NEW MICROBES IN HUMANS
“Lascolabacillus massiliensis”: a new species isolated from the human gut M. Beye, S. Bakour, S. I. Traore, D. Raoult and P.-E. Fournier Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille cedex 5, France
Abstract We report here the main characteristics of “Lascolabacillus massiliensis” strain SIT8 (CSUR P1560) that was isolated from the stool of a healthy 28-month-old boy. New Microbes and New Infections © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. Keywords: Culturomics, taxonomy, Lascolabacillus massiliensis, new species Original Submission: 4 March 2016; Revised Submission: 10 March 2016; Accepted: 14 March 2016 Article published online: 19 March 2016
Corresponding author: P.-E. Fournier, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 bd Jean Moulin, 13385 Marseille cedex 5, France E-mail: [email protected]
In 2015, as part of a culturomics study of the human microbiome [1], we isolated from the stool of a healthy 28-monthold Senegalese boy a bacterial strain that could not be identified by our systematic matrix-assisted laser desorptionionization time-of-flight screening (http://www.mediterraneeinfection.com/article.php?laref=256&titre=urms-database) on a MicroFlex spectrometer (Bruker Daltonics, Bremen, Germany) [2]. The patient’s parents gave informed signed
consent, and the agreement of the National Ethics Committee of Senegal and the local ethics committee of the IFR48 (Marseille, France) were obtained under numbers 11-017 and 09-022, respectively. The initial growth was obtained after 10 days of culture in a 5% sheep blood-enriched sheep rumen medium in aerobic atmosphere at 37°C. The bacterium was sub-cultured on 5% sheep blood-enriched Columbia agar (bioMérieux, Marcy l’Etoile, France) and grew in 24 hours at 37°C in both aerobic and anaerobic conditions. Agar-grown colonies were pale grey and 1.5 mm in diameter. Bacterial cells were Gram-negative, rod-shaped and polymorphic, ranging in length from 1.5 to 10 μm. Strain SIT8 was catalaseand oxidase-negative. The 16S rRNA gene was sequenced using the fD1-rP2 primers as previously described, using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain SIT8 exhibited a 94.14% sequence identity with Proteiniphilum acetatigenes strain TB107 (GenBank accession NR_043154), the phylogenetically closest species with standing in nomenclature (Fig. 1), which putatively classifies it as a member of a new genus within the family Porphyromonadaceae in the phylum Bacteroidetes [3]. Proteiniphilum acetatigenes was described in 2005 [4]. This obligately anaerobic bacterium was isolated from a bioreactor treating brewery wastewater. The P. acetatigenes cells are Gram-negative rods that do not exhibit oxidase and catalase activities. Another closely related species, Petrimonas sulfuriphila, isolated from a biodegraded oil reservoir, is also an obligately anaerobic Gram-negative rod-shaped bacterium [5]. In contrast with Proteiniphilum acetatigenes and Petrimonas sulfuriphila, strain SIT8 is facultatively anaerobic and associated with humans. However, among the other closely related genera, the Dysgonomonas genus also contains facultatively anaerobic species such as Dysgonomonas gadei and Dysgonomonas capnocytophagoides (6). These two species are Gram-negative coccobacilli that variably express catalase but not oxidase, and were also obtained from human specimens [6]. Strain SIT8 exhibiting a 16S rRNA sequence divergence > 5% with its phylogenetically closest species with standing in nomenclature [7], we propose the creation of the new genus Lascolabacillus gen. nov. in honour of the French bacteriologist Bernard La Scola for his contributions to clinical microbiology. Strain SIT8 is the type strain of the new species Lascolabacillus massiliensis gen. nov., sp. nov.
New Microbe and New Infect 2016; 11: 91–92 New Microbes and New Infections © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) http://dx.doi.org/10.1016/j.nmni.2016.03.002
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FIG. 1. Phylogenetic tree showing the position of Lascolabacillus massiliensis strain SIT8 (underlined) relative to other phylogenetically close members of the family Porphyromonadaceae. GenBank Accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were 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 values >70% were displayed. The scale bar indicates a 2% nucleotide sequence divergence.
Nucleotide sequence accession number. The 16S rRNA gene sequence was deposited in GenBank under Accession number LN827535. Deposit in a culture collection. Strain SIT8 was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P1560.
Conflict of Interest The authors certify that they do not have any conflict of interest in relation to this research.
Acknowledgements This research is funded by the Mediterranée-Infection Foundation.
References [1] 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. [2] Seng P, Abat C, Rolain JM, Colson P, Lagier JC, Gouriet F, et al. Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2013;51:2182–94. [3] Euzeby J. Validation list N°143. Int J Syst Evol Microbiol 2012;62:1–4. [4] Chen S, Dong X. Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater. Int J Syst Evol Microbiol 2005;55:2257–61. [5] Grabowski A, Tindall BJ, Bardin V, Blanchet D, Jeanthon C. Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir. Int J Syst Evol Microbiol 2005;55:1113–21. [6] Hofstad T, Olsen I, Eribe ER, Falsen E, Collins MD, Lawson PA. Dysgonomonas gen. nov. to accommodate Dysgonomonas gadei sp. nov., an organism isolated from a human gall bladder, and Dysgonomonas capnocytophagoides (formerly CDC group DF-3). Int J Syst Evol Microbiol 2000;50:2189–95. [7] Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007;17:377–86.
New Microbes and New Infections © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases, NMNI, 11, 91–92 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
“Lascolabacillus massiliensis”: a new species isolated from the human gut M. Beye, S. Bakour, S. I. Traore, D. Raoult and P.-E. Fournier Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille cedex 5, France
Abstract We report here the main characteristics of “Lascolabacillus massiliensis” strain SIT8 (CSUR P1560) that was isolated from the stool of a healthy 28-month-old boy. New Microbes and New Infections © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. Keywords: Culturomics, taxonomy, Lascolabacillus massiliensis, new species Original Submission: 4 March 2016; Revised Submission: 10 March 2016; Accepted: 14 March 2016 Article published online: 19 March 2016
Corresponding author: P.-E. Fournier, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 bd Jean Moulin, 13385 Marseille cedex 5, France E-mail: [email protected]
In 2015, as part of a culturomics study of the human microbiome [1], we isolated from the stool of a healthy 28-monthold Senegalese boy a bacterial strain that could not be identified by our systematic matrix-assisted laser desorptionionization time-of-flight screening (http://www.mediterraneeinfection.com/article.php?laref=256&titre=urms-database) on a MicroFlex spectrometer (Bruker Daltonics, Bremen, Germany) [2]. The patient’s parents gave informed signed
consent, and the agreement of the National Ethics Committee of Senegal and the local ethics committee of the IFR48 (Marseille, France) were obtained under numbers 11-017 and 09-022, respectively. The initial growth was obtained after 10 days of culture in a 5% sheep blood-enriched sheep rumen medium in aerobic atmosphere at 37°C. The bacterium was sub-cultured on 5% sheep blood-enriched Columbia agar (bioMérieux, Marcy l’Etoile, France) and grew in 24 hours at 37°C in both aerobic and anaerobic conditions. Agar-grown colonies were pale grey and 1.5 mm in diameter. Bacterial cells were Gram-negative, rod-shaped and polymorphic, ranging in length from 1.5 to 10 μm. Strain SIT8 was catalaseand oxidase-negative. The 16S rRNA gene was sequenced using the fD1-rP2 primers as previously described, using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain SIT8 exhibited a 94.14% sequence identity with Proteiniphilum acetatigenes strain TB107 (GenBank accession NR_043154), the phylogenetically closest species with standing in nomenclature (Fig. 1), which putatively classifies it as a member of a new genus within the family Porphyromonadaceae in the phylum Bacteroidetes [3]. Proteiniphilum acetatigenes was described in 2005 [4]. This obligately anaerobic bacterium was isolated from a bioreactor treating brewery wastewater. The P. acetatigenes cells are Gram-negative rods that do not exhibit oxidase and catalase activities. Another closely related species, Petrimonas sulfuriphila, isolated from a biodegraded oil reservoir, is also an obligately anaerobic Gram-negative rod-shaped bacterium [5]. In contrast with Proteiniphilum acetatigenes and Petrimonas sulfuriphila, strain SIT8 is facultatively anaerobic and associated with humans. However, among the other closely related genera, the Dysgonomonas genus also contains facultatively anaerobic species such as Dysgonomonas gadei and Dysgonomonas capnocytophagoides (6). These two species are Gram-negative coccobacilli that variably express catalase but not oxidase, and were also obtained from human specimens [6]. Strain SIT8 exhibiting a 16S rRNA sequence divergence > 5% with its phylogenetically closest species with standing in nomenclature [7], we propose the creation of the new genus Lascolabacillus gen. nov. in honour of the French bacteriologist Bernard La Scola for his contributions to clinical microbiology. Strain SIT8 is the type strain of the new species Lascolabacillus massiliensis gen. nov., sp. nov.
New Microbe and New Infect 2016; 11: 91–92 New Microbes and New Infections © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) http://dx.doi.org/10.1016/j.nmni.2016.03.002
92
New Microbes and New Infections, Volume 11 Number C, May 2016
NMNI
FIG. 1. Phylogenetic tree showing the position of Lascolabacillus massiliensis strain SIT8 (underlined) relative to other phylogenetically close members of the family Porphyromonadaceae. GenBank Accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were 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 values >70% were displayed. The scale bar indicates a 2% nucleotide sequence divergence.
Nucleotide sequence accession number. The 16S rRNA gene sequence was deposited in GenBank under Accession number LN827535. Deposit in a culture collection. Strain SIT8 was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P1560.
Conflict of Interest The authors certify that they do not have any conflict of interest in relation to this research.
Acknowledgements This research is funded by the Mediterranée-Infection Foundation.
References [1] 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. [2] Seng P, Abat C, Rolain JM, Colson P, Lagier JC, Gouriet F, et al. Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2013;51:2182–94. [3] Euzeby J. Validation list N°143. Int J Syst Evol Microbiol 2012;62:1–4. [4] Chen S, Dong X. Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater. Int J Syst Evol Microbiol 2005;55:2257–61. [5] Grabowski A, Tindall BJ, Bardin V, Blanchet D, Jeanthon C. Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir. Int J Syst Evol Microbiol 2005;55:1113–21. [6] Hofstad T, Olsen I, Eribe ER, Falsen E, Collins MD, Lawson PA. Dysgonomonas gen. nov. to accommodate Dysgonomonas gadei sp. nov., an organism isolated from a human gall bladder, and Dysgonomonas capnocytophagoides (formerly CDC group DF-3). Int J Syst Evol Microbiol 2000;50:2189–95. [7] Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007;17:377–86.
New Microbes and New Infections © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases, NMNI, 11, 91–92 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
