Accepted Manuscript
Isolation of a new species Peptoniphilus phoceensis from the human gut
Gaël Mourembou, Sory Ibrahima Traore, Jaishriram Rathored, Saber Khelaifia, Jean Christophe Lagier, Caroline Michelle, Didier Raoult, Matthieu Million
PII: S2052-2975(16)30011-7 DOI: 10.1016/j.nmni.2016.04.002 Reference: NMNI 154
To appear in: New Microbes and New Infections Received Date: 23 March 2016
Revised Date: 30 March 2016 Accepted Date: 5 April 2016
Please cite this article as: Mourembou G, Traore SI, Rathored J, Khelaifia S, Lagier JC, Michelle C, Raoult D, Million M, Isolation of a new species Peptoniphilus phoceensis from the human gut, New Microbes and New Infections (2016), doi: 10.1016/j.nmni.2016.04.002.
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1 Isolation of a new species Peptoniphilus phoceensis from the human gut
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Running head: Peptoniphilus phoceensis sp. nov.
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Gaël Mourembou1,2, Sory Ibrahima Traore1, Jaishriram Rathored1, Saber Khelaifia1, Jean 3
Christophe Lagier,1 Caroline Michelle,1 Didier Raoult1,3, Matthieu Million1*
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1. Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 5
Marseille, France 6
2. Ecole Doctorale Régionale d’Afrique Centrale, B.P. 876 Franceville, Gabon 7
3.Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz 8
University, Jeddah, Saudi Arabia 9
*Corresponding author: Matthieu MILLION, Aix Marseille Université, URMITE, UM63, 10
CNRS 7278, IRD 198, INSERM 1095, Marseille, France, E-mail:
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Keywords: Peptoniphilus phoceensis sp. nov., taxonogenomics, culturomics, gut microbiota, 13
human 14
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Isolation of a new species Peptoniphilus phoceensis from the human gut 1
Running head: Peptoniphilus phoceensis sp. nov.
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2 Abstract
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Taxonogenomics coupled with culturomics lead to descriptions of new bacteria. Thanks to 4
this strategy, we report the main characteristics of “Peptoniphilus phoceensis” strain SIT 15, a 5
new bacterium isolated from a stool sample of a one-year-old healthy Senegalese boy.
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Culturomics, recently developed alternative to traditional culture methods, improve the 7
likelihood of detecting bacteria (1,2). Applied to a stool sample from a healthy one-year-old 8
male from Senegal, a bacterium strain SIT15 was isolated but Matrix-Assisted laser 9
desorption-ionization time-of-fligh (MALDI-TOF MS) failed to provide its systematic 10
identification (http://www.mediterraneeinfection.com/ article.php?laref=256&titre=urms- 11
database) on a Microflex spectrometer (Bruker Daltonics, Germany). The stool was collected 12
in 2014 after the protocol was accepted by the National ethics committee of Senegal and IFR 13
48 (Marseille, France) under numbers 11-017 and 09-12-022, respectively. Parents’ informed 14
and signed consent was obtained. Strain SIT15 was isolated after 15 days of culture in a 15
sterile bottle containing a marine medium (bioMérieux, Marcy l’Etoile, France) followed by a 16
subculture in 5% sheep blood-enriched Columbia agar (bioMérieux,) under anaerobic 17
conditions at 37°C (4-6). Gram-positive coccus, strain SIT 15 exhibited catalase activity 18
without oxidase and grows after 24 hours. Individual colonies are opaque and have a diameter 19
of 1 mm on agar plates and individual cells exhibit a diameter of 1.5 µm. Motile and non 20
spore-forming, it grows between 28°C-40°C (optimal at 37°C) and supports salinity around 21
0% (0-5%) and pH ranging between 6 and 8.5. The identification was completed by 22
sequencing the 16S rRNA using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, 23
France) and an adequate set of primer rP2-fD1 (4-6). The 16S rRNA sequence obtained was 24
corrected and assembled using ChromasPro 1.34 (Technelysium Pty. Ltd., Tewantin, 25
Australia), then a BLASTn was performed against online GenBank database 26
(http://blast.ncbi.nlm.nih.gov.gate1. inist.fr/Blast. cgi). The results demonstrate that the 16S 27
rRNA sequence of strain SIT15 (Genbank accession LN881605) exhibited 96.95% of identity 28
with the closest species Peptoniphilus grossensis strain ph5 (Figure1) (7). This value is lower 29
than the threshold recommended to delineate a new species (8), therefore the strain SIT15 was 30
putatively classified as a new species called Peptoniphilus phoceensis sp nov. strain SIT15, 31
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4 belonging to the genus Peptoniphilus within the family Peptoniphilaceae created in 2014 by 32
Johnson (9).
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The closest species of P. phoceensis (P. grossensis strain ph5, Peptoniphilus obesi strain ph1, 34
Peptoniphilus timonensis strain JC401, and Peptoniphilus gorbachii strain WAL10418) are 35
anaerobic Gram positive without oxidase and nitrate reductase activities (7). P. grossensis 36
strain ph5, P. obesi strain ph1, and P. timonensis strain JC401 are non-motile (7). In contrast 37
to strain SIT15, P. grossensis strain ph5 and P. timonensis strain JC401 can produce 38
endospores (7).
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The divergence of 16S rRNA sequences between P. phoceensis strain SIT15 and the 40
phylogenetically closest species was more than 2%, exceeding the threshold value of 1.3%
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recommended (8). Thus, we propose the creation of the new species P. phoceensis sp. nov for 42
“Phocaea”, the Hellenic city of the sailors who settled in Marseille (France), 2600 years ago, 43
where this bacterium was isolated. Strain SIT 15T is the type strain of the new species 44
Peptoniphilus phoceensis sp. nov.
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Description of gut anaerobes, previously shown to be depleted in malnutrition (10), is of 46
critical importance to decipher the links between gut microbiota and human health.
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Nucleotide sequence accession number. The 16S rRNA gene sequence was deposited in 48
GenBank under accession number LN881605.
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Deposit in a culture collection. Strain SIT 15 was deposited in the Collection de Souches de 50
l’Unité des Rickettsies (CSUR) under number P2336.
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Acknowledgments 52
We thank Mediterranee-Infection foundation for financial support and Karolina Griffiths for 53
English correction.
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6 References
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8 Figure legend
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Figure 1: Phylogenetic tree highlighting the position of Peptoniphilus phoceensis strain 85
SIT15.
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The scale bar represents 0.02% nucleotide sequence divergence.
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