1
|
Banerjee A, Kang CY, An M, Koff BB, Sunder S, Kumar A, Tenuta LMA, Stockbridge RB. Fluoride export is required for the competitive fitness of pathogenic microorganisms in dental biofilm models. mBio 2024; 15:e0018424. [PMID: 38624207 PMCID: PMC11077948 DOI: 10.1128/mbio.00184-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024] Open
Abstract
Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species Streptococcus mutans and Candida albicans extrude intracellular fluoride using a CLCF F-/H+ antiporter and FEX fluoride channel, respectively, whereas oral commensal eubacteria, such as Streptococcus gordonii, export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using S. mutans with the genetic knockout of the CLCF transporter, exposure to low fluoride concentrations decreased S. mutans counts, synergistically reduced the populations of C. albicans, increased the relative proportion of oral commensal S. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with C. albicans with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride but to a lesser degree. Imaging studies indicate that S. mutans is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time. Biochemical purification of the S. mutans CLCF transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms and that S. mutans is especially susceptible to fluoride toxicity. IMPORTANCE Dental caries is a globally prevalent condition that occurs when pathogenic species, including Streptococcus mutans and Candida albicans, outcompete beneficial species, such as Streptococcus gordonii, in the dental biofilm. Fluoride is routinely used in oral hygiene to prevent dental caries. Fluoride also has antimicrobial properties, although most microbes possess fluoride exporters to resist its toxicity. This work shows that sensitization of cariogenic species S. mutans and C. albicans to fluoride by genetic knockout of fluoride exporters alters the microbial composition and pathogenic properties of dental biofilms. These results suggest that the development of drugs that inhibit fluoride exporters could potentiate the anticaries effect of fluoride in over-the-counter products like toothpaste and mouth rinses. This is a novel strategy to treat dental caries.
Collapse
Affiliation(s)
- Aditya Banerjee
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chia-Yu Kang
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Minjun An
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - B. Ben Koff
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sham Sunder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Randy B. Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
2
|
Montecillo JAV, Billacura MP, Billacura MDG. Reclassification of Aestuariicella albida as Pseudomaricurvus albidus comb. nov. and Aestuariicella hydrocarbonica as Pseudomaricurvus hydrocarbonicus comb. nov. Based on Comparative Genomics and Molecular Synapomorphies. Curr Microbiol 2024; 81:159. [PMID: 38689166 DOI: 10.1007/s00284-024-03683-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/30/2024] [Indexed: 05/02/2024]
Abstract
The genus Aestuariicella has been recently reclassified as a member of the family Cellvibrionaceae. However, the taxonomic position of the genus as a distinct member of the family has not been clarified. In the present study, we performed multilayered analyses anchored on genome sequences to clarify the relationship between the genera Aestuariicella and Pseudomaricurvus within the family Cellvibrionaceae. Phylogenetic analyses based on 16S rRNA gene, RNA polymerase beta subunit (RpoB) protein, and core gene sequences showed a well-supported tight cluster formed by the members of the two genera. Moreover, the analysis of the average amino acid identity (AAI) revealed that the members of the two genera shared 68.16-79.48% AAI, values which were within the range of observed AAI (≥ 67.23%) among the members of the same genus within the family Cellvibrionaceae. Members of the two genera also shared several common characteristics. Furthermore, molecular synapomorphies in a form of conserved signature indels were identified in six protein sequences that were exclusively shared by the members of the two genera. Based on the phylogenetic and molecular evidence presented here, we propose the reclassification of the species Aestuariicella albida and Aestuariicella hydrocarbonica as Pseudomaricurvus albidus comb. nov. and Pseudomaricurvus hydrocarbonicus comb. nov., respectively.
Collapse
Affiliation(s)
- Jake Adolf V Montecillo
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| | - Merell P Billacura
- Department of Chemistry, Mindanao State University-Main Campus, 9700, Marawi, Lanao del Sur, Philippines
| | - Maria Distressa G Billacura
- Department of Chemistry, Mindanao State University-Iligan Institute of Technology, Andres Bonifacio Avenue, Tibanga, 9200, Iligan, Lanao del Norte, Philippines
| |
Collapse
|
3
|
Ma J, Wu H, Ma Z, Wu Z. Bacterial and host factors involved in zoonotic Streptococcal meningitis. Microbes Infect 2024:105335. [PMID: 38582147 DOI: 10.1016/j.micinf.2024.105335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
Zoonotic streptococci cause several invasive diseases with high mortality rates, especially meningitis. Numerous studies elucidated the meningitis pathogenesis of zoonotic streptococci, some specific to certain bacterial species. In contrast, others are shared among different bacterial species, involving colonization and invasion of mucosal barriers, survival in the bloodstream, breaching the blood-brain and/or blood-cerebrospinal fluid barrier to access the central nervous system, and triggering inflammation of the meninges. This review focuses on the recent advancements in comprehending the molecular and cellular events of five major zoonotic streptococci responsible for causing meningitis in humans or animals, including Streptococcus agalactiae, Streptococcus equi subspecies zooepidemicus, Streptococcus suis, Streptococcus dysgalactiae, and Streptococcus iniae. The underlying mechanism was summarized into four themes, including 1) bacterial survival in blood, 2) brain microvascular endothelial cell adhesion and invasion, 3) penetration of the blood-brain barrier, and 4) activation of the immune system and inflammatory reaction within the brain. This review may contribute to developing therapeutics to prevent or mitigate injury of streptococcal meningitis and improve risk stratification.
Collapse
Affiliation(s)
- Jiale Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China; WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Huizhen Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China; WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Zhe Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China.
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China; WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China; Guangdong Provincial Key Laboratory of Research on the Technology of Pig-breeding and Pig-disease Prevention, Guangzhou 511400, China.
| |
Collapse
|
4
|
Taylor SL, Crabbé A, Hoffman LR, Chalmers JD, Rogers GB. Understanding the clinical implications of the "non-classical" microbiome in chronic lung disease: a viewpoint. Eur Respir J 2024; 63:2302281. [PMID: 38387999 DOI: 10.1183/13993003.02281-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/21/2024] [Indexed: 02/24/2024]
Affiliation(s)
- Steven L Taylor
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Luke R Hoffman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Geraint B Rogers
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| |
Collapse
|
5
|
Banerjee A, Kang CY, An M, Koff BB, Sunder S, Kumar A, Tenuta LMA, Stockbridge RB. Fluoride export is required for competitive fitness of pathogenic microorganisms in dental biofilm models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576223. [PMID: 38293214 PMCID: PMC10827179 DOI: 10.1101/2024.01.18.576223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species Streptococcus mutans and Candida albicans extrude intracellular fluoride using a CLCF F-/H+ antiporter and FEX fluoride channel, respectively, whereas commensal eubacteria, such as Streptococcus gordonii, export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using S. mutans with genetic knockout of the CLCF transporter, exposure to low fluoride concentrations decreased S. mutans counts, synergistically reduced the populations of C. albicans, increased the relative proportion of commensal S. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with C. albicans with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride, but to a lesser degree. Imaging studies indicate that S. mutans is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time, and biochemical purification the S. mutans CLCF transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms, and that S. mutans is especially susceptible to fluoride toxicity.
Collapse
Affiliation(s)
- Aditya Banerjee
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chia-Yu Kang
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Minjun An
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - B. Ben Koff
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sham Sunder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Randy B. Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
6
|
Wright MJ, Bai G. Bacterial second messenger cyclic di-AMP in streptococci. Mol Microbiol 2023; 120:791-804. [PMID: 37898560 DOI: 10.1111/mmi.15187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/10/2023] [Accepted: 10/15/2023] [Indexed: 10/30/2023]
Abstract
Cyclic dimeric adenosine monophosphate (c-di-AMP) has been well studied in bacteria, including those of the genus Streptococcus, since the first recognition of this dinucleotide in 2008. Streptococci possess a sole diadenylate cyclase, CdaA, and distinct c-di-AMP phosphodiesterases. Interestingly, cdaA is required for viability of some streptococcal species but not all when streptococci are grown in standard laboratory media. Bacteria of this genus also have distinct c-di-AMP effector proteins, diverse c-di-AMP-signaling pathways, and subsequent biological outcomes. In streptococci, c-di-AMP may influence bacterial growth, morphology, biofilm formation, competence program, drug resistance, and bacterial pathogenesis. c-di-AMP secreted by streptococci has also been shown to interact with the mammalian host and induces immune responses including type I interferon production. In this review, we summarize the reported c-di-AMP networks in seven species of the genus Streptococcus, which cause diverse clinical manifestations, and propose future perspectives to investigate the signaling molecule in these streptococcal pathogens.
Collapse
Affiliation(s)
- Michael J Wright
- Department of Internal Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| |
Collapse
|
7
|
Volokhov DV, Zagorodnyaya TA, Furtak VA, Nattanmai G, Randall L, Jose S, Gao Y, Eisenberg T, Delmonte P, Blom J, Mitchell KK. Streptococcus sciuri sp. nov., Staphylococcus marylandisciuri sp. nov. and Staphylococcus americanisciuri sp. nov., isolated from faeces of eastern grey squirrel ( Sciurus carolinensis). Int J Syst Evol Microbiol 2023; 73. [PMID: 37578899 DOI: 10.1099/ijsem.0.006015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
One novel Streptococcus strain (SQ9-PEAT) and two novel Staphylococcus strains (SQ8-PEAT and GRT3T) were isolated from faeces of a wild eastern grey squirrel. The strains were non-spore-forming, non-motile Gram-positive cocci, facultative anaerobes. The genomes for these strains were sequenced. The 16S rRNA gene and core-genome-based phylogenetic analyses showed that strain SQ9-PEAT was closely related to Streptococcus hyointestinalis, strain SQ8-PEAT to Staphylococcus pettenkoferi and Staphylococcus argensis, and strain GRT3T to Staphylococcus rostri, Staphylococcus muscae and Staphylococcus microti. Average nucleotide identity and pairwise digital DNA-DNA hybridization values calculated for these novel strains compared to type strain genomes of phylogenetically related species within the genera Streptococcus and Staphylococcus clearly revealed that strain SQ9-PEAT represents a novel species of the genus Streptococcus and strains SQ8-PEAT and GRT3T represent two novel species of the genus Staphylococcus. Phenotypical features of these novel type strains differed from the features of the type strains of other phylogenetically related species. MALDI-TOF mass spectrometry supported identification of these novel species. Based on these data, we propose one novel species of the genus Streptococcus, for which the name Streptococcus sciuri sp. nov. with the type strain SQ9-PEAT (=DSM 114656T=CCUG 76426T=NCTC 14727T) is proposed, and two novel species of the genus Staphylococcus, for which the names Staphylococcus marylandisciuri sp. nov. with the type strain SQ8-PEAT (=DSM 114685T=CCUG 76423T=NCTC 14723T) and Staphylococcus americanisciuri sp. nov. with the type strain GRT3T (=DSM 114696T=CCUG 76427T=NCTC 14722T) are proposed. The genome G+C contents are 38.29, 36.49 and 37.26 mol% and complete draft genome sizes are 1 692 266, 2 371 088 and 2 237 001 bp for strains SQ9-PEAT, SQ8-PEAT and GRT3T, respectively.
Collapse
Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tatiana A Zagorodnyaya
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Geetha Nattanmai
- Bacteriology Laboratory, Wadsworth Center, the New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Linnell Randall
- Bacteriology Laboratory, Wadsworth Center, the New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Sherly Jose
- Bacteriology Laboratory, Wadsworth Center, the New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tobias Eisenberg
- Hessian State Laboratory (LHL), Department of Veterinary Medicine, Schubertstrasse 60, 35392 Giessen, Germany
| | - Pierluigi Delmonte
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD 20740, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich Buff Ring 58, 35392 Giessen, Germany
| | - Kara K Mitchell
- Bacteriology Laboratory, Wadsworth Center, the New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| |
Collapse
|
8
|
Diouf FS, Beye M, Gaye M, Mbaye B, Alibar S, Sarr M, Dubourg G, Lagier JC, Sokhna C, Fenollar F, Fournier PE, Lo CI. Description of Streptococcus thalassemiae sp. nov., a Bacterium Isolated from Human Blood. Int J Microbiol 2023; 2023:3802590. [PMID: 37559874 PMCID: PMC10409578 DOI: 10.1155/2023/3802590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 08/11/2023] Open
Abstract
Blood is a precious biological liquid that is normally sterile. Therefore, bacteria in the bloodstream are shown a priori anomaly. A blood culture is systematically performed to diagnose the cause of the bacteremia. Indeed, a patient received in our service had a thalassemia major and underwent a genoidentical transplant. Then, a blood test was performed to diagnose a four-day fever. In this context, we have isolated strain Marseille-Q2617 from the blood sample. It revealed a new bacterial strain that belongs to the genus Streptococcus. It is a Gram-positive coccus, nonmotile, and nonspore forming. The major fatty acid found is hexadecanoic acid, with 49.5%. A taxonomic method was used to characterize the strain by studying their phenotypic, phylogenetic, and genomic characteristics. In addition, sequence analysis of the 16S rRNA gene shows that the strain Marseille-Q2617 has 99.94% sequence similarity to Streptococcus mitis. Average nucleotide identity (ANI) analysis for strain Marseille-Q2617T showed the highest similarity of 92.9% with S. mitis. The DNA-DNA hybridization value obtained (50.2%) between strain Marseille-Q2607 and S. mitis, its closest related species, was below the recommended threshold (<70%). Strain Marseille-Q2617T has a genome size of 2.02 Mbp with 40.5 mol% of G + C content. Based on these results, we propose a new species of the genus Streptococcus, for which the name Streptococcus thalassemiae sp. nov., Marseille-Q2617T (=CSUR Q2617 = CECT 30109) was proposed.
Collapse
Affiliation(s)
- Fatou Samba Diouf
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Mamadou Beye
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Mapenda Gaye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Babacar Mbaye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Stephane Alibar
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Mariema Sarr
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Gregory Dubourg
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Florence Fenollar
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| |
Collapse
|
9
|
Dama AC, Kim KS, Leyva DM, Lunkes AP, Schmid NS, Jijakli K, Jensen PA. BacterAI maps microbial metabolism without prior knowledge. Nat Microbiol 2023; 8:1018-1025. [PMID: 37142775 DOI: 10.1038/s41564-023-01376-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/29/2023] [Indexed: 05/06/2023]
Abstract
Training artificial intelligence (AI) systems to perform autonomous experiments would vastly increase the throughput of microbiology; however, few microbes have large enough datasets for training such a system. In the present study, we introduce BacterAI, an automated science platform that maps microbial metabolism but requires no prior knowledge. BacterAI learns by converting scientific questions into simple games that it plays with laboratory robots. The agent then distils its findings into logical rules that can be interpreted by human scientists. We use BacterAI to learn the amino acid requirements for two oral streptococci: Streptococcus gordonii and Streptococcus sanguinis. We then show how transfer learning can accelerate BacterAI when investigating new environments or larger media with up to 39 ingredients. Scientific gameplay and BacterAI enable the unbiased, autonomous study of organisms for which no training data exist.
Collapse
Affiliation(s)
- Adam C Dama
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kevin S Kim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Danielle M Leyva
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Annamarie P Lunkes
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Noah S Schmid
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Kenan Jijakli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul A Jensen
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
10
|
Gupta RS, Kanter-Eivin DA. AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159410 DOI: 10.1099/ijsem.0.005844] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.
Collapse
Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
| | - David A Kanter-Eivin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
| |
Collapse
|
11
|
Montecillo JAV. Phylogenomics and molecular marker-based analyses of the order Nevskiales: Proposal for the creation of Steroidobacterales ord. nov. and Peristeroidobacter gen. nov. Res Microbiol 2023:104057. [PMID: 37037310 DOI: 10.1016/j.resmic.2023.104057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 04/12/2023]
Abstract
The order Nevskiales, class Gammaproteobacteria, encompasses four families Algiphilaceae, Salinisphaeraceae, Nevskiaceae, and Steroidobacteraceae. The taxonomy of this order is structured from the inferences derived from the 16S rRNA gene and genome-based phylogenetic tree analyses. However, previous taxonomic studies of the order failed to incorporate most of the representatives from other established orders within the class Gammaproteobacteria. Other divergent members within the class Gammaproteobacteria were therefore overlooked. In this study, the taxonomy of the order Nevskiales was revisited using genome-based analyses with an expanded scope of outgroups representing the vast majority of the diversity within the class Gammaproteobacteria. Results from the phylogenetic analyses strongly supported the exclusion of the family Steroidobacteraceae from the order Nevskiales and further implied the assignment of the family into a novel order. In addition, the analyses also supported the reclassification of Steroidobacter gossypii, Steroidobacter soli, Steroidobacter agariperforans, and Steroidobacter agaridevorans into a novel genus. The identified conserved signature indels in 33 protein sequences further reinforced the new taxonomic assignments. Furthermore, the results of the average nucleotide identity and average amino acid identity analyses, together with the phenotypic and genomic characteristics among the members of the genus Steroidobacter also provided evidence supporting the reclassification of the four Steroidobacter species. Based on these results, the family Steroidobacteraceae is proposed to be assigned into a novel order Steroidobacterales ord. nov., and the species S. gossypii, S. soli, S. agariperforans, and S. agaridevorans are proposed to be moved into a novel genus Peristeroidobacter gen. nov. within the family Steroidobacteraceae.
Collapse
Affiliation(s)
- Jake Adolf V Montecillo
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| |
Collapse
|
12
|
Montecillo JAV. Phylogenomics and comparative genomic analyses support the creation of the novel family Ignatzschineriaceae fam. nov. comprising the genera Ignatzschineria and Wohlfahrtiimonas within the order Cardiobacteriales. Res Microbiol 2023; 174:103988. [PMID: 35973557 DOI: 10.1016/j.resmic.2022.103988] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/08/2022] [Accepted: 08/05/2022] [Indexed: 01/11/2023]
Abstract
The genera Ignatzschineria and Wohlfahrtiimonas were originally classified as members of the family Xanthomonadaceae, order Xanthomonadales of the class Gammaproteobacteria. With the recent taxonomic revisions in the order Xanthomonadales, the two genera were left unclassified in both family and order level. As members of these genera were considered emerging pathogens, their proper classification is therefore relevant. Here, a phylogenomics and comparative genomic approach was used to ascertain the taxonomic position of the two genera. Result showed that the members of the two genera formed a highly supported monophyletic clade with the members of the order Cardiobacteriales. This close affiliation was further supported by the results of the comparative analysis of the 16S rRNA sequence similarity values. The comparative analyses of the 16S rRNA sequence similarity and average amino acid identity values also implied that the two genera represent a single novel family. Conserved signature indels (CSIs) in seven protein sequences were exclusively shared by the members of the novel family. In addition, four CSIs were also found to be useful in delimiting members of the two genera at the genus level. To accommodate the two genera in a single family within the order Cardiobacteriales, the name Ignatzschineriaceae fam. nov. is proposed.
Collapse
Affiliation(s)
- Jake Adolf V Montecillo
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| |
Collapse
|
13
|
Berbel D, González-Díaz A, López de Egea G, Càmara J, Ardanuy C. An Overview of Macrolide Resistance in Streptococci: Prevalence, Mobile Elements and Dynamics. Microorganisms 2022; 10:2316. [PMID: 36557569 PMCID: PMC9783990 DOI: 10.3390/microorganisms10122316] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Streptococcal infections are usually treated with beta-lactam antibiotics, but, in case of allergic patients or reduced antibiotic susceptibility, macrolides and fluoroquinolones are the main alternatives. This work focuses on studying macrolide resistance rates, genetic associated determinants and antibiotic consumption data in Spain, Europe and also on a global scale. Macrolide resistance (MR) determinants, such as ribosomal methylases (erm(B), erm(TR), erm(T)) or active antibiotic efflux pumps and ribosomal protectors (mef(A/E)-mrs(D)), are differently distributed worldwide and associated with different clonal lineages and mobile genetic elements. MR rates vary together depending on clonal dynamics and on antibiotic consumption applying selective pressure. Among Streptococcus, higher MR rates are found in the viridans group, Streptococcus pneumoniae and Streptococcus agalactiae, and lower MR rates are described in Streptococcus pyogenes. When considering different geographic areas, higher resistance rates are usually found in East-Asian countries and milder or lower in the US and Europe. Unfortunately, the availability of data varies also between countries; it is scarce in low- and middle- income countries from Africa and South America. Thus, surveillance studies of macrolide resistance rates and the resistance determinants involved should be promoted to complete global knowledge among macrolide resistance dynamics.
Collapse
Affiliation(s)
- Dàmaris Berbel
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Aida González-Díaz
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Guillem López de Egea
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Jordi Càmara
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
- Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, 08007 Barcelona, Spain
| |
Collapse
|
14
|
Teng JLL, Ma Y, Chen JHK, Luo R, Foo CH, Li TT, Fong JYH, Yao W, Wong SSY, Fung KSC, Lau SKP, Woo PCY. Streptococcus oriscaviae sp. nov. Infection Associated with Guinea Pigs. Microbiol Spectr 2022; 10:e0001422. [PMID: 35510851 PMCID: PMC9241640 DOI: 10.1128/spectrum.00014-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/17/2022] [Indexed: 11/20/2022] Open
Abstract
Pet bite-related infections are commonly caused by the pet's oral flora transmitted to the animal handlers through the bite wounds. In this study, we isolated a streptococcus, HKU75T, in pure culture from the purulent discharge collected from a guinea pig bite wound in a previously healthy young patient. HKU75T was alpha-hemolytic on sheep blood agar and agglutinated with Lancefield group D and group G antisera. API 20 STREP showed that the most likely identity for HKU75T was S. suis I with 85.4% confidence while Vitek 2 showed that HKU75T was unidentifiable. MALDI-TOF MS identified HKU75T as Streptococcus suis (score of 1.86 only). 16S rRNA gene sequencing showed that HKU75T was most closely related to S. parasuis (98.3% nucleotide identity), whereas partial groEL and rpoB gene sequencing showed that it was most closely related to S. suis (81.8% and 89.8% nucleotide identity respectively). Whole genome sequencing and intergenomic distance determined by ANI revealed that there was <85% identity between the genome of HKU75T and those of all other known Streptococcus species. Genome classification using concatenated sequences of 92 bacterial core genes showed that HKU75T belonged to the Suis group. groEL gene sequences identical to that of HKU75T could be directly amplified from the oral cavities of the two guinea pigs owned by the patient. HKU75T is a novel Streptococcus species, which we propose to be named S. oriscaviae. The oral cavity of guinea pigs is presumably a reservoir of S. oriscaviae. Some of the reported S. suis strains isolated from clinical specimens may be S. oriscaviae. IMPORTANCE We reported the discovery of a novel Streptococcus species, propose to be named Streptococcus oriscaviae, from the pus collected from a guinea pig bite wound in a healthy young patient. The bacterium was initially misidentified as S. suis/S. parasuis by biochemical tests, mass spectrometry. and housekeeping genes sequencing. Its novelty was confirmed by whole genome sequencing. Comparative genomic studies showed that S. oriscaviae belongs to the Suis group. S. oriscaviae sequences were detected in the oral cavities of the two guinea pigs owned by the patient, suggesting that the oral cavity of guinea pigs could be a reservoir of S. oriscaviae. Some of the reported S. suis strains may be S. oriscaviae. Further studies are warranted to refine our knowledge on this novel Streptococcus species.
Collapse
Affiliation(s)
- Jade L. L. Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuanchao Ma
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jonathan H. K. Chen
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Chuen-Hing Foo
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Tsz Tuen Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jordan Y. H. Fong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Weiming Yao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Samson S. Y. Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kitty S. C. Fung
- Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
15
|
Stewart GC. Streptococcus
and
Enterococcus. Vet Microbiol 2022. [DOI: 10.1002/9781119650836.ch26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
16
|
Kumar S, Bansal K, Sethi SK. Reclassification of Streptococcus ilei as a later heterotypic synonym of Streptococcus koreensis based on whole-genome sequence analysis. Arch Microbiol 2022; 204:408. [PMID: 35727397 DOI: 10.1007/s00203-022-02979-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/01/2022]
Abstract
The genus Streptococcus, a member of family Streptococcaceae, is known for its wide range of industrial, clinical and human relevance. Among the species of genus Streptococcus two members, namely Streptococcus koreensis and Streptococcus ilei, were isolated from subgingival dental plaque and human small intestinal fluid, respectively. The 16S rRNA gene sequence similarity of the type strains of these members shows a similarity of 99.87%. In this study, we performed a systematic study to clarify the taxonomic assignment of these two species. Genome similarity assessment based on whole-genome sequence information such as average nucleotide identity using orthoANI and fastANI, digital DNA-DNA hybridization value between S. koreensis and S. ilei were 96.31, 96.60, 86.4 and 97.63, respectively. All these genome similarity values clearly exceeded the species delineation cutoffs. Phylogenetic assessment using 16S rRNA gene and whole-genome information using PhyloPhlAn, which uses around 400 conserved genes across bacterial phyla, provides additional evidence for these members forming a monophyletic clade in the phylogenetic tree. Pan genome analysis suggests a very large core genome (n = 1374) and the presence of no unique gene between the genomes of S. koreensis and S. ilei. Additionally, we found highly syntenic genomes of type strains of these two species. Based on these evidences, we propose S. ilei should be reclassified as a later heterotypic synonym of S. koreensis.
Collapse
Affiliation(s)
- Sanjeet Kumar
- School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, 768004, India
| | - Kanika Bansal
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Santosh Kumar Sethi
- School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, 768004, India.
| |
Collapse
|
17
|
Kumar S, Sethi SK. Genome-based reclassification of Streptococcus ursoris as a later heterotypic synonym of Streptococcus ratti. Arch Microbiol 2022; 204:405. [PMID: 35723755 DOI: 10.1007/s00203-022-03012-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Among the species of genus Streptococcus two members namely Streptococcus ratti and Streptococcus ursoris were isolated from oral cavity of rat and bear, respectively. Type strain of these members shows a 16S rRNA gene sequence similarity of 98.9%. Based on systematic phylo-taxonogenomics investigations, we could deduce the taxonomic assignment of the members of these species. Genome similarity assessment among the type strain of these members using average nucleotide identity (orthoANI and fastANI), digital DNA-DNA hybridization and average amino acid identity (AAI) were 98.5, 98.3, 88, and 98.3% respectively. All these values exceed the species delineation cutoffs suggesting a unified species. Phylogenetic tree obtained using 16S rRNA gene sequence also indicates the monophyletic nature of the member strains. Such monophyletic taxonomic positioning of the strains was further complemented with the whole genome-based phylogenomic tree. Based on these evidences, we propose S. ursoris should be reclassified as a later heterotypic synonym of S. ratti.
Collapse
Affiliation(s)
- Sanjeet Kumar
- School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, 768004, India
| | - Santosh K Sethi
- School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, 768004, India.
| |
Collapse
|
18
|
Krieger MC, Merritt J, Raghavan R. Genome-Wide Identification of Novel sRNAs in Streptococcus mutans. J Bacteriol 2022; 204:e0057721. [PMID: 35285723 PMCID: PMC9017351 DOI: 10.1128/jb.00577-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/10/2022] [Indexed: 11/20/2022] Open
Abstract
Streptococcus mutans is a major pathobiont involved in the development of dental caries. Its ability to utilize numerous sugars and to effectively respond to environmental stress promotes S. mutans proliferation in oral biofilms. Because of their quick action and low energetic cost, noncoding small RNAs (sRNAs) represent an ideal mode of gene regulation in stress response networks, yet their roles in oral pathogens have remained largely unexplored. We identified 15 novel sRNAs in S. mutans and show that they respond to four stress-inducing conditions commonly encountered by the pathogen in human mouth: sugar-phosphate stress, hydrogen peroxide exposure, high temperature, and low pH. To better understand the role of sRNAs in S. mutans, we further explored the function of the novel sRNA SmsR4. Our data demonstrate that SmsR4 regulates the enzyme IIA (EIIA) component of the sorbitol phosphotransferase system, which transports and phosphorylates the sugar alcohol sorbitol. The fine-tuning of EIIA availability by SmsR4 likely promotes S. mutans growth while using sorbitol as the main carbon source. Our work lays a foundation for understanding the role of sRNAs in regulating gene expression in stress response networks in S. mutans and highlights the importance of the underexplored phenomenon of posttranscriptional gene regulation in oral bacteria. IMPORTANCE Small RNAs (sRNAs) are important gene regulators in bacteria, but the identities and functions of sRNAs in Streptococcus mutans, the principal bacterium involved in the formation of dental caries, are unknown. In this study, we identified 15 putative sRNAs in S. mutans and show that they respond to four common stress-inducing conditions present in human mouth: sugar-phosphate stress, hydrogen peroxide exposure, high temperature, and low pH. We further show that the novel sRNA SmsR4 likely modulates sorbitol transport into the cell by regulating SMU_313 mRNA, which encodes the EIIA subunit of the sorbitol phosphotransferase system. Gaining a better understanding of sRNA-based gene regulation may provide new opportunities to develop specific inhibitors of S. mutans growth, thereby improving oral health.
Collapse
Affiliation(s)
- Madeline C. Krieger
- Department of Biology, Portland State University, Portland, Oregon, USA
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Rahul Raghavan
- Department of Biology, Portland State University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, The University of Texas at San Antonio, San Antonio, Texas, USA
| |
Collapse
|
19
|
Belman S, Chaguza C, Kumar N, Lo S, Bentley SD. A new perspective on ancient Mitis group streptococcal genetics. Microb Genom 2022; 8. [PMID: 35225216 PMCID: PMC8942026 DOI: 10.1099/mgen.0.000753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mitis group Streptococcus are human obligate bacteria residing in the nasopharynx and oral cavity. They comprise both commensal and pathogenic species with the most well-known being Streptococcus pneumoniae – a leading cause of meningitis and pneumonia. A primary difference between the commensal and pathogenic species is the presence of the polysaccharide capsule – a major virulence factor in S. pneumoniae, also present in other commensal species. Our current understanding of the evolutionary divergence of the pathogenic and commensal species has been inferred from extant strains. Ancient genomes can further elucidate streptococcal evolutionary history. We extracted streptococcal genome reads from a 5700-year-old ancient metagenome and worked towards characterizing them. Due to excessive within- and between-species recombination common among streptococci we were unable to parse individual species. Further, the composite reads of the ancient metagenome do not fit within the diversity of any specific extant species. Using a capsular gene database and AT-content analysis we determined that this ancient metagenome is missing polysaccharide synthesis genes integral to streptococcal capsule formation. The presence of multiple zinc metalloproteases suggests that adaptation to host IgA1 had begun and the presence of other virulence factors further implies development of close host–microbe interactions, though the absence of a capsule suggests an inability to cause invasive disease. The presence of specific virulence factors such as pneumolysin implies stable maintenance of such genes through streptococcal evolution that may strengthen their value as anti-pneumococcal vaccine antigens, while maintaining awareness of their potential presence in commensal species. Following from Jensen et al.’s initial analysis we provide historical context for this long time human nasopharyngeal resident, the Mitis group Streptococcus.
Collapse
Affiliation(s)
- Sophie Belman
- Department of Genetics, University of Cambridge, Cambridge, UK
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Chrispin Chaguza
- Yale School of Medicine, New Haven, CT, USA
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Stephanie Lo
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | | |
Collapse
|
20
|
Lemaire C, Le Gallou B, Lanotte P, Mereghetti L, Pastuszka A. Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci. Front Microbiol 2022; 13:828031. [PMID: 35173702 PMCID: PMC8841824 DOI: 10.3389/fmicb.2022.828031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/10/2022] [Indexed: 12/26/2022] Open
Abstract
Streptococci form a wide group of bacteria and are involved in both human and animal pathologies. Among pathogenic isolates, differences have been highlighted especially concerning their adaptation and virulence profiles. CRISPR-Cas systems have been identified in bacteria and many streptococci harbor one or more systems, particularly subtypes I-C, II-A, and III-A. Since the demonstration that CRISPR-Cas act as an adaptive immune system in Streptococcus thermophilus, a lactic bacteria, the diversity and role of CRISPR-Cas were extended to many germs and functions were enlarged. Among those, the genome editing tool based on the properties of Cas endonucleases is used worldwide, and the recent attribution of the Nobel Prize illustrates the importance of this tool in the scientific world. Another application is CRISPR loci analysis, which allows to easily characterize isolates in order to understand the interactions of bacteria with their environment and visualize species evolution. In this review, we focused on the distribution, diversity and roles of CRISPR-Cas systems in the main pathogenic streptococci.
Collapse
Affiliation(s)
- Coralie Lemaire
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - Brice Le Gallou
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - Philippe Lanotte
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
- *Correspondence: Philippe Lanotte,
| | - Laurent Mereghetti
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - Adeline Pastuszka
- Université de Tours, INRAE, Infectiologie et Santé Publique, BRMF, Tours, France
- Service de Bactériologie-Virologie, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| |
Collapse
|
21
|
Volokhov DV, Zagorodnyaya TA, Shen Z, Blom J, Furtak VA, Eisenberg T, Fan P, Jeong KC, Gao Y, Zhang S, Amselle M. Streptococcus vicugnae sp. nov., isolated from faeces of alpacas ( Vicugna pacos) and cattle ( Bos taurus), Streptococcus zalophi sp. nov., and Streptococcus pacificus sp. nov., isolated from respiratory tract of California sea lions ( Zalophus californianus). Int J Syst Evol Microbiol 2021; 71. [PMID: 33999792 DOI: 10.1099/ijsem.0.004826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four novel independent strains of Streptococcus spp. were isolated from faeces of alpaca (SL1232T), cattle (KCJ4950), and from respiratory tract of wild California sea lions (CSL7508T, CSL7591T). The strains were indole-, oxidase- and catalase-negative, non-spore-forming, non-motile Gram-positive cocci in short and long chains, facultative anaerobes. The 16S rRNA gene of SL1232T and KCJ4950 shared 99.40-99.60% nucleotide similarity to strains of S. equinus, S. lutetiensis, S. infantarius, and the 16S rRNA gene of CSL7508T and CSL7591T demonstrated 98.72 and 98.92% similarity, respectively, to S. marimammalium. All other known Streptococcus species had the 16S rRNA gene sequence similarities of ≤95%. The genomes were sequenced for the novel strains. Average nucleotide identity (ANI) analysis for strains SL1232T and KCJ4950, showed the highest similarity to S. equinus, S. lutetiensis, and S. infantarius with 85.21, 87.17, 88.47, 85.54, 87.47 and 88.89%, respectively, and strains CSL7508T and CSL7591T to S. marimammalium with 87.16 and 83.97%, respectively. Results of ANI were confirmed by pairwise digital DNA-DNA hybridization and phylogeny, which also revealed that the strains belong to three novel species of the genus Streptococcus. Phenotypical features of the novel species were in congruence with closely related members of the genus Streptococcus and gave negative reactions with the tested Lancefield serological groups (A-D, F and G). MALDI-TOF mass spectrometry supported identification of the species. Based on these data, we propose three novel species of the genus Streptococcus, for which the name Streptococcus vicugnae sp. nov. is proposed with the type strain SL1232T (=NCTC 14341T=DSM 110741T=CCUG 74371T), Streptococcus zalophi sp. nov. is proposed with the type strain CSL7508T (=NCTC 14410T=DSM 110742T=CCUG 74374T) and Streptococcus pacificus sp. nov. is proposed with the type strain CSL7591T (=NCTC 14455T=DSM 111148T=CCUG 74655T). The genome G+C content is 36.89, 34.85, and 35.34 % and draft genome sizes are 1906993, 1581094 and 1656080 bp for strains SL1232T, CSL7508T, and CSL7591T, respectively.
Collapse
Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tatiana A Zagorodnyaya
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Zhenyu Shen
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 East Campus Loop, Columbia, MO 65211, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich Buff Ring 58, 35392, Giessen, Germany
| | - Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tobias Eisenberg
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Frankfurter Strasse 89-91, 35392 Giessen, Germany.,Hessian State Laboratory (LHL), Department of Veterinary Medicine, Schubertstrasse 60, 35392, Giessen, Germany
| | - Peixin Fan
- Department of Animal Sciences, Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32611, USA
| | - Kwangcheol Casey Jeong
- Department of Animal Sciences, Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32611, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Shuping Zhang
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 East Campus Loop, Columbia, MO 65211, USA
| | - Megan Amselle
- American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110, USA
| |
Collapse
|
22
|
Li JW, Wyllie RM, Jensen PA. A Novel Competence Pathway in the Oral Pathogen Streptococcus sobrinus. J Dent Res 2021; 100:542-548. [PMID: 33876976 DOI: 10.1177/0022034520979150] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Streptococcus sobrinus is an etiologic cause of dental caries (tooth decay) in humans. Our knowledge of S. sobrinus is scant despite the organism's important role in oral health. It is widely believed that S. sobrinus lacks the natural competence pathways that are used by other streptococci to regulate growth, virulence, and quorum sensing. The lack of natural competence has also prevented genetic manipulation of S. sobrinus, limiting our knowledge of its pathogenicity. We discovered that most strains of S. sobrinus contain a new class of the ComRS competence system. Although S. sobrinus is typically placed among the mutans group streptococci, the S. sobrinus ComRS system is most similar to the competence pathways in the salivarius group. Unlike all other ComRS systems, the S. sobrinus pathway contains 2 copies of the transcriptional regulator ComR and has a peptide pheromone (XIP) that lacks any aromatic amino acids. Synthetic XIP enables transformation of S. sobrinus with plasmid or linear DNA, and we leverage this newfound genetic tractability to confirm that only 1 of the ComR homologs is required for induced competence while the other appears to suppress competence. Exogenous XIP increases the expression of bacteriocin gene clusters and produces an antimicrobial response that inhibits growth of S. mutans. We also identified 2 strains of S. sobrinus that appear to be "cheaters" by either not responding to or not producing XIP. We show how a recombination event in the nonresponsive strain could restore function of the ComRS pathway but delete the gene encoding XIP. Thus, the S. sobrinus ComRS pathway provides new tools for studying this pathogen and offers a lens into the evolution of ecological cheaters.
Collapse
Affiliation(s)
- J W Li
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - R M Wyllie
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - P A Jensen
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
23
|
Lannes-Costa PS, de Oliveira JSS, da Silva Santos G, Nagao PE. A current review of pathogenicity determinants of Streptococcus sp. J Appl Microbiol 2021; 131:1600-1620. [PMID: 33772968 DOI: 10.1111/jam.15090] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/16/2021] [Accepted: 03/24/2021] [Indexed: 12/16/2022]
Abstract
The genus Streptococcus comprises important pathogens, many of them are part of the human or animal microbiota. Advances in molecular genetics, taxonomic approaches and phylogenomic studies have led to the establishment of at least 100 species that have a severe impact on human health and are responsible for substantial economic losses to agriculture. The infectivity of the pathogens is linked to cell-surface components and/or secreted virulence factors. Bacteria have evolved sophisticated and multifaceted adaptation strategies to the host environment, including biofilm formation, survival within professional phagocytes, escape the host immune response, amongst others. This review focuses on virulence mechanism and zoonotic potential of Streptococcus species from pyogenic (S. agalactiae, S. pyogenes) and mitis groups (S. pneumoniae).
Collapse
Affiliation(s)
- P S Lannes-Costa
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - J S S de Oliveira
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - G da Silva Santos
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - P E Nagao
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
24
|
Sadowy E, Hryniewicz W. Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods. Eur J Clin Microbiol Infect Dis 2020; 39:2247-2256. [PMID: 32710352 PMCID: PMC7669753 DOI: 10.1007/s10096-020-03991-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.
Collapse
Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| |
Collapse
|
25
|
Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753-5798. [PMID: 33112222 DOI: 10.1099/ijsem.0.004475] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.
Collapse
Key Words
- classification of Bacillus species
- conserved signature indels
- emendation of genus Bacillus
- genus Bacillus and the family Bacillaceae
- novel Bacillaceae genera Alteribacter, Ectobacillus, Evansella, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Niallia, Priestia, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sutcliffiella and Weizmannia
- phylogenomic and comparative genomic analyses
Collapse
Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| |
Collapse
|
26
|
Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406-438. [PMID: 31617837 DOI: 10.1099/ijsem.0.003775] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.
Collapse
Affiliation(s)
- Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| |
Collapse
|
27
|
Gupta RS, Patel S. Robust Demarcation of the Family Caryophanaceae ( Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures. Front Microbiol 2020; 10:2821. [PMID: 32010063 PMCID: PMC6971209 DOI: 10.3389/fmicb.2019.02821] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.
Collapse
Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| |
Collapse
|
28
|
Chan AWY, Naphtali J, Schellhorn HE. High-throughput DNA sequencing technologies for water and wastewater analysis. Sci Prog 2019; 102:351-376. [PMID: 31818206 PMCID: PMC10424514 DOI: 10.1177/0036850419881855] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Conventional microbiological water monitoring uses culture-dependent techniques to screen indicator microbial species such as Escherichia coli and fecal coliforms. With high-throughput, second-generation sequencing technologies becoming less expensive, water quality monitoring programs can now leverage the massively parallel nature of second-generation sequencing technologies for batch sample processing to simultaneously obtain compositional and functional information of culturable and as yet uncultured microbial organisms. This review provides an introduction to the technical capabilities and considerations necessary for the use of second-generation sequencing technologies, specifically 16S rDNA amplicon and whole-metagenome sequencing, to investigate the composition and functional potential of microbiomes found in water and wastewater systems.
Collapse
Affiliation(s)
| | - James Naphtali
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | |
Collapse
|
29
|
Turner CE, Bubba L, Efstratiou A. Pathogenicity Factors in Group C and G Streptococci. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0020-2018. [PMID: 31111818 PMCID: PMC11026075 DOI: 10.1128/microbiolspec.gpp3-0020-2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Indexed: 11/20/2022] Open
Abstract
Initially recognized zoonoses, streptococci belonging to Lancefield group C (GCS) and G (GGS) were subsequently recognised as human pathogens causing a diverse range of symptoms, from asymptomatic carriage to life threatening diseases. Their taxonomy has changed during the last decade. Asymptomatic carriage is <4% amongst the human population and invasive infections are often in association with chronic diseases such as diabetes, cardiovascular diseases or chronic skin infections. Other clinical manifestations include acute pharyngitis, pneumonia, endocarditis, bacteraemia and toxic-shock syndrome. Post streptococcal sequalae such as rheumatic fever and acute glomerulonephritis have also been described but mainly in developed countries and amongst specific populations. Putative virulence determinants for these organisms include adhesins, toxins, and other factors that are essential for dissemination in human tissues and for interference with the host immune responses. High nucleotide similarities among virulence genes and their association with mobile genetic elements supports the hypothesis of extensive horizontal gene transfer events between the various pyogenic streptococcal species belonging to Lancefield groups A, C and G. A better understanding of the mechanisms of pathogenesis should be apparent by whole-genome sequencing, and this would result in more effective clinical strategies for the pyogenic group in general.
Collapse
Affiliation(s)
- Claire E Turner
- Department of Molecular Biology & Biotechnology, The Florey Institute, University of Sheffield, Sheffield, UK
| | - Laura Bubba
- Reference Microbiology Division, National Infection Service, Public Health England, London, United Kingdom
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Androulla Efstratiou
- Reference Microbiology Division, National Infection Service, Public Health England, London, United Kingdom
| |
Collapse
|