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Nganou-Makamdop K, Douek DC. The Gut and the Translocated Microbiomes in HIV Infection: Current Concepts and Future Avenues. Pathog Immun 2024; 9:168-194. [PMID: 38807656 PMCID: PMC11132393 DOI: 10.20411/pai.v9i1.693] [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: 03/05/2024] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
It is widely acknowledged that HIV infection results in disruption of the gut's mucosal integrity partly due a profound loss of gastrointestinal CD4+ T cells that are targets of the virus. In addition, systemic inflammation and immune activation that drive disease pathogenesis are reduced but not normalized by antiretroviral therapy (ART). It has long been postulated that through the process of microbial translocation, the gut microbiome acts as a key driver of systemic inflammation and immune recovery in HIV infection. As such, many studies have aimed at characterizing the gut microbiota in order to unravel its influence in people with HIV and have reported an association between various bacterial taxa and inflammation. This review assesses both contra-dictory and consistent findings among several studies in order to clarify the overall mechanisms by which the gut microbiota in adults may influence immune recovery in HIV infection. Independently of the gut microbiome, observations made from analysis of microbial products in the blood provide direct insight into how the translocated microbiome may drive immune recovery. To help better understand strengths and limitations of the findings reported, this review also highlights the numerous factors that can influence microbiome studies, be they experimental methodologies, and host-intrinsic or host-extrinsic factors. Altogether, a fuller understanding of the interplay between the gut microbiome and immunity in HIV infection may contribute to preventive and therapeutic approaches.
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Affiliation(s)
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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2
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Igarashi K, Kato S. Reductive Transformation of Fe(III) (oxyhydr)Oxides by Mesophilic Homoacetogens in the Genus Sporomusa. Front Microbiol 2021; 12:600808. [PMID: 33633701 PMCID: PMC7901989 DOI: 10.3389/fmicb.2021.600808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/04/2021] [Indexed: 01/10/2023] Open
Abstract
Microbial reduction of iron contributes to the dissolution and transformation of iron-containing minerals in nature. Diverse groups of homoacetogenic bacteria (homoacetogens) have been reported to reduce insoluble Fe(III) oxides, such as hydrous ferric oxide (HFO), an Fe(III) mineral commonly found in soils and sediments. Several members of genus Sporomusa reportedly oxidize Fe(0), indicating the presence of an extracellular electron-uptake mechanism. However, the ability of the genus to reduce insoluble Fe(III) oxides is limited, and the underlying reduction mechanism remains to be elucidated. In this study, the HFO reduction ability of three Sporomusa spp. (Sporomusa sp. strain GT1, Sporomusa sphaeroides, and Sporomusa ovata) and a homoacetogen of a different genus (Acetobacterium woodii) were assayed under organotrophic (ethanol) and lithotrophic (H2 + CO2) conditions without a chelator or reducing reagent. All tested homoacetogens showed acetogenic growth and concomitant reduction of HFO under both organotrophic and lithotrophic conditions. Analysis of the growth stoichiometry showed that Fe(III) reduction does not support direct energy conservation, thereby indicating that Fe(III) reduction is a side reaction of acetogenesis to dissipate the excess reducing power. HFO was reduced to a soluble Fe(II) form by microbial activity. In addition, we observed that strain GT1, S. sphaeroides, and S. ovata reduced crystalline Fe(III) oxides, and HFO was reductively transformed into magnetite (Fe3O4) under phosphate-limiting conditions. Separation of HFO by a dialysis membrane still permitted Fe(II) production, although the reduction rate was decreased, suggesting that Fe(III) reduction is at least partially mediated by soluble redox compound(s) secreted from the cells. Finally, culture experiments and comparative genomic analysis suggested that electron transfer by flavins and multiheme c-type cytochrome were not directly correlated with Fe(III) reduction activity. This study reveals the capability of Sporomusa spp. in the reductive transformation of iron mineral and indicates the potential involvement of these organisms in iron and other mineral cycles in nature.
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Affiliation(s)
- Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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Megrian D, Taib N, Witwinowski J, Beloin C, Gribaldo S. One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide. Mol Microbiol 2020; 113:659-671. [PMID: 31975449 DOI: 10.1111/mmi.14469] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/24/2022]
Abstract
How, when and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.
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Affiliation(s)
- Daniela Megrian
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.,Ecole Doctorale Complexité du vivant, Sorbonne University, Paris, France
| | - Najwa Taib
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.,Hub Bioinformatics and Biostatistics, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Jerzy Witwinowski
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Christophe Beloin
- Department of Microbiology, Genetics of Biofilm Unit, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
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Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition. Nat Ecol Evol 2020; 4:1661-1672. [PMID: 33077930 DOI: 10.1038/s41559-020-01299-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/05/2020] [Indexed: 11/08/2022]
Abstract
The transition between cell envelopes with one membrane (Gram-positive or monoderm) and those with two membranes (Gram-negative or diderm) is a fundamental open question in the evolution of Bacteria. Evidence of the presence of two independent diderm lineages, the Halanaerobiales and the Negativicutes, within the classically monoderm Firmicutes has blurred the monoderm/diderm divide and specifically anticipated that other members with an outer membrane (OM) might exist in this phylum. Here, by screening 1,639 genomes of uncultured Firmicutes for signatures of an OM, we highlight a third and deep branching diderm clade, the Limnochordia, strengthening the hypothesis of a diderm ancestor and the occurrence of independent transitions leading to the monoderm phenotype. Phyletic patterns of over 176,000 protein families constituting the Firmicutes pan-proteome identify those that strongly correlate with the diderm phenotype and suggest the existence of new potential players in OM biogenesis. In contrast, we find practically no largely conserved core of monoderms, a fact possibly linked to different ways of adapting to repeated OM losses. Phylogenetic analysis of a concatenation of main OM components totalling nearly 2,000 amino acid positions illustrates the common origin and vertical evolution of most diderm bacterial envelopes. Finally, mapping the presence/absence of OM markers onto the tree of Bacteria shows the overwhelming presence of diderm phyla and the non-monophyly of monoderm ones, pointing to an early origin of two-membraned cells and the derived nature of the Gram-positive envelope following multiple OM losses.
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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6
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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7
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Ajibola O, Rowan AD, Ogedengbe CO, Mshelia MB, Cabral DJ, Eze AA, Obaro S, Belenky P. Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents. Sci Rep 2019; 9:829. [PMID: 30696838 PMCID: PMC6351658 DOI: 10.1038/s41598-018-36709-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/25/2018] [Indexed: 12/11/2022] Open
Abstract
Urogenital schistosomiasis is a neglected tropical disease caused by the parasite Schistosoma haematobium, which resides in the vasculature surrounding the urogenital system. Previous work has suggested that helminthic infections can affect the intestinal microbiome, and we hypothesized that S. haematobium infection could result in an alteration of immune system-microbiota homeostasis and impact the composition of the gut microbiota. To address this question, we compared the fecal microbiomes of infected and uninfected schoolchildren from the Argungu Local Government Area of Kebbi State, Nigeria, detecting significant differences in community composition between the two groups. Most remarkably, we observed a decreased abundance of Firmicutes and increased abundance of Proteobacteria - a shift in community structure which has been previously associated with dysbiosis. More specifically, we detected a number of changes in lower taxa reminiscent of inflammation-associated dysbiosis, including decreases in Clostridiales and increases in Moraxellaceae, Veillonellaceae, Pasteurellaceae, and Desulfovibrionaceae. Functional potential analysis also revealed an enrichment in orthologs of urease, which has been linked to dysbiosis and inflammation. Overall, our analysis indicates that S. haematobium infection is associated with perturbations in the gut microbiota and may point to microbiome disruption as an additional consequence of schistosome infection.
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Affiliation(s)
- Olumide Ajibola
- Department of Microbiology, Faculty of Science, Federal University Birnin Kebbi, Birnin Kebbi, Kebbi State, Nigeria.
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.
| | - Aislinn D Rowan
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Clement O Ogedengbe
- Department of Medical Biochemistry, College of Medicine, University of Nigeria - Enugu Campus, Enugu, Nigeria
| | - Mari B Mshelia
- Department of Microbiology, Faculty of Science, Federal University Birnin Kebbi, Birnin Kebbi, Kebbi State, Nigeria
| | - Damien J Cabral
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Anthonius A Eze
- Department of Medical Biochemistry, College of Medicine, University of Nigeria - Enugu Campus, Enugu, Nigeria
| | - Stephen Obaro
- Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- International Foundation Against Infectious Diseases in Nigeria, Department of Pediatrics, Bayero University Kano, Kano, Nigeria
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, USA.
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8
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Li X, Zhao Q, Wang X, Li Y, Zhou Q. Surfactants selectively reallocated the bacterial distribution in soil bioelectrochemical remediation of petroleum hydrocarbons. JOURNAL OF HAZARDOUS MATERIALS 2018; 344:23-32. [PMID: 29028494 DOI: 10.1016/j.jhazmat.2017.09.050] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/30/2017] [Accepted: 09/27/2017] [Indexed: 06/07/2023]
Abstract
Soil contaminated by aged petroleum hydrocarbons is faced with scarcity of electron acceptors, low activity of functional microbes and inefficient electron transfer, which hinder the bioremediation application. The soil microbial fuel cell (MFC) simultaneously solves these problems with bioelectricity production. In this study, five types of surfactants were introduced to enhance the bioavailability of aged petroleum hydrocarbon in soils. The ampholytic surfactant (lecithos) was optimal due to the highest bioelectricity generation (0.321Cd-1g-1) and promoted hydrocarbon degradation (328%), while the nonionic (glyceryl monostearate) and cationic (cetyltrimethylammonium bromide) surfactants were inefficient. The surfactants induced a special microbial enrichment affiliated with Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Chloroflexi, Planctomycetes and Acidobacteria (93%-99% of total) in soil MFCs. The anionic surfactant (sodium dodecyl sulfate) exhibited the strongest selectivity, and α-proteobacteria and γ-proteobacteria abundances decreased while Clostridia increased, much like the result obtained with the biosurfactant β-cyclodextrin. Furthermore, Bacillus abundance was increased in connected soil MFCs, except addition of lecithos in which Clostridium increased to 14.88% from 3.61% in the control. The high correlations among Bacillus, Phenylobacterium, Solibacillus (0.9162-0.9577) and among Alcaligenes, Dysgonomonas, Sedimentibacter (0.9538-0.9966) indicated a metabolic network of microorganisms in the soil bioelectrochemical remediation system.
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Affiliation(s)
- Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, No. 31 Fukang Road, Nankai District, Tianjin 300191, China.
| | - Qian Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, No. 31 Fukang Road, Nankai District, Tianjin 300191, China.
| | - Xin Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
| | - Yongtao Li
- Agro-Environmental Protection Institute, Ministry of Agriculture, MOA Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, No. 31 Fukang Road, Nankai District, Tianjin 300191, China.
| | - Qixing Zhou
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
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Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo S. Outer Membrane Proteome of Veillonella parvula: A Diderm Firmicute of the Human Microbiome. Front Microbiol 2017; 8:1215. [PMID: 28713344 PMCID: PMC5491611 DOI: 10.3389/fmicb.2017.01215] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/14/2017] [Indexed: 12/24/2022] Open
Abstract
Veillonella parvula is a biofilm-forming commensal found in the lungs, vagina, mouth, and gastro-intestinal tract of humans, yet it may develop into an opportunistic pathogen. Furthermore, the presence of Veillonella has been associated with the development of a healthy immune system in infants. Veillonella belongs to the Negativicutes, a diverse clade of bacteria that represent an evolutionary enigma: they phylogenetically belong to Gram-positive (monoderm) Firmicutes yet maintain an outer membrane (OM) with lipopolysaccharide similar to classic Gram-negative (diderm) bacteria. The OMs of Negativicutes have unique characteristics including the replacement of Braun's lipoprotein by OmpM for tethering the OM to the peptidoglycan. Through phylogenomic analysis, we have recently provided bioinformatic annotation of the Negativicutes diderm cell envelope. We showed that it is a unique type of envelope that was present in the ancestor of present-day Firmicutes and lost multiple times independently in this phylum, giving rise to the monoderm architecture; however, little experimental data is presently available for any Negativicutes cell envelope. Here, we performed the first experimental proteomic characterization of the cell envelope of a diderm Firmicute, producing an OM proteome of V. parvula. We initially conducted a thorough bioinformatics analysis of all 1,844 predicted proteins from V. parvula DSM 2008's genome using 12 different localization prediction programs. These results were complemented by protein extraction with surface exposed (SE) protein tags and by subcellular fractionation, both of which were analyzed by liquid chromatography tandem mass spectrometry. The merging of proteomics and bioinformatics results allowed identification of 78 OM proteins. These include a number of receptors for TonB-dependent transport, the main component of the BAM system for OM protein biogenesis (BamA), the Lpt system component LptD, which is responsible for insertion of LPS into the OM, and several copies of the major OmpM protein. The annotation of V. parvula's OM proteome markedly extends previous inferences on the nature of the cell envelope of Negativicutes, including the experimental evidence of a BAM/TAM system for OM protein biogenesis and of a complete Lpt system for LPS transport to the OM. It also provides important information on the role of OM components in the lifestyle of Veillonella, such as a possible gene cluster for O-antigen synthesis and a large number of adhesins. Finally, many OM hypothetical proteins were identified, which are priority targets for further characterization.
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Affiliation(s)
- Daniel I. Poppleton
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut PasteurParis, France
| | - Magalie Duchateau
- Unité de Spectrométrie de Masse Structurale et Protéomique, Plateforme Protéomique, Départment de Biologie Structurale et Chime, Institut Pasteur, USR 2000 Centre National de la Recherche ScientifiqueParis, France
| | - Véronique Hourdel
- Unité de Spectrométrie de Masse Structurale et Protéomique, Plateforme Protéomique, Départment de Biologie Structurale et Chime, Institut Pasteur, USR 2000 Centre National de la Recherche ScientifiqueParis, France
| | - Mariette Matondo
- Unité de Spectrométrie de Masse Structurale et Protéomique, Plateforme Protéomique, Départment de Biologie Structurale et Chime, Institut Pasteur, USR 2000 Centre National de la Recherche ScientifiqueParis, France
| | - Jennifer Flechsler
- Pflanzliche Entwicklungsbiologie und Elektronenmikroskopie, Department I. Botanik, Biozentrum der LMU MünchenPlanegg-Martinsried, Germany
| | - Andreas Klingl
- Pflanzliche Entwicklungsbiologie und Elektronenmikroskopie, Department I. Botanik, Biozentrum der LMU MünchenPlanegg-Martinsried, Germany
| | - Christophe Beloin
- Unité de Génétique des Biofilms, Département de Microbiologie, Institut PasteurParis, France
| | - Simonetta Gribaldo
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut PasteurParis, France
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10
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Antunes LC, Poppleton D, Klingl A, Criscuolo A, Dupuy B, Brochier-Armanet C, Beloin C, Gribaldo S. Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes. eLife 2016; 5. [PMID: 27580370 PMCID: PMC5007114 DOI: 10.7554/elife.14589] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/21/2016] [Indexed: 12/22/2022] Open
Abstract
One of the major unanswered questions in evolutionary biology is when and how the transition between diderm (two membranes) and monoderm (one membrane) cell envelopes occurred in Bacteria. The Negativicutes and the Halanaerobiales belong to the classically monoderm Firmicutes, but possess outer membranes with lipopolysaccharide (LPS-OM). Here, we show that they form two phylogenetically distinct lineages, each close to different monoderm relatives. In contrast, their core LPS biosynthesis enzymes were inherited vertically, as in the majority of bacterial phyla. Finally, annotation of key OM systems in the Halanaerobiales and the Negativicutes shows a puzzling combination of monoderm and diderm features. Together, these results support the hypothesis that the LPS-OMs of Negativicutes and Halanaerobiales are remnants of an ancient diderm cell envelope that was present in the ancestor of the Firmicutes, and that the monoderm phenotype in this phylum is a derived character that arose multiple times independently through OM loss. DOI:http://dx.doi.org/10.7554/eLife.14589.001 The cell envelope is one of the evolutionarily oldest parts of a bacterium. This structure – made up of a cell wall and either one or two cell membranes – surrounds the bacterial cell, maintaining the cell’s structure and providing an interface through which bacteria can sense their environment and communicate. Bacteria can be broadly classed based on the number of cell membranes that their envelope consists of. Bacteria that have a single cell membrane are known as “monoderm”, whereas those with two membranes are termed “diderm”. The number of membranes that bacteria have can affect how well they resist antibacterial compounds. When, how and why bacteria switched between monoderm and diderm cell envelopes are some of the major unanswered questions in evolutionary biology. The textbook example of a monoderm cell envelope can be found in bacteria called Firmicutes. This group includes some notoriously harmful bacteria such as Staphylococcus, which can cause conditions ranging from abscesses to pneumonia. However, some Firmicutes possess two cell membranes. It was unclear how these unusual diderm Firmicutes developed a second membrane, and how they are related to their monoderm relatives. Antunes, Poppleton et al. set out to answer these questions by analyzing the information contained in the thousands of bacterial genomes that have already been described. The results indicate that Firmicutes originally had diderm envelopes, and that species with monoderm envelopes arose independently several times through the loss of their outermost membrane. Future work is needed to investigate the driving forces and the precise mechanism that led most Firmicutes to lose their outer membrane. Also, further characterization of diderm Firmicutes will provide key information about the biology of these poorly understood bacteria. DOI:http://dx.doi.org/10.7554/eLife.14589.002
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Affiliation(s)
- Luisa Cs Antunes
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Daniel Poppleton
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Andreas Klingl
- Plant Development and Electron Microscopy, Department of Biology I, Biocenter LMU, Munich, Germany
| | - Alexis Criscuolo
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Département de Microbiologie, Institut Pasteur, Paris
| | | | - Christophe Beloin
- Unité de Génétique des Biofilms, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
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Tocheva EI, Ortega DR, Jensen GJ. Sporulation, bacterial cell envelopes and the origin of life. Nat Rev Microbiol 2016; 14:535-542. [PMID: 28232669 DOI: 10.1038/nrmicro.2016.85] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron cryotomography (ECT) enables the 3D reconstruction of intact cells in a near-native state. Images produced by ECT have led to the proposal that an ancient sporulation-like event gave rise to the second membrane in diderm bacteria. Tomograms of sporulating monoderm and diderm bacterial cells show how sporulation can lead to the generation of diderm cells. Tomograms of Gram-negative and Gram-positive cell walls and purified sacculi suggest that they are more closely related than previously thought and support the hypothesis that they share a common origin. Mapping the distribution of cell envelope architectures onto a recent phylogenetic tree of life indicates that the diderm cell plan, and therefore the sporulation-like event that gave rise to it, must be very ancient. One explanation for this model is that during the cataclysmic transitions of the early Earth, cellular evolution may have gone through a bottleneck in which only spores survived, which implies that the last bacterial common ancestor was a spore.
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Affiliation(s)
- Elitza I Tocheva
- Department of Stomatology and the Department of Biochemistry and Molecular Medicine, Université de Montréal, P. O. Box 6128 Station Centre-Ville, Montreal, Québec H3C 3J7, Canada
| | - Davi R Ortega
- Department of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
| | - Grant J Jensen
- Howard Hughes Medical Institute, Department of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
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12
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Putker F, Bos MP, Tommassen J. Transport of lipopolysaccharide to the Gram-negative bacterial cell surface. FEMS Microbiol Rev 2015; 39:985-1002. [DOI: 10.1093/femsre/fuv026] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 12/15/2022] Open
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13
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Campbell C, Adeolu M, Gupta RS. Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov. Int J Syst Evol Microbiol 2015; 65:3203-3215. [PMID: 25999592 DOI: 10.1099/ijs.0.000347] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.
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Affiliation(s)
- Chantal Campbell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Mobolaji Adeolu
- 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
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