- Email: [email protected]
“Nigerium massiliense” gen. nov., sp. nov., a new bacterium isolated from the gut from a patient with acute malnutrition
Human Microbiome Journal 1 (2016) 12–13
Contents lists available at ScienceDirect
Human Microbiome Journal journal homepage: www.elsevier.com/locate/humic
‘‘Nigerium massiliense” gen. nov., sp. nov., a new bacterium isolated from the gut from a patient with acute malnutrition Sory Ibrahima Traore a, Souleymane Brah b, Jeremy Delerce a, Pierre Edouard Fournier a, Didier Raoult a,c, Sophie Edouard a,⇑ a Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France b Hôpital National de Niamey, Niamey, Niger c Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
a r t i c l e
i n f o
Article history: Received 15 July 2016 Revised 12 August 2016 Accepted 16 August 2016 Available online 20 August 2016
a b s t r a c t We propose the main characteristics of a new bacterium named ‘‘Nigerium massiliense” strain SIT5 (CSURP1302) that was isolated from the stool of a 2-year-old Nigerian child suffering from kwashiorkor, a form of severe acute malnutrition. Ó 2016 Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Culturomics Taxonomy Genomics Taxono-genomics ‘‘Nigerium massiliense”
In 2014, we used a culturomics approach [1] with the objective of drawing an exhaustive repertoire of the bacteria present in the human gut of a 2-year-old child suffering from kwashiorkor, a form of acute severe malnutrition. The parents of the patient provided signed informed consent and the study was validated by the ethics committee of the Institut Federatif de Recherche IFR48 under number 09-022. We isolated a bacterial strain from the stool of the child that could not be identified (score < 1.7) by our systematic matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS) screening on a Microflex spectrometer (Bruker Daltonics, Brenen, Germany) [2]. Therefore, we sequenced the 16S rRNA gene of the bacteria using fD1-rP2 primers and a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France) for identification [3]. The initial growth was obtained on blood agar at 37 °C (bioMérieux, Marcy l’Etoile, France) after 21 days of incubation of the specimen in a Columbia broth medium [4], at 28 °C in anaerobic atmosphere. The strain forms small smooth and transparent colonies on blood agar with a diameter of 0.2–0.4 mm. The strain grows also in aerobic conditions. Bacterial cells were Gram-positive cocci ranging in diameter from 0.8 to 1 lm. Strain SIT5 was catalasepositive and oxidase-negative. ⇑ Corresponding author. E-mail address: [email protected] (S. Edouard).
This 16S RNA sequence of the strain SIT5 exhibited 93.02% of similarity with Propioniciclava tarda strain WR061 (Genbank accession number NR112669.1), the phylogenetically closest species with standing nomenclature (Fig. 1), which putatively classifies it as a new genus named Nigerium within the family Propionibacteriaceae in the phylum Actinobacteria. P. tarda is a facultative anaerobic Gram positive rod isolated for the first time in 2011 from a ricestraw residue in a methanogenic reactor treating waste from cattle farms in Japan [5]. Strain SIT5 exhibited a similarity rate with P. tarda and the others closest species lower than the 95% cut-off gene sequence established for the definition of new bacterial genera [6,7]. Consequently, Nigerium massiliense gen. nov., sp. nov., strain SIT5, was classified as new genus that we named Nigerium (ni.ger.i’um. N.L. neutr. gen. n, referring to Niger, name of the country where the child lives and where the sample was collected). The strain SIT5 is the type strain of the new species ‘‘Nigerium massiliense” gen. nov., sp. nov. (mas. il.i.en’se. L. gen. neutr. n. massiliense, of Massilia, the Latin name of Marseille, the place where the strain SIT5 was isolated). MALDI-TOF-MS spectrum accession number The MALDI-TOF-MS spectrum of ‘‘Nigerium massiliense” available at http://mediterranee-infection.com/article.php?laref=256& titre=urms-database.
http://dx.doi.org/10.1016/j.humic.2016.08.001 2452-2317/Ó 2016 Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
S.I. Traore et al. / Human Microbiome Journal 1 (2016) 12–13
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Fig. 1. Phylogenetic tree showing the position of ‘‘Nigerium massiliense” strain SIT5 relative to other phylogenetically-close neighbours. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Only the bootstraps score at least 90% were retained. The scale bar indicates a 1% nucleotide sequence divergence.
Nucleotide sequence accession number
References
The 16S rRNA gene sequence was deposited in Genbank under accession number LK985392.1.
[1] Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012;18:1185–93. [2] Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009;49:543–51. [3] Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 2000;38:3623–30. [4] Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult D. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015;28:237–64. [5] Sugawara Y, Ueki A, Abe K, Kaku N, Watanabe K, Ueki K. Propioniciclava tarda gen. nov., sp. nov., isolated from a methanogenic reactor treating waste from cattle farms. Int J Syst Evol Microbiol 2011;61:2298–303. [6] Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–51. [7] Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152.
Deposit in a culture collection Strain SIT5 was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P1302.
Conflict of interest None to declare.
Funding sources This work was funded by Méditerranée-Infection Foundation.
Contents lists available at ScienceDirect
Human Microbiome Journal journal homepage: www.elsevier.com/locate/humic
‘‘Nigerium massiliense” gen. nov., sp. nov., a new bacterium isolated from the gut from a patient with acute malnutrition Sory Ibrahima Traore a, Souleymane Brah b, Jeremy Delerce a, Pierre Edouard Fournier a, Didier Raoult a,c, Sophie Edouard a,⇑ a Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France b Hôpital National de Niamey, Niamey, Niger c Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
a r t i c l e
i n f o
Article history: Received 15 July 2016 Revised 12 August 2016 Accepted 16 August 2016 Available online 20 August 2016
a b s t r a c t We propose the main characteristics of a new bacterium named ‘‘Nigerium massiliense” strain SIT5 (CSURP1302) that was isolated from the stool of a 2-year-old Nigerian child suffering from kwashiorkor, a form of severe acute malnutrition. Ó 2016 Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Culturomics Taxonomy Genomics Taxono-genomics ‘‘Nigerium massiliense”
In 2014, we used a culturomics approach [1] with the objective of drawing an exhaustive repertoire of the bacteria present in the human gut of a 2-year-old child suffering from kwashiorkor, a form of acute severe malnutrition. The parents of the patient provided signed informed consent and the study was validated by the ethics committee of the Institut Federatif de Recherche IFR48 under number 09-022. We isolated a bacterial strain from the stool of the child that could not be identified (score < 1.7) by our systematic matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS) screening on a Microflex spectrometer (Bruker Daltonics, Brenen, Germany) [2]. Therefore, we sequenced the 16S rRNA gene of the bacteria using fD1-rP2 primers and a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France) for identification [3]. The initial growth was obtained on blood agar at 37 °C (bioMérieux, Marcy l’Etoile, France) after 21 days of incubation of the specimen in a Columbia broth medium [4], at 28 °C in anaerobic atmosphere. The strain forms small smooth and transparent colonies on blood agar with a diameter of 0.2–0.4 mm. The strain grows also in aerobic conditions. Bacterial cells were Gram-positive cocci ranging in diameter from 0.8 to 1 lm. Strain SIT5 was catalasepositive and oxidase-negative. ⇑ Corresponding author. E-mail address: [email protected] (S. Edouard).
This 16S RNA sequence of the strain SIT5 exhibited 93.02% of similarity with Propioniciclava tarda strain WR061 (Genbank accession number NR112669.1), the phylogenetically closest species with standing nomenclature (Fig. 1), which putatively classifies it as a new genus named Nigerium within the family Propionibacteriaceae in the phylum Actinobacteria. P. tarda is a facultative anaerobic Gram positive rod isolated for the first time in 2011 from a ricestraw residue in a methanogenic reactor treating waste from cattle farms in Japan [5]. Strain SIT5 exhibited a similarity rate with P. tarda and the others closest species lower than the 95% cut-off gene sequence established for the definition of new bacterial genera [6,7]. Consequently, Nigerium massiliense gen. nov., sp. nov., strain SIT5, was classified as new genus that we named Nigerium (ni.ger.i’um. N.L. neutr. gen. n, referring to Niger, name of the country where the child lives and where the sample was collected). The strain SIT5 is the type strain of the new species ‘‘Nigerium massiliense” gen. nov., sp. nov. (mas. il.i.en’se. L. gen. neutr. n. massiliense, of Massilia, the Latin name of Marseille, the place where the strain SIT5 was isolated). MALDI-TOF-MS spectrum accession number The MALDI-TOF-MS spectrum of ‘‘Nigerium massiliense” available at http://mediterranee-infection.com/article.php?laref=256& titre=urms-database.
http://dx.doi.org/10.1016/j.humic.2016.08.001 2452-2317/Ó 2016 Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
S.I. Traore et al. / Human Microbiome Journal 1 (2016) 12–13
13
Fig. 1. Phylogenetic tree showing the position of ‘‘Nigerium massiliense” strain SIT5 relative to other phylogenetically-close neighbours. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Only the bootstraps score at least 90% were retained. The scale bar indicates a 1% nucleotide sequence divergence.
Nucleotide sequence accession number
References
The 16S rRNA gene sequence was deposited in Genbank under accession number LK985392.1.
[1] Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012;18:1185–93. [2] Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009;49:543–51. [3] Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 2000;38:3623–30. [4] Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult D. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015;28:237–64. [5] Sugawara Y, Ueki A, Abe K, Kaku N, Watanabe K, Ueki K. Propioniciclava tarda gen. nov., sp. nov., isolated from a methanogenic reactor treating waste from cattle farms. Int J Syst Evol Microbiol 2011;61:2298–303. [6] Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–51. [7] Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152.
Deposit in a culture collection Strain SIT5 was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P1302.
Conflict of interest None to declare.
Funding sources This work was funded by Méditerranée-Infection Foundation.