1
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Detomasi TC, Batka AE, Valastyan JS, Hydorn MA, Craik CS, Bassler BL, Marletta MA. Proteases influence colony aggregation behavior in Vibrio cholerae. J Biol Chem 2023; 299:105386. [PMID: 37898401 PMCID: PMC10709122 DOI: 10.1016/j.jbc.2023.105386] [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: 07/10/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Aggregation behavior provides bacteria protection from harsh environments and threats to survival. Two uncharacterized proteases, LapX and Lap, are important for Vibrio cholerae liquid-based aggregation. Here, we determined that LapX is a serine protease with a preference for cleavage after glutamate and glutamine residues in the P1 position, which processes a physiologically based peptide substrate with a catalytic efficiency of 180 ± 80 M-1s-1. The activity with a LapX substrate identified by a multiplex substrate profiling by mass spectrometry screen was 590 ± 20 M-1s-1. Lap shares high sequence identity with an aminopeptidase (termed VpAP) from Vibrio proteolyticus and contains an inhibitory bacterial prepeptidase C-terminal domain that, when eliminated, increases catalytic efficiency on leucine p-nitroanilide nearly four-fold from 5.4 ± 4.1 × 104 M-1s-1 to 20.3 ± 4.3 × 104 M-1s-1. We demonstrate that LapX processes Lap to its mature form and thus amplifies Lap activity. The increase is approximately eighteen-fold for full-length Lap (95.7 ± 5.6 × 104 M-1s-1) and six-fold for Lap lacking the prepeptidase C-terminal domain (11.3 ± 1.9 × 105 M-1s-1). In addition, substrate profiling reveals preferences for these two proteases that could inform in vivo function. Furthermore, purified LapX and Lap restore the timing of the V. cholerae aggregation program to a mutant lacking the lapX and lap genes. Both proteases must be present to restore WT timing, and thus they appear to act sequentially: LapX acts on Lap, and Lap acts on the substrate involved in aggregation.
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Affiliation(s)
- Tyler C Detomasi
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Allison E Batka
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Julie S Valastyan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; The Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Molly A Hydorn
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; The Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Michael A Marletta
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
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2
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Silale A, Zhu Y, Witwinowski J, Smith RE, Newman KE, Bhamidimarri SP, Baslé A, Khalid S, Beloin C, Gribaldo S, van den Berg B. Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes. Nat Commun 2023; 14:7152. [PMID: 37932269 PMCID: PMC10628300 DOI: 10.1038/s41467-023-42601-y] [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: 02/10/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
The outer membrane (OM) in diderm, or Gram-negative, bacteria must be tethered to peptidoglycan for mechanical stability and to maintain cell morphology. Most diderm phyla from the Terrabacteria group have recently been shown to lack well-characterised OM attachment systems, but instead have OmpM, which could represent an ancestral tethering system in bacteria. Here, we have determined the structure of the most abundant OmpM protein from Veillonella parvula (diderm Firmicutes) by single particle cryogenic electron microscopy. We also characterised the channel properties of the transmembrane β-barrel of OmpM and investigated the structure and PG-binding properties of its periplasmic stalk region. Our results show that OM tethering and nutrient acquisition are genetically linked in V. parvula, and probably other diderm Terrabacteria. This dual function of OmpM may have played a role in the loss of the OM in ancestral bacteria and the emergence of monoderm bacterial lineages.
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Affiliation(s)
- Augustinas Silale
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Yiling Zhu
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Jerzy Witwinowski
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Robert E Smith
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Kahlan E Newman
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Satya P Bhamidimarri
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Arnaud Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Christophe Beloin
- Institut Pasteur, Université de Paris Cité, Genetics of Biofilms Laboratory, Paris, France.
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Bert van den Berg
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK.
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3
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Merritt J, Kreth J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies. FEMS Microbiol Rev 2023; 47:fuac050. [PMID: 36549660 PMCID: PMC10719069 DOI: 10.1093/femsre/fuac050] [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: 08/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Advancements in DNA sequencing technologies within the last decade have stimulated an unprecedented interest in the human microbiome, largely due the broad diversity of human diseases found to correlate with microbiome dysbiosis. As a direct consequence of these studies, a vast number of understudied and uncharacterized microbes have been identified as potential drivers of mucosal health and disease. The looming challenge in the field is to transition these observations into defined molecular mechanistic studies of symbiosis and dysbiosis. In order to meet this challenge, many of these newly identified microbes will need to be adapted for use in experimental models. Consequently, this review presents a comprehensive overview of the molecular microbiology tools and techniques that have played crucial roles in genetic studies of the bacteria found within the human oral microbiota. Here, we will use specific examples from the oral microbiome literature to illustrate the biology supporting these techniques, why they are needed in the field, and how such technologies have been implemented. It is hoped that this information can serve as a useful reference guide to help catalyze molecular microbiology studies of the many new understudied and uncharacterized species identified at different mucosal sites in the body.
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Affiliation(s)
- Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
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4
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Tataru C, Peras M, Rutherford E, Dunlap K, Yin X, Chrisman BS, DeSantis TZ, Wall DP, Iwai S, David MM. Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism. Sci Rep 2023; 13:11353. [PMID: 37443184 PMCID: PMC10345091 DOI: 10.1038/s41598-023-38228-0] [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: 10/12/2022] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
While healthy gut microbiomes are critical to human health, pertinent microbial processes remain largely undefined, partially due to differential bias among profiling techniques. By simultaneously integrating multiple profiling methods, multi-omic analysis can define generalizable microbial processes, and is especially useful in understanding complex conditions such as Autism. Challenges with integrating heterogeneous data produced by multiple profiling methods can be overcome using Latent Dirichlet Allocation (LDA), a promising natural language processing technique that identifies topics in heterogeneous documents. In this study, we apply LDA to multi-omic microbial data (16S rRNA amplicon, shotgun metagenomic, shotgun metatranscriptomic, and untargeted metabolomic profiling) from the stool of 81 children with and without Autism. We identify topics, or microbial processes, that summarize complex phenomena occurring within gut microbial communities. We then subset stool samples by topic distribution, and identify metabolites, specifically neurotransmitter precursors and fatty acid derivatives, that differ significantly between children with and without Autism. We identify clusters of topics, deemed "cross-omic topics", which we hypothesize are representative of generalizable microbial processes observable regardless of profiling method. Interpreting topics, we find each represents a particular diet, and we heuristically label each cross-omic topic as: healthy/general function, age-associated function, transcriptional regulation, and opportunistic pathogenesis.
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Affiliation(s)
- Christine Tataru
- Department of Microbiology, Oregon State University, SW Campus Way, Corvallis, USA.
| | - Marie Peras
- Second Genome Inc, 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Erica Rutherford
- Second Genome Inc, 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Kaiti Dunlap
- Department of Bioengineering, Serra Mall, Stanford, USA
| | - Xiaochen Yin
- Second Genome Inc, 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | | | - Todd Z DeSantis
- Second Genome Inc, 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Dennis P Wall
- Department of Biomedical Data Science, Serra Mall, Stanford, USA
- Department of Pediatrics (Systems Medicine), Stanford, 1265 Welch Road, Stanford, USA
| | - Shoko Iwai
- Second Genome Inc, 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Maude M David
- Department of Microbiology, Oregon State University, SW Campus Way, Corvallis, USA.
- School of Pharmacy, Oregon State University, SW Campus Way, Corvallis, USA.
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Chekli Y, Stevick RJ, Kornobis E, Briolat V, Ghigo JM, Beloin C. Escherichia coli Aggregates Mediated by Native or Synthetic Adhesins Exhibit Both Core and Adhesin-Specific Transcriptional Responses. Microbiol Spectr 2023; 11:e0069023. [PMID: 37039668 PMCID: PMC10269875 DOI: 10.1128/spectrum.00690-23] [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: 02/17/2023] [Accepted: 03/20/2023] [Indexed: 04/12/2023] Open
Abstract
Bacteria can rapidly tune their physiology and metabolism to adapt to environmental fluctuations. In particular, they can adapt their lifestyle to the close proximity of other bacteria or the presence of different surfaces. However, whether these interactions trigger transcriptomic responses is poorly understood. We used a specific setup of E. coli strains expressing native or synthetic adhesins mediating bacterial aggregation to study the transcriptomic changes of aggregated compared to nonaggregated bacteria. Our results show that, following aggregation, bacteria exhibit a core response independent of the adhesin type, with differential expression of 56.9% of the coding genome, including genes involved in stress response and anaerobic lifestyle. Moreover, when aggregates were formed via a naturally expressed E. coli adhesin (antigen 43), the transcriptomic response of the bacteria was more exaggerated than that of aggregates formed via a synthetic adhesin. This suggests that the response to aggregation induced by native E. coli adhesins could have been finely tuned during bacterial evolution. Our study therefore provides insights into the effect of self-interaction in bacteria and allows a better understanding of why bacterial aggregates exhibit increased stress tolerance. IMPORTANCE The formation of bacterial aggregates has an important role in both clinical and ecological contexts. Although these structures have been previously shown to be more resistant to stressful conditions, the genetic basis of this stress tolerance associated with the aggregate lifestyle is poorly understood. Surface sensing mediated by different adhesins can result in various changes in bacterial physiology. However, whether adhesin-adhesin interactions, as well as the type of adhesin mediating aggregation, affect bacterial cell physiology is unknown. By sequencing the transcriptomes of aggregated and nonaggregated cells expressing native or synthetic adhesins, we characterized the effects of aggregation and adhesin type on E. coli physiology.
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Affiliation(s)
- Yankel Chekli
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Rebecca J. Stevick
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Etienne Kornobis
- Hub de Bioinformatique et Biostatistique-Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
- Plate-forme Technologique Biomics—Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Valérie Briolat
- Hub de Bioinformatique et Biostatistique-Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
- Plate-forme Technologique Biomics—Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Christophe Beloin
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
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6
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Zha F, Pang R, Huang S, Zhang J, Wang J, Chen M, Xue L, Ye Q, Wu S, Yang M, Gu Q, Ding Y, Wu Q, Zhang H. Proteomic analysis reveals the non-coding small RNA Qrr5 influences autoaggregation and growth competition in Vibrio parahaemolyticus. J Proteomics 2023; 279:104866. [PMID: 36918054 DOI: 10.1016/j.jprot.2023.104866] [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: 10/25/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 03/13/2023]
Abstract
Vibrio parahaemolyticus, a sea-born bacterial pathogen, is a primary inducement of food-borne gastroenteritis. Previous studies have shown that non-coding small RNA plays a vital role in the regulation of multiple biological processes in pathogenic bacteria, especially autoaggregation and growth competition. However, the inherent mechanisms have not yet to be fully understood. As important regulators in Vibrios, the involvement of Qrr sRNAs in V. parahaemolyticus is largely unknown. Here, we carried out the Qrr5 deletion mutant and utilized a proteomic method to describe global proteomic alterations in response to Qrr5 deletion. A total of 297 significantly expressed proteins were determined between the Qrr5 deletion mutant and wild-type strain, among which 137 proteins were upregulated and 160 proteins were downregulated. The upregulated proteins principally participated in membrane transporters and signal transcription, while the downregulated proteins participated in the two-component system and transcription factor binding. Notably, transcriptional regulator LysR, outer membrane protein OmpA, and conjugal transfer protein TraA-related proteins were upregulated, causing the promotion of autoaggregation ability and growth competition ability against E. coli. This study provides insights into the regulatory network of sRNA in this bacterium, which will facilitate further explorations of important biological processes in pathogenic bacteria. SIGNIFICANCE: sRNA Qrr5 is an important regulator involved in bacterial multiple physiological processes, including auto-aggregation and growth competition among food-borne pathogens Vibrio parahaemolyticus. Here, utilizing a TMT-labeling proteomic approach, we identified 137 proteins were upregulated and 160 proteins were downregulated between the Qrr5 deletion mutant and wild-type strain. The upregulated proteins were involved in membrane transporters and signal transcription, while downregulated proteins were involved in the two-component system and transcription factor binding. Moreover, the LysR, OmpA, and TraA proteins were significantly upregulated, causing the promotion of autoaggregation and commensal growth competition ability. The mechanism of how Qrr5 regulates the targeted genes remains unclarified and need great efforts to explore.
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Affiliation(s)
- Fei Zha
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Shixuan Huang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Meiyan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China.
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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Lu Y, Li Z, Peng X. Regulatory effects of oral microbe on intestinal microbiota and the illness. Front Cell Infect Microbiol 2023; 13:1093967. [PMID: 36816583 PMCID: PMC9928999 DOI: 10.3389/fcimb.2023.1093967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Over the past decade, the association between oral health, intestinal microbiota, and systemic diseases has been further validated. Some oral microbial species have been isolated from pathological intestine mucosa or feces and identified as biomarkers for intestinal diseases. A small proportion of oral microbiome passes through or colonizes the lower gastrointestinal tract, even in healthy individuals. Opportunistic pathogens from the oral cavity may expand and participate in the occurrence and progression of intestinal diseases when the anatomical barrier is disrupted. These disruptors interact with the intestinal microbiota, disturbing indigenous microorganisms, and mucosal barriers through direct colonization, blood circulation, or derived metabolite pathways. While interacting with the host's immune system, oral-derived pathogens stimulate inflammation responses and guide the transition of the intestinal microenvironment from a healthy state to a pre-disease state. Therefore, the oral-gut microbiome axis sheds light on new clinical therapy options, and gastrointestinal tract ecology balance necessitates simultaneous consideration of both oral and gut microbiomes. This review summarizes possible routes of oral microbes entering the intestine and the effects of certain oral bacteria on intestinal microbiota and the host's immune responses.
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Abram AM, Szewczyk MM, Park SG, Sam SS, Eldana HB, Koria FJ, Ferracciolo JM, Young LA, Qadir H, Bonham AJ, Yang F, Zora JS, Abdulelah SA, Patel NA, Koleilat A, Saleh MA, Alhabeil JA, Khan S, Tripathi A, Palanci JG, Krukonis ES. A Co-Association of Streptococcus mutans and Veillonella parvula/dispar in Root Caries Patients and In Vitro Biofilms. Infect Immun 2022; 90:e0035522. [PMID: 36129298 PMCID: PMC9584289 DOI: 10.1128/iai.00355-22] [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] [Indexed: 11/20/2022] Open
Abstract
Root caries in geriatric patients is a growing problem as more people are maintaining their natural teeth into advanced age. We determined the levels of various bacterial species previously implicated in root caries disease or health using quantitative real-time PCR in a pilot study of 7 patients with 1 to 4 root caries lesions per person. Levels of 12 different species on diseased roots compared to healthy (contralateral control) roots were measured. Four species were found at significantly higher levels on diseased roots (Streptococcus mutans, Veillonella parvula/dispar, Actinomyces naeslundii/viscosus, and Capnocytophaga granulosa) compared across all plaque samples. The level of colonization by these species varied dramatically (up to 1,000-fold) between patients, indicating different patients have different bacteria contributing to root caries disease. Neither of the two species previously reported to correlate with healthy roots (C. granulosa and Delftia acidovorans) showed statistically significant protective roles in our population, although D. acidovorans showed a trend toward higher levels on healthy teeth (P = 0.08). There was a significant positive correlation between higher levels of S. mutans and V. parvula/dispar on the same diseased teeth. In vitro mixed biofilm studies demonstrated that co-culturing S. mutans and V. parvula leads to a 50 to 150% increase in sucrose-dependent biofilm mass compared to S. mutans alone, depending on the growth conditions, while V. parvula alone did not form in vitro biofilms. The presence of V. parvula also decreased the acidification of S. mutans biofilms when grown in artificial saliva and enhanced the health of mixed biofilms.
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Affiliation(s)
- Amber M. Abram
- Department of Biology, University of Detroit Mercy, Detroit, Michigan, USA
| | | | - Seon G. Park
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Sumita S. Sam
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Haya B. Eldana
- Department of Biology, University of Detroit Mercy, Detroit, Michigan, USA
| | - Fadi J. Koria
- Department of Biology, University of Detroit Mercy, Detroit, Michigan, USA
| | | | - Laura A. Young
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Hina Qadir
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Aaron J. Bonham
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Fei Yang
- Natural Products Discovery Core, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan S. Zora
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Sara A. Abdulelah
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Neil A. Patel
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Ayah Koleilat
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Malaka A. Saleh
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Jamal A. Alhabeil
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Shameel Khan
- University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Ashootosh Tripathi
- Natural Products Discovery Core, University of Michigan, Ann Arbor, Michigan, USA
| | - John G. Palanci
- Division of Restorative Dentistry, University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
| | - Eric S. Krukonis
- Division of Integrated Biomedical Sciences, University of Detroit Mercy School of Dentistry, Detroit, Michigan, USA
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9
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Vidal-Veuthey B, González D, Cárdenas JP. Role of microbial secreted proteins in gut microbiota-host interactions. Front Cell Infect Microbiol 2022; 12:964710. [PMID: 35967863 PMCID: PMC9373040 DOI: 10.3389/fcimb.2022.964710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022] Open
Abstract
The mammalian gut microbiota comprises a variety of commensals including potential probiotics and pathobionts, influencing the host itself. Members of the microbiota can intervene with host physiology by several mechanisms, including the secretion of a relatively well-reported set of metabolic products. Another microbiota influence mechanism is the use of secreted proteins (i.e., the secretome), impacting both the host and other community members. While widely reported and studied in pathogens, this mechanism remains understood to a lesser extent in commensals, and this knowledge is increasing in recent years. In the following minireview, we assess the current literature covering different studies, concerning the functions of secretable proteins from members of the gut microbiota (including commensals, pathobionts, and probiotics). Their effect on host physiology and health, and how these effects can be harnessed by postbiotic products, are also discussed.
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Affiliation(s)
- Boris Vidal-Veuthey
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Huechuraba, Chile
| | - Dámariz González
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Huechuraba, Chile
| | - Juan P. Cárdenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Huechuraba, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- *Correspondence: Juan P. Cárdenas,
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10
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Comparison of the Oral Microbiota Structure among People from the Same Ethnic Group Living in Different Environments. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6544497. [PMID: 35800217 PMCID: PMC9256442 DOI: 10.1155/2022/6544497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 11/20/2022]
Abstract
The characteristics of the oral microbiota may depend on oral health, age, diet, and geography, but the influence of the geographic setting on the oral microbiota has received limited attention. The characteristics of oral microbiota have been reported to differ between urban and rural environments. In order to minimize the influence of genetic background, we recruited 54 volunteers from the same ethnic group, living in urban and rural areas of Gansu Province, China. We collected dental plaque samples and divided them into four groups according to the participant's area of residence and dental caries status. We sequenced the 16S rRNA of these samples using the Pacific Biosciences sequencing platform and analyzed the correlation between the geographic area and the characteristics of the oral microbiota. Analysis of the alpha and beta diversity revealed that there were significant differences in diversity and composition of dental plaque microflora among the four groups. Cluster analysis revealed that geographic area played an important role in determining the oral microbiota. Network analysis of oral microorganisms showed that geographic differences had major influence on the composition characteristics and internal structure of oral microorganisms. We found that some dominant strains which may play a key role in maintaining oral health, such as Streptococcus oralis, Capnocytophaga sputigena, Porphyromonas catoniae, Corynebacterium matruchotii, Haemophilus parainfluenzae, and Prevotella loescheii, were less affected by the geographic setting. These results provide a deeper understanding of factors influencing the composition of the oral microbiota and could contribute to early diagnosis and effective prevention of dental caries in different settings.
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Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
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Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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An ancient divide in outer membrane tethering systems in bacteria suggests a mechanism for the diderm-to-monoderm transition. Nat Microbiol 2022; 7:411-422. [PMID: 35246664 DOI: 10.1038/s41564-022-01066-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/24/2022] [Indexed: 11/08/2022]
Abstract
Recent data support the hypothesis that Gram-positive bacteria (monoderms) arose from Gram-negative ones (diderms) through loss of the outer membrane (OM), but how this happened remains unknown. As tethering of the OM is essential for cell envelope stability in diderm bacteria, its destabilization may have been involved in this transition. In the present study, we present an in-depth analysis of the four known main OM-tethering systems across the Tree of Bacteria (ToB). We show that the presence of such systems follows the ToB with a bimodal distribution matching the deepest phylogenetic divergence between Terrabacteria and Gracilicutes. Whereas the lipoprotein peptidoglycan-associated lipoprotein (Pal) is restricted to the Gracilicutes, along with a more sporadic occurrence of OmpA, and Braun's lipoprotein is present only in a subclade of Gammaproteobacteria, diderm Terrabacteria display, as the main system, the OmpM protein. We propose an evolutionary scenario whereby OmpM represents a simple, ancestral OM-tethering system that was later replaced by one based on Pal after the emergence of the Lol machinery to deliver lipoproteins to the OM, with OmpA as a possible transition state. We speculate that the existence of only one main OM-tethering system in the Terrabacteria would have allowed the multiple OM losses specifically inferred in this clade through OmpM perturbation, and we provide experimental support for this hypothesis by inactivating all four ompM gene copies in the genetically tractable diderm Firmicute Veillonella parvula. High-resolution imaging and tomogram reconstructions reveal a non-lethal phenotype in which vast portions of the OM detach from the cells, forming huge vesicles with an inflated periplasm shared by multiple dividing cells. Together, our results highlight an ancient shift of OM-tethering systems in bacterial evolution and suggest a mechanism for OM loss and the multiple emergences of the monoderm phenotype from diderm ancestors.
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Nwoko ESQA, Okeke IN. Bacteria autoaggregation: how and why bacteria stick together. Biochem Soc Trans 2021; 49:1147-1157. [PMID: 34110370 PMCID: PMC8286834 DOI: 10.1042/bst20200718] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/02/2021] [Accepted: 05/12/2021] [Indexed: 12/16/2022]
Abstract
Autoaggregation, adherence between identical bacterial cells, is important for colonization, kin and kind recognition, and survival of bacteria. It is directly mediated by specific interactions between proteins or organelles on the surfaces of interacting cells or indirectly by the presence of secreted macromolecules such as eDNA and exopolysaccharides. Some autoaggregation effectors are self-associating and present interesting paradigms for protein interaction. Autoaggregation can be beneficial or deleterious at specific times and niches. It is, therefore, typically regulated through transcriptional or post-transcriptional mechanisms or epigenetically by phase variation. Autoaggregation can contribute to bacterial adherence, biofilm formation or other higher-level functions. However, autoaggregation is only required for these phenotypes in some bacteria. Thus, autoaggregation should be detected, studied and measured independently using both qualitative and quantitative in vitro and ex vivo methods. If better understood, autoaggregation holds the potential for the discovery of new therapeutic targets that could be cost-effectively exploited.
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Affiliation(s)
- El-shama Q. A. Nwoko
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
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