Moulin, 13385, Marseille cedex 05, France
M AN U
* Corresponding author: Pr. Didier Raoult: [email protected]
Running head: Gorbachella massiliensis gen. nov., sp. nov., Fenollaria timonensis sp. nov.,
TE D
Intestinimonas timonensis sp. nov., Collinsella ihuae sp. nov.
AC C
EP
Keywords: Gorbachella massiliensis, Fenollaria timonensis, Intestinimonas timonensis, Collinsella ihuae, gut microbiota
ACCEPTED MANUSCRIPT Abstract:
2
We report here the main characteristics of “Gorbachella massiliensis” GD7T gen. nov., sp.
3
nov., “Fenollaria timonensis” GD5T sp. nov., “Intestinimonas timonensis” GD4T sp. nov.,
4
and “Collinsella ihuae” sp. nov. GD8T isolated from one fresh stool of a French volunteer.
5
We used a bacterial culturomics approach combined with taxono-genomics.
RI PT
1
6
In our study concerning the intolerant oxygen species from human gut microbiota, we
8
isolated in 2015 using a bacterial culturomics approach four bacteria that could not be
9
identified
by
matrix-assisted
laser
SC
7
desorption-ionization
mass
spectrometry
(http://www.mediterraner-infection.com/article.php?laref=256&titre=urms-database)
11
Microflex spectrometer (Bruker Daltonics, Brenen, Germany) (1,2). These species were
12
isolated from the same fresh stool from a healthy volunteer. The individual has signed
13
informed consent and the study has been validated by the Ethics Committee of the IFR48
14
Federative Research Institute under the number 09-022.
on
a
TE D
M AN U
10
Strain GD7T was isolated from a dilution of the fresh sample. The species was grown
16
after 48 hours on Columbia agar supplemented with 5% sheep blood at 37°C under strict
17
anaerobic conditions. The colonies appeared translucent and rough, non-hemolytic, non-
18
motile, non-spore forming, with 1 mm size. The cells were Gram-negative, rod-shaped. The
19
strain did not show catalase or oxidase activity. The 16S rRNA gene was sequenced using
20
fD1-rP2 primers as described previously using a 3130-XL sequencer (Applied Biosciences,
21
Saint Aubin, France) (3). The strain GD7T had a 16S rRNA gene sequence identity of 93.4%
22
with Subdoligranulum variabile strain BI 114T (NR_028997), the phylogenetically closest
23
species with standing in nomenclature (Figure 1). This similarity < 98.65% leads us to
24
putatively classify GD7T as a new member in the Ruminococcaceae family of Firmicutes (4).
25
Therefore we propose the creation of the new genus “Gorbachella” (Gor.ba.chel'la. NL gen
AC C
EP
15
ACCEPTED MANUSCRIPT 26
fem, in honor of the microbiologist Sherwood Gorbach (Tufts University School of Medicine,
27
Boston, Massachusetts, USA)). GD7T is the type strain of the species Gorbachella
28
massiliensis (ma.ssi.li.en’sis L. adj. fem to Massilia, the latin name of Marseille, France,
29
where this strain was isolated). Strain GD5T was isolated from the fresh sample after 48-h anaerobic growth on
31
Columbia agar supplemented with 5% sheep blood at 37°C. The colonies appeared to be
32
translucent, rough, non-hemolytic, motile, non-spore forming, with 1 mm size. The cells were
33
rod-shaped with Gram-negative staining. Oxidase and catalase activities were negative. Strain
34
GD5T showed 97.4% sequence homology with the 16S RNA of Fenollaria massiliensis strain
35
9401234T (NR_133038) (Figure 2) (5). So we propose to classify GD5T as a new species
36
within the genus Fenollaria in the phylum Firmicutes (4). GD5T is the type strain of the
37
species “Fenollaria timonensis” (ti.mo.nen’sis L. adj. fem to Timone, the name of the main
38
hospital of Marseille, France, where this strain was isolated).
M AN U
SC
RI PT
30
Strain GD4T was isolated after 48-h anaerobic growth on Columbia agar
40
supplemented with 5% sheep blood and 5% rumen fluid at 37°C. The colonies appeared
41
translucent, rough, non-hemolytic, motile, non-spore forming, with 1 mm size. The cells were
42
Gram-negative. Catalase and oxidase activities were negative. Strain GD4T presented a
43
sequence identity of 97.08% with 16S rRNA sequence of Intestinimonas butyriciproducens
44
DSM 26588T (NR_118554), the closest species with a validly name (Figure 1). We propose to
45
putatively classify GD4T as a new member of the genus Intestinimonas in the phylum
46
Firmicutes (4). GD4T is the type strain of the species “Intestinimonas timonensis”
47
(ti.mo.nen’sis L. adj. fem to Timone, the name of the main hospital of Marseille, France,
48
where this strain was isolated).
AC C
EP
TE D
39
49
“Collinsella ihuae” strain GD8T was isolated after 48-h anaerobic growth on
50
Columbia agar supplemented with 5% sheep blood and 5% rumen fluid at 37°C. Colonies
ACCEPTED MANUSCRIPT appeared as microcolonies rough, non-hemolytic, motile, non-spore forming, with 0.5 mm
52
size. The cells were rod-shaped with Gram-positive staining. Catalase and oxidase activities
53
were negative. The 16S rRNA sequence of the strain GD8T presented a identity of 96.2% with
54
the 16S rRNA sequence of Collinsella tanakaei strain JCM 16071 (NR_113273), the closest
55
phylogenetic species with nomenclature (Figure 3) (6). Then we propose the creation of the
56
new species “Collinsella ihuae” within the phylum Actinobacteria (4). GD8T is the type strain
57
of the species “Collinsella ihuae” (i.hu.ae L. adj. fem to Institut Hospitalo-Universitaire
58
(IHU), the name of the name of the laboratory (Marseille, France) where this strain was
59
isolated).
60
MALDI-TOF-MS spectra accession numbers
61
The MALDI-TOF-MS spectra of these species are available at http://mediterranee-
62
infection.com/article.php? laref=256&titre=urms-database.
63
(Last access 2016/12/07)
64
Nucleotide sequence accession number
65
The 16S r RNA gene sequences were deposited in Genbank under accession numbers:
66
“Gorbachella massiliensis” GD7T (LN870316), “Fenollaria timonensis” GD5T (LN881613),
67
“Intestinimonas timonensis” GD4T (LN870298) and “Collinsella ihuae” GD8T (LN881598).
68
Deposit in a culture collection.
69
The strains were deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR,
70
WDCM 875) under numbers “Gorbachella massiliensis” GD7T (P2021), “Fenollaria
71
timonensis” GD5T (P2133), “Intestinimonas timonensis” GD4T (P2010) and “Collinsella
72
ihuae” GD8T (P2019).
73
Conflict of interest:
74
None to declare.
75
Funding sources:
AC C
EP
TE D
M AN U
SC
RI PT
51
ACCEPTED MANUSCRIPT 76
This work was funded by Fondation Mediterrannée-Infection.
AC C
EP
TE D
M AN U
SC
RI PT
77
ACCEPTED MANUSCRIPT Figure legend
79
Figure 1: Phylogenetic tree showing the position of “Intestinimonas timonensis” GD4T and
80
“Gorbachella massiliensis” GD7T relative to other phylogenetically-close neighbors.
81
Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained with
82
kimura two parameter models using the maximum-likelihood method within the MEGA
83
software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the
84
analysis 1,000 times to generate a majority consensus tree. Only bootstrap values >95% are
85
displayed. The scale bar indicates a 2% nucleotide sequence divergence.
86
Figure 2: Phylogenetic tree showing the position of “Fenollaria timonensis” GD5T relative to
87
other phylogenetically-close neighbors. Alignment and phylogenetic inferences were done as
88
described for Figure 1.
89
Figure 3: Phylogenetic tree showing the position of “Collinsella ihuae” GD8T relative to
90
other phylogenetically-close neighbors. Alignment and phylogenetic inferences were done as
91
described for Figure 1. The scale bar indicates a 1% nucleotide sequence divergence.
AC C
EP
TE D
M AN U
SC
RI PT
78
ACCEPTED MANUSCRIPT 92
References
93
1. Lagier J-C, Hugon P, Khelaifia S, Fournier P-E, La Scola B, Raoult D. The rebirth of
94
culture in microbiology through the example of culturomics to study human gut
95
microbiota. Clin Microbiol Rev. 2015 Jan;28(1):237–64. 2. Lagier J-C, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P, et al. Culture of
RI PT
96 97
previously uncultured members of the human gut microbiota by culturomics. Nat
98
Microbiol. 2016 Nov 7;1:16203.
3. Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D. 16S ribosomal DNA
SC
99
sequence analysis of a large collection of environmental and clinical unidentifiable
101
bacterial isolates. J Clin Microbiol. 2000 Oct;38(10):3623–30.
M AN U
100
102
4. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average
103
nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of
104
prokaryotes. Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):346–51. 4. Pagnier I, Croce O, Robert C, Raoult D, La Scola B. Non-contiguous finished genome
TE D
105 106
sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of
107
anaerobic bacterium. Stand Genomic Sci. 2014 Jun 15;9(3):704–17. 5. Nagai F, Watanabe Y, Morotomi M. Slackia piriformis sp. nov. and Collinsella tanakaei
EP
108
sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces. Int J
110
Syst Evol Microbiol. 2010 Nov;60(Pt 11):2639–46.
111
AC C
109
ACCEPTED MANUSCRIPT
Clostridium orbiscindens DSM 6740T (Y18187)
100 100
Eubacterium plautii CCUG 28093T (AY724678) Pseudoflavonifractor capillosus ATCC 29799T (AY136666)
100
RI PT
Intestinimonas timonensis GD4T (LN870298) Intestinimonas butyriciproducens DSM 26588T (KC311367)
99
Clostridium viride DSM 6836T (X81125)
SC
Oscillibacter valericigenes DSM 18026T (AB238598)
100
Oscillibacter ruminantium GH1T (JF750939)
M AN U
100
Sporobacter termitidis DSM 10068T (Z49863)
Papillibacter cinnaminovorans DSM 12816T (AF167711)
96
TE D
Anaerotruncus colihominis 14565T (AJ315980) Hydrogenoanaerobacterium saccharovorans SW512T (EU158190)
100
EP
Anaerofilum agile DSM 4272T (X98011)
100 99
AC C
100
Gorbachella massiliensis GD7T (LN870316) Faecalibacterium prausnitzii ATCC 27768T (AJ413954) Gemmiger formicilis ATCC 27749T (GU562446) 100
0.02
Anaerofilum pentosovorans DSM 7168T (X97852)
Subdoligranulum variabile BI 114T (AJ518869)
ACCEPTED MANUSCRIPT
Peptoniphilus grossensis ph5 (NR125605) Peptoniphilus hareii DSM 10020T (Y07839)
100 100
Peptoniphilus lacrimalis CCUG 31350T (AF542230)
RI PT
Anaerosphaera aminiphila DSM 21120T (AB298735) Peptoniphilus asaccharolyticus CCUG 9988T (AF542228) 96
100
Peptoniphilus indolicus DSM 20464T (AY153431)
SC
Peptoniphilus ivorii DSM 10022T (Y07840)
M AN U
Bacteroides coagulans EUH 581-73T (HF558387) Fenollaria timonensis GD5T (LN881613)
98 100
Fenollaria massiliensis 9401234T (NR133038)
Keratinibaculum paraultunense KD-1T (KC188660) Clostridium ultunense DSM 10521T (Z69293)
TE D
100
Sporanaerobacter acetigenes Lup33T (AF358114.2)
EP
Soehngenia saccharolytica DSM 12858T (AY353956) Tissierella creatinophila DSM 6911T (X80227)
99
AC C
Tissierella carlieri LBN 295T (GQ461821)
99
Clostridium hastiforme DSM 5675T (X80841) 100 Tissierella praeacuta NCTC 11158T (X80832)
Sporobacterium olearium DSM 12504T (AF116854) 100
0.02
Clostridium butyricum VPI3266T (AJ458420)
ACCEPTED MANUSCRIPT
Collinsella tanakaei DSM 22478T (AB490807) RI PT
Collinsella aerofaciens DSM 3979T (AB011816)
Collinsella ihuae GD8 (LN881598) M AN U
SC
T
TE D
Collinsella instestinalis DSM 13280T (AB031063) Collinsella stercoris DSM 13279T (AB031061) AC C
EP
100
0.01
Coriobacterium glomerans DSM 20642T (X79048)
S2052-2975(17)30005-7
DOI:
10.1016/j.nmni.2017.01.005
Reference:
NMNI 293
To appear in:
New Microbes and New Infections
Received Date: 9 December 2016 Revised Date:
5 January 2017
Accepted Date: 9 January 2017
Please cite this article as: Durand GA, Cadoret F, Lagier JC, Fournier PE, Raoult D, Description of “Gorbachella massiliensis” gen. nov., sp. nov., “Fenollaria timonensis” sp. nov., “Intestinimonas timonensis” sp. nov., “Collinsella ihuae” sp. nov. isolated from healthy fresh stools with culturomics, New Microbes and New Infections (2017), doi: 10.1016/j.nmni.2017.01.005. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
ACCEPTED MANUSCRIPT Description of “Gorbachella massiliensis” gen. nov., sp. nov., “Fenollaria timonensis” sp. nov., “Intestinimonas timonensis” sp. nov., “Collinsella ihuae” sp. nov. isolated from healthy fresh stools with culturomics
RI PT
G.A. Durand, F. Cadoret, J.C. Lagier, P.E. Fournier and D. Raoult*
Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 27 Boulevard Jean
SC
Moulin, 13385, Marseille cedex 05, France
M AN U
* Corresponding author: Pr. Didier Raoult: [email protected]
Running head: Gorbachella massiliensis gen. nov., sp. nov., Fenollaria timonensis sp. nov.,
TE D
Intestinimonas timonensis sp. nov., Collinsella ihuae sp. nov.
AC C
EP
Keywords: Gorbachella massiliensis, Fenollaria timonensis, Intestinimonas timonensis, Collinsella ihuae, gut microbiota
ACCEPTED MANUSCRIPT Abstract:
2
We report here the main characteristics of “Gorbachella massiliensis” GD7T gen. nov., sp.
3
nov., “Fenollaria timonensis” GD5T sp. nov., “Intestinimonas timonensis” GD4T sp. nov.,
4
and “Collinsella ihuae” sp. nov. GD8T isolated from one fresh stool of a French volunteer.
5
We used a bacterial culturomics approach combined with taxono-genomics.
RI PT
1
6
In our study concerning the intolerant oxygen species from human gut microbiota, we
8
isolated in 2015 using a bacterial culturomics approach four bacteria that could not be
9
identified
by
matrix-assisted
laser
SC
7
desorption-ionization
mass
spectrometry
(http://www.mediterraner-infection.com/article.php?laref=256&titre=urms-database)
11
Microflex spectrometer (Bruker Daltonics, Brenen, Germany) (1,2). These species were
12
isolated from the same fresh stool from a healthy volunteer. The individual has signed
13
informed consent and the study has been validated by the Ethics Committee of the IFR48
14
Federative Research Institute under the number 09-022.
on
a
TE D
M AN U
10
Strain GD7T was isolated from a dilution of the fresh sample. The species was grown
16
after 48 hours on Columbia agar supplemented with 5% sheep blood at 37°C under strict
17
anaerobic conditions. The colonies appeared translucent and rough, non-hemolytic, non-
18
motile, non-spore forming, with 1 mm size. The cells were Gram-negative, rod-shaped. The
19
strain did not show catalase or oxidase activity. The 16S rRNA gene was sequenced using
20
fD1-rP2 primers as described previously using a 3130-XL sequencer (Applied Biosciences,
21
Saint Aubin, France) (3). The strain GD7T had a 16S rRNA gene sequence identity of 93.4%
22
with Subdoligranulum variabile strain BI 114T (NR_028997), the phylogenetically closest
23
species with standing in nomenclature (Figure 1). This similarity < 98.65% leads us to
24
putatively classify GD7T as a new member in the Ruminococcaceae family of Firmicutes (4).
25
Therefore we propose the creation of the new genus “Gorbachella” (Gor.ba.chel'la. NL gen
AC C
EP
15
ACCEPTED MANUSCRIPT 26
fem, in honor of the microbiologist Sherwood Gorbach (Tufts University School of Medicine,
27
Boston, Massachusetts, USA)). GD7T is the type strain of the species Gorbachella
28
massiliensis (ma.ssi.li.en’sis L. adj. fem to Massilia, the latin name of Marseille, France,
29
where this strain was isolated). Strain GD5T was isolated from the fresh sample after 48-h anaerobic growth on
31
Columbia agar supplemented with 5% sheep blood at 37°C. The colonies appeared to be
32
translucent, rough, non-hemolytic, motile, non-spore forming, with 1 mm size. The cells were
33
rod-shaped with Gram-negative staining. Oxidase and catalase activities were negative. Strain
34
GD5T showed 97.4% sequence homology with the 16S RNA of Fenollaria massiliensis strain
35
9401234T (NR_133038) (Figure 2) (5). So we propose to classify GD5T as a new species
36
within the genus Fenollaria in the phylum Firmicutes (4). GD5T is the type strain of the
37
species “Fenollaria timonensis” (ti.mo.nen’sis L. adj. fem to Timone, the name of the main
38
hospital of Marseille, France, where this strain was isolated).
M AN U
SC
RI PT
30
Strain GD4T was isolated after 48-h anaerobic growth on Columbia agar
40
supplemented with 5% sheep blood and 5% rumen fluid at 37°C. The colonies appeared
41
translucent, rough, non-hemolytic, motile, non-spore forming, with 1 mm size. The cells were
42
Gram-negative. Catalase and oxidase activities were negative. Strain GD4T presented a
43
sequence identity of 97.08% with 16S rRNA sequence of Intestinimonas butyriciproducens
44
DSM 26588T (NR_118554), the closest species with a validly name (Figure 1). We propose to
45
putatively classify GD4T as a new member of the genus Intestinimonas in the phylum
46
Firmicutes (4). GD4T is the type strain of the species “Intestinimonas timonensis”
47
(ti.mo.nen’sis L. adj. fem to Timone, the name of the main hospital of Marseille, France,
48
where this strain was isolated).
AC C
EP
TE D
39
49
“Collinsella ihuae” strain GD8T was isolated after 48-h anaerobic growth on
50
Columbia agar supplemented with 5% sheep blood and 5% rumen fluid at 37°C. Colonies
ACCEPTED MANUSCRIPT appeared as microcolonies rough, non-hemolytic, motile, non-spore forming, with 0.5 mm
52
size. The cells were rod-shaped with Gram-positive staining. Catalase and oxidase activities
53
were negative. The 16S rRNA sequence of the strain GD8T presented a identity of 96.2% with
54
the 16S rRNA sequence of Collinsella tanakaei strain JCM 16071 (NR_113273), the closest
55
phylogenetic species with nomenclature (Figure 3) (6). Then we propose the creation of the
56
new species “Collinsella ihuae” within the phylum Actinobacteria (4). GD8T is the type strain
57
of the species “Collinsella ihuae” (i.hu.ae L. adj. fem to Institut Hospitalo-Universitaire
58
(IHU), the name of the name of the laboratory (Marseille, France) where this strain was
59
isolated).
60
MALDI-TOF-MS spectra accession numbers
61
The MALDI-TOF-MS spectra of these species are available at http://mediterranee-
62
infection.com/article.php? laref=256&titre=urms-database.
63
(Last access 2016/12/07)
64
Nucleotide sequence accession number
65
The 16S r RNA gene sequences were deposited in Genbank under accession numbers:
66
“Gorbachella massiliensis” GD7T (LN870316), “Fenollaria timonensis” GD5T (LN881613),
67
“Intestinimonas timonensis” GD4T (LN870298) and “Collinsella ihuae” GD8T (LN881598).
68
Deposit in a culture collection.
69
The strains were deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR,
70
WDCM 875) under numbers “Gorbachella massiliensis” GD7T (P2021), “Fenollaria
71
timonensis” GD5T (P2133), “Intestinimonas timonensis” GD4T (P2010) and “Collinsella
72
ihuae” GD8T (P2019).
73
Conflict of interest:
74
None to declare.
75
Funding sources:
AC C
EP
TE D
M AN U
SC
RI PT
51
ACCEPTED MANUSCRIPT 76
This work was funded by Fondation Mediterrannée-Infection.
AC C
EP
TE D
M AN U
SC
RI PT
77
ACCEPTED MANUSCRIPT Figure legend
79
Figure 1: Phylogenetic tree showing the position of “Intestinimonas timonensis” GD4T and
80
“Gorbachella massiliensis” GD7T relative to other phylogenetically-close neighbors.
81
Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained with
82
kimura two parameter models using the maximum-likelihood method within the MEGA
83
software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the
84
analysis 1,000 times to generate a majority consensus tree. Only bootstrap values >95% are
85
displayed. The scale bar indicates a 2% nucleotide sequence divergence.
86
Figure 2: Phylogenetic tree showing the position of “Fenollaria timonensis” GD5T relative to
87
other phylogenetically-close neighbors. Alignment and phylogenetic inferences were done as
88
described for Figure 1.
89
Figure 3: Phylogenetic tree showing the position of “Collinsella ihuae” GD8T relative to
90
other phylogenetically-close neighbors. Alignment and phylogenetic inferences were done as
91
described for Figure 1. The scale bar indicates a 1% nucleotide sequence divergence.
AC C
EP
TE D
M AN U
SC
RI PT
78
ACCEPTED MANUSCRIPT 92
References
93
1. Lagier J-C, Hugon P, Khelaifia S, Fournier P-E, La Scola B, Raoult D. The rebirth of
94
culture in microbiology through the example of culturomics to study human gut
95
microbiota. Clin Microbiol Rev. 2015 Jan;28(1):237–64. 2. Lagier J-C, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P, et al. Culture of
RI PT
96 97
previously uncultured members of the human gut microbiota by culturomics. Nat
98
Microbiol. 2016 Nov 7;1:16203.
3. Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D. 16S ribosomal DNA
SC
99
sequence analysis of a large collection of environmental and clinical unidentifiable
101
bacterial isolates. J Clin Microbiol. 2000 Oct;38(10):3623–30.
M AN U
100
102
4. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average
103
nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of
104
prokaryotes. Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):346–51. 4. Pagnier I, Croce O, Robert C, Raoult D, La Scola B. Non-contiguous finished genome
TE D
105 106
sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of
107
anaerobic bacterium. Stand Genomic Sci. 2014 Jun 15;9(3):704–17. 5. Nagai F, Watanabe Y, Morotomi M. Slackia piriformis sp. nov. and Collinsella tanakaei
EP
108
sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces. Int J
110
Syst Evol Microbiol. 2010 Nov;60(Pt 11):2639–46.
111
AC C
109
ACCEPTED MANUSCRIPT
Clostridium orbiscindens DSM 6740T (Y18187)
100 100
Eubacterium plautii CCUG 28093T (AY724678) Pseudoflavonifractor capillosus ATCC 29799T (AY136666)
100
RI PT
Intestinimonas timonensis GD4T (LN870298) Intestinimonas butyriciproducens DSM 26588T (KC311367)
99
Clostridium viride DSM 6836T (X81125)
SC
Oscillibacter valericigenes DSM 18026T (AB238598)
100
Oscillibacter ruminantium GH1T (JF750939)
M AN U
100
Sporobacter termitidis DSM 10068T (Z49863)
Papillibacter cinnaminovorans DSM 12816T (AF167711)
96
TE D
Anaerotruncus colihominis 14565T (AJ315980) Hydrogenoanaerobacterium saccharovorans SW512T (EU158190)
100
EP
Anaerofilum agile DSM 4272T (X98011)
100 99
AC C
100
Gorbachella massiliensis GD7T (LN870316) Faecalibacterium prausnitzii ATCC 27768T (AJ413954) Gemmiger formicilis ATCC 27749T (GU562446) 100
0.02
Anaerofilum pentosovorans DSM 7168T (X97852)
Subdoligranulum variabile BI 114T (AJ518869)
ACCEPTED MANUSCRIPT
Peptoniphilus grossensis ph5 (NR125605) Peptoniphilus hareii DSM 10020T (Y07839)
100 100
Peptoniphilus lacrimalis CCUG 31350T (AF542230)
RI PT
Anaerosphaera aminiphila DSM 21120T (AB298735) Peptoniphilus asaccharolyticus CCUG 9988T (AF542228) 96
100
Peptoniphilus indolicus DSM 20464T (AY153431)
SC
Peptoniphilus ivorii DSM 10022T (Y07840)
M AN U
Bacteroides coagulans EUH 581-73T (HF558387) Fenollaria timonensis GD5T (LN881613)
98 100
Fenollaria massiliensis 9401234T (NR133038)
Keratinibaculum paraultunense KD-1T (KC188660) Clostridium ultunense DSM 10521T (Z69293)
TE D
100
Sporanaerobacter acetigenes Lup33T (AF358114.2)
EP
Soehngenia saccharolytica DSM 12858T (AY353956) Tissierella creatinophila DSM 6911T (X80227)
99
AC C
Tissierella carlieri LBN 295T (GQ461821)
99
Clostridium hastiforme DSM 5675T (X80841) 100 Tissierella praeacuta NCTC 11158T (X80832)
Sporobacterium olearium DSM 12504T (AF116854) 100
0.02
Clostridium butyricum VPI3266T (AJ458420)
ACCEPTED MANUSCRIPT
Collinsella tanakaei DSM 22478T (AB490807) RI PT
Collinsella aerofaciens DSM 3979T (AB011816)
Collinsella ihuae GD8 (LN881598) M AN U
SC
T
TE D
Collinsella instestinalis DSM 13280T (AB031063) Collinsella stercoris DSM 13279T (AB031061) AC C
EP
100
0.01
Coriobacterium glomerans DSM 20642T (X79048)