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Hussain A, Patwekar U, Mongad DS, Nimonkar Y, Mundhe S, Paul D, Prakash O, Shouche YS. Functional antagonism and insights into the biosynthetic potential of human gut-derived microbes. Int J Antimicrob Agents 2024; 63:107091. [PMID: 38242249 DOI: 10.1016/j.ijantimicag.2024.107091] [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: 03/12/2023] [Revised: 12/09/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
The specialised small molecules encoded by commensal microbes mediate distinct functional interactions. However, there is a landscape of antagonistic interactions mediated by specialised strains and their small molecules. Herein, the antagonistic landscape within a collection of 330 human gut-derived commensal microbial strains was elucidated to evaluate antimicrobial interactions as a defensive contributor, and gain new insights into structure-related functions. The potential antagonistic gut-derived strains displayed strain-specific selective inhibition. This is in contrast to common antimicrobial drugs, which typically wipe out a broad range of species and are usually found in environmental microbes. Genome sequencing of representative gut strains revealed the presence of significant biosynthetic gene clusters (BGCs) encoding compound families that contribute to antagonistic activities, and are important in host defence and maintaining gut homeostasis. Subsets of these BGCs were abundant in metagenomic sequencing data from healthy individuals. Furthermore, the cell culture secretome of these strains revealed potential biomarkers linked to hallmark pathways. These microorganisms have biosynthetic novelty and are a source of biologically significant natural products. Such natural products are essential in the development of new antimicrobial agents to reduce the usage of broad-spectrum antibiotics and combat antimicrobial resistance.
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Affiliation(s)
| | - Umera Patwekar
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | | | - Yogesh Nimonkar
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | - Swapnil Mundhe
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | - Dhiraj Paul
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | - Om Prakash
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | - Yogesh S Shouche
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
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Nimonkar YS, Godambe T, Kulkarni A, Patel T, Paul D, Paul D, Rale V, Prakash O. Oligotrophy vs. copiotrophy in an alkaline and saline habitat of Lonar Lake. Front Microbiol 2022; 13:939984. [PMID: 35992701 PMCID: PMC9386271 DOI: 10.3389/fmicb.2022.939984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10–20 mg carbon L−1) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level altered the selection of organisms from the same sample. Our data indicate that copiotrophic microorganisms dominate the eutrophic Lonar Lake, which is also supported by the past metagenomics studies from the same site. We also reported that quick depletion of carbon from oligotrophic medium worked as a limiting factor, inducing cell death after 2–3 generations and preventing the development of visible colonies on plates and sufficient optical density in liquid medium. Therefore, a long-term supply of low levels of carbon, followed by isolation on enriched media, can serve as a good strategy in isolation of novel taxa of microorganism, with industrial or environmental importance.
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Affiliation(s)
- Yogesh S. Nimonkar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Tejashree Godambe
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Apurva Kulkarni
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Tarachand Patel
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Dhreej Paul
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Debarati Paul
- Amity Institute of Biotechnology, Amity University Uttar Pradesh (AUUP), Noida, India
| | - Vinay Rale
- Symbiosis School of Biological Sciences (SSBS) Symbiosis International (Deemed University) & Symbiosis Centre for Research & Innovation (SCRI), Symbiosis International (Deemed University), Pune, India
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
- *Correspondence: Om Prakash ;
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Two-Dimensional Cell Separation: a High-Throughput Approach to Enhance the Culturability of Bacterial Cells from Environmental Samples. Microbiol Spectr 2022; 10:e0000722. [PMID: 35467387 PMCID: PMC9248899 DOI: 10.1128/spectrum.00007-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Culture-independent sequence data from various environmental samples have revealed an immense microbial diversity of environmental, clinical, and industrial importance that has not yet been cultured. Cultivation is imperative to validate findings emerging from cultivation-independent molecular data and exploit the isolated organisms for biotechnological purposes. Efforts have been made to boost the cultivability of microbes from environmental samples by use of a range of techniques and instrumentation. The manuscript presents a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. By employing gradient centrifugation combined with serial dilution (“two-dimensional cell separation”), significantly higher numbers of genera (>2-fold higher) and species (>3-fold higher) were isolated from environmental samples, including soil, anaerobic sludge, and landfill leachate, than from using serial dilution alone. This simple and robust protocol can be modified for any environment and culture medium and provides access to untapped microbial diversity. IMPORTANCE In the manuscript, we have developed a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. The method used gradient centrifugation combined with serial dilution (two-dimensional cell separation) to improve taxum recovery from samples. This simple and robust protocol can be modified for any environment and culture medium and provides access to untapped microbial diversity. This approach can be incorporated with less labor and complexity in laboratories with minimal instrumentation. As cultivation is a workflow that is well suited to lower-resource microbiology labs, we believe improvements in cultivability can increase opportunities for scientific collaborations between low-resource labs and groups focused on high-resource cultivation-independent methodologies.
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Antibiotic susceptibility of human gut-derived facultative anaerobic bacteria is different under aerobic versus anaerobic test conditions. Microbes Infect 2021; 23:104847. [PMID: 34116163 DOI: 10.1016/j.micinf.2021.104847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/24/2021] [Accepted: 05/29/2021] [Indexed: 11/23/2022]
Abstract
Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC) testing. The results demonstrated that 7-strains had a similar pattern of drug resistance under both conditions, while the remaining ten strains had significant differences in resistance patterns between aerobic and anaerobic conditions for at least one antibiotic. We conclude that successful antibiotic therapy for host-associated pathogens requires proper assessment of the oxygen condition of the growth environment and MIC testing of each pathogen under anaerobic and aerobic conditions.
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Tsilifis C, Pareja-Cebrian L. Neonatal Thoracic Infection with Mixta. Infect Prev Pract 2021; 3:100114. [PMID: 34368734 PMCID: PMC8335919 DOI: 10.1016/j.infpip.2021.100114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/06/2021] [Indexed: 11/05/2022] Open
Abstract
The Erwiniaceae are a family of gram-negative, aerobic coliforms which are pathogenic to a number of plants. Recently described within this family are the Pantoea, strains of which have been associated with infection in immunocompromised children and post-surgical meningitis but also colonisation of a healthy human subject's gastrointestinal tract, as well as a variety of agricultural diseases. In 2015, a further clade of this family was established as the genus Mixta. In this case report, we describe infection of the pleural space and lung parenchyma with members of Mixta in a term neonate following an anastomic leak post-primary repair of congenital trache-oesophageal fistula, causing a respiratory and cardiovascular deterioration. Mixta were identified by MALDI-TOF. The child made a full recovery with use of intravenous piperacillin-tazobactam. The Mixta genus must be added to a list of opportunistic pathogens responsible for infection following perforation of the gastrointestinal tract.
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Affiliation(s)
- Christo Tsilifis
- Paediatric Immunology and Infectious Diseases, Great North Children's Hospital, Royal Victoria Infirmary, Newcastle Upon Tyne, United Kingdom.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Lucia Pareja-Cebrian
- Department of Microbiology and Virology, Royal Victoria Infirmary, Newcastle Upon Tyne, United Kingdom
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A Re-evaluation of the Taxonomy and Classification of the Type III Secretion System in a Pathogenic Bacterium Causing Soft Rot Disease of Pleurotus eryngii. Curr Microbiol 2020; 78:179-189. [PMID: 33123750 DOI: 10.1007/s00284-020-02253-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
Pantoea beijingensis, a gram-negative pathogenic bacterium, causes soft rot disease in the fungus Pleurotus eryngii in China. However, the taxonomic classification of this pathogen is controversial due to close relationships between bacteria of the genera Pantoea and Erwinia. This study aimed to resolve the identity of P. beijingensis using phylogenomic and systematic analyses of Pantoea and Erwinia by whole-genome sequencing. Single-copy orthologs identified from the Erwinia/Pantoea core genomes were used to delineate Erwinia/Pantoea phylogeny. P. beijingensis LMG27579T clustered within a single Erwinia clade. A whole-genome-based phylogenetic tree and average nucleotide and amino-acid identity values indicate that P. beijingensis LMG27579T should be renamed Erwinia beijingensis. The hrp/hrc genes encoding type III secretion system (T3SS) proteins in Erwinia and Pantoea were divided into five groups according to gene contents and organization. Neighbor-joining-inferred phylogenetic trees based on concatenated HrcU, HrcN, and HrcR in the main hrp/hrc cluster showed that E. beijingensis T3SS proteins are closely related to those in Ewingella americana, implying that E. beijingensis and E. americana have a recent common hrp/hrc gene ancestor. Furthermore, T3SS proteins of Erwinia and Pantoea were clustered in different clades separated by other bacterial T3SS proteins. Thus, T3SS genes in Pantoea and Erwinia strains might have been acquired by horizontal gene transfer. Overall, our findings clarify the taxonomy of the bacterium causing soft rot in P. eryngii, as well as the genetic structure and classification of the hrp/hrc T3SS virulence factor. We propose that T3SS acquisition is important for E. beijingensis emergence and pathogenesis.
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Xia M, Wang J, Huo YX, Yang Y. Mixta tenebrionis sp. nov., isolated from the gut of the plastic-eating mealworm Tenebrio molitor L. Int J Syst Evol Microbiol 2020; 70:790-796. [PMID: 31675291 DOI: 10.1099/ijsem.0.003826] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, BIT-26T, was isolated from the gut of plastic-eating mealworm Tenebrio molitor L. The taxonomic position of this new isolate was investigated by using a polyphasic approach. Cells of the strain were Gram-stain-negative, facultatively anaerobic, motile rods with peritrichous flagella. The 16S rRNA gene sequence (1412 bp) of strain BIT-26T showed the highest similarity (97.4 %) to Erwinia piriflorinigrans CFBP 5888T, followed by Citrobacter sedlakii NBRC 105722T (97.3 %), Mixta calida LMG 25383T (97.3 %), Cronobacter muytjensii ATCC 51329T (97.2 %) and Mixta theicola QC88-366 T (97.2 %). The results of phylogenetic analyses, based on the 16S rRNA gene and concatenated sequences of four housekeeping genes (atpD, gyrB, infB and rpoB), placed strain BIT-26T within the genus Mixta of the family Erwiniaceae. This affiliation was also supported by the chemotaxonomic data. Strain BIT-26T had similar predominant fatty acids, including C12 : 0, C14 : 0, C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c, to species of the genus Mixta. In silico DNA-DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain BIT-26T from other species of the genus Mixta with validly published names. Therefore, strain BIT-26T is considered to represent a novel species, for which the name Mixta tenebrionis sp. nov is proposed. The type strain is BIT-26T (=CGMCC 1.17041T=KCTC 72449T).
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Affiliation(s)
- Mengli Xia
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Jialei Wang
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yi-Xin Huo
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
- Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yu Yang
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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Pantoea endophytica sp. nov., novel endophytic bacteria isolated from maize planting in different geographic regions of northern China. Syst Appl Microbiol 2019; 42:488-494. [PMID: 31204142 DOI: 10.1016/j.syapm.2019.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/24/2019] [Accepted: 06/01/2019] [Indexed: 01/24/2023]
Abstract
Four endophytic bacterial strains were isolated from root, stem and leaf of maize planted in different regions of northern China. The four strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. Furthermore, the average nucleotide identity (ANI) values among them were higher than 95%, suggesting they all belong to one species. Based on 16S rRNA gene phylogeny, the four strains were clustered together with Pantoea rodasii LMG 26273T and Pantoea rwandensis LMG 26275T, but on a separate branch. Multilocus sequence analysis (MLSA) indicated that the four strains form a novel Pantoea species. Authenticity of the novel species was confirmed by ANI comparisons between strain 596T and its closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. The genome size of 596T was 5.1Mbp, comprising 4896 predicted genes with DNA G+C content of 57.8mol%. The respiratory quinone was ubiquinone-8 (Q-8) and the polar lipid profile consisted of phosphatidylethanolamin, diphosphatidylglycerol, phosphatidylglycerol, unidentified aminophospholipid and unidentified phospholipid. The major fatty acids of strain 596T were C16:0, summed feature 2 (C12:0 aldehyde), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, the four isolates are considered to represent a novel species of the genus Pantoea, for which the name Pantoea endophytica sp. nov., is proposed, with 596T (=DSM 100,785T=CGMCC 1.15280T) as type strain.
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Palmer M, Steenkamp ET, Coetzee MPA, Avontuur JR, Chan WY, van Zyl E, Blom J, Venter SN. Mixta gen. nov., a new genus in the Erwiniaceae. Int J Syst Evol Microbiol 2018; 68:1396-1407. [DOI: 10.1099/ijsem.0.002540] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Marike Palmer
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin P. A. Coetzee
- DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Juanita R. Avontuur
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai-Yin Chan
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Biotechnology Platform (BTP), Agricultural Research Council Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort, South Africa
| | - Elritha van Zyl
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Stephanus N. Venter
- DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
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Genomic and physiological analyses of an indigenous strain, Enterococcus faecium 17OM39. Funct Integr Genomics 2018; 18:385-399. [PMID: 29556852 DOI: 10.1007/s10142-018-0596-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 02/16/2018] [Accepted: 02/26/2018] [Indexed: 12/30/2022]
Abstract
The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity. The strain was able to tolerate bile salts and showed bile salt hydrolytic (BSH) activity, exopolysaccharide production and adherence to human HT-29 cell line. Importantly, partial haemolytic activity was detected and the strain was susceptible to the human serum. Genomics investigation of strain 17OM39 revealed the presence of diverse genes encoding for proteolytic enzymes, stress response systems and the ability to produce essential amino acids, vitamins and antimicrobial compound Bacteriocin-A. No virulence factors and plasmids were found in this genome of the strain 17OM39. Collectively, these physiological and genomic features of 17OM39 confirm the potential of this strain as a candidate probiotic.
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Dhotre DP, Rajabal V, Sharma A, Kulkarni GJ, Prakash O, Vemuluri VR, Joseph N, Rahi P, Shouche YS. Reclassification of Phycicola gilvus (Lee et al. 2008) and Leifsonia pindariensis (Reddy et al. 2008) as Microterricola gilva comb. nov. and Microterricola pindariensis comb. nov. and emended description of the genus Microterricola. Int J Syst Evol Microbiol 2017; 67:2766-2772. [PMID: 28857730 DOI: 10.1099/ijsem.0.002019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of Microterricola viridarii JCM 15926T, Phycicola gilvus DSM 18319T and Leifsonia pindariensis JCM 15132T were re-examined. Phylogenetic analysis and 16S rRNA gene sequence similarities revealed that all three strains are closely related with each other and form a monophyletic cluster with high sequence similarity (99.2 -99.9 %). A dendrogram constructed based on the protein spectra generated by matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy also displayed close clustering of these three strains. The fatty acid profiles of three strains were very similar to each other and contained branched fatty acids (anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0) as the predominant cellular fatty acids. The polar lipid profiles of the three stains were similar and consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as major polar lipids and an unknown lipid. Comparisons of morphological, chemotaxonomic and physiological data of Microterricola viridarii JCM 15926T, Leifsonia pindariensis JCM 15132T and Phycicola gilvus DSM 18319T are in agreement with the features of a common genus. DNA-DNA hybridization data generated during this study showed less than 70 % reassociation value with each other indicating that they are different at species level. Based on the present study, we conclude that Phycicola gilvus DSM 18319T and Leifsonia pindariensis JCM 15132T should be reclassified under the genus Microterricola, since this genus has the nomenclatural priority, and reclassified as Microterricolagilva comb. nov. (type strain SSWW-21T=DSM 18319T=KCTC 19185T=JCM 30550T) and Microterricolapindariensis comb. nov. (type strain PON10T=LMG 24222T=JCM 15132T=MTCC9128T). An emended description of the genus Microterricola is also presented.
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Affiliation(s)
- Dhiraj Prakash Dhotre
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Vaheesan Rajabal
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Avinash Sharma
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Girish J Kulkarni
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Venkata Ramana Vemuluri
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Neetha Joseph
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
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13
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Palmer M, Steenkamp ET, Coetzee MPA, Chan WY, van Zyl E, De Maayer P, Coutinho TA, Blom J, Smits THM, Duffy B, Venter SN. Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella. Antonie van Leeuwenhoek 2017; 110:1287-1309. [PMID: 28255640 DOI: 10.1007/s10482-017-0852-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/23/2017] [Indexed: 11/29/2022]
Abstract
Investigation of the evolutionary relationships between related bacterial species and genera with a variety of lifestyles have gained popularity in recent years. For analysing the evolution of specific traits, however, a robust phylogeny is essential. In this study we examined the evolutionary relationships among the closely related genera Erwinia, Tatumella and Pantoea, and also attempted to resolve the species relationships within Pantoea. To accomplish this, we used the whole genome sequence data for 35 different strains belonging to these three genera, as well as nine outgroup taxa. Multigene datasets consisting of the 1039 genes shared by these 44 strains were then generated and subjected to maximum likelihood phylogenetic analyses, after which the results were compared to those using conventional multi-locus sequence analysis (MLSA) and ribosomal MLSA (rMLSA) approaches. The robustness of the respective phylogenies was then explored by considering the factors typically responsible for destabilizing phylogenetic trees. We found that the nucleotide datasets employed in the MLSA, rMLSA and 1039-gene datasets contained significant levels of homoplasy, substitution saturation and differential codon usage, all of which likely gave rise to the observed lineage specific rate heterogeneity. The effects of these factors were much less pronounced in the amino acid dataset for the 1039 genes, which allowed reconstruction of a fully supported and resolved phylogeny. The robustness of this amino acid tree was also supported by different subsets of the 1039 genes. In contrast to the smaller datasets (MLSA and rMLSA), the 1039 amino acid tree was also not as sensitive to long-branch attraction. The robust and well-supported evolutionary hypothesis for the three genera, which confidently resolved their various inter- and intrageneric relationships, represents a valuable resource for future studies. It will form the basis for studies aiming to understand the forces driving the divergence and maintenance of lineages, species and biological traits in this important group of bacteria.
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Affiliation(s)
- Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI),, University of Pretoria, Pretoria, South Africa
| | - Wai-Yin Chan
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Elritha van Zyl
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Pieter De Maayer
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Teresa A Coutinho
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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14
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Pantoea alhagi, a novel endophytic bacterium with ability to improve growth and drought tolerance in wheat. Sci Rep 2017; 7:41564. [PMID: 28128318 PMCID: PMC5269684 DOI: 10.1038/srep41564] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
A novel strain LTYR-11ZT that exhibited multiple plant growth promoting (PGP) traits was isolated from the surface-sterilized leaves of Alhagi sparsifolia Shap. (Leguminosae), which reprsents one of the top drought tolerant plants in north-west China. Phylogenetic analysis of 16S rRNA gene sequences and multilocus sequence analysis based on partial sequences of atpD, gyrB, infB and rpoB genes revealed that strain LTYR-11ZT was a member of the genus Pantoea, with Pantoea theicola NBRC 110557T and Pantoea intestinalis DSM 28113T as the closest phylogenetic relatives. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analysis confirmed that strain LTYR-11ZT represents a novel species of the genus Pantoea, for which we propose the name Pantoea alhagi sp. nov. Confocal microscopy observation revealed that strain LTYR-11ZT effectively colonizes the rhizoplane of both Arabidopsis and wheat. Strain LTYR-11ZT was able to promote the growth of wheat enhancing its resistance to drought stress. Strain LTYR-11ZT led to increased accumulation of soluble sugars, decreased accumulation of proline and malondialdehyde (MDA), and decreased degradation of chlorophyll in leaves of drought-stressed wheat. Our findings will contribute to the development of a novel biotechnological agent to improve the adaptation of crop plants to drought in arid ecosystems.
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15
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Munson E, Carroll KC. What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015. J Clin Microbiol 2017; 55:24-42. [PMID: 27795334 PMCID: PMC5228236 DOI: 10.1128/jcm.01379-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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16
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Janda JM. Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2015. Diagn Microbiol Infect Dis 2016; 86:123-7. [DOI: 10.1016/j.diagmicrobio.2016.06.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 12/23/2022]
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17
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Pantoea hericii sp. nov., Isolated from the Fruiting Bodies of Hericium erinaceus. Curr Microbiol 2016; 72:738-43. [PMID: 26897127 DOI: 10.1007/s00284-016-1011-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/10/2016] [Indexed: 10/22/2022]
Abstract
Three Gram-negative, facultatively anaerobic bacterial isolates were obtained from the fruiting bodies of the edible mushroom Hericium erinaceus showing symptoms of soft rot disease in Beijing, China. Sequences of partial 16S rRNA gene placed these isolates in the genus Pantoea. Multilocus sequence analysis based on the partial sequences of atpD, gyrB, infB and rpoB revealed P. eucalypti and P. anthophila as their closest phylogenetic relatives and indicated that these isolates constituted a possible novel species. DNA-DNA hybridization studies confirmed the classification of these isolates as a novel species and phenotypic tests allowed for differentiation from the closest phylogenetic neighbours. The name Pantoea hericii sp. nov. [Type strain LMG 28847(T) = CGMCC 1.15224(T) = JZB 2120024(T)] is proposed.
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