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Wang Y, Xu X, Chen H, Yang F, Xu B, Wang K, Liu Q, Liang G, Zhang R, Jiao X, Zhang Y. Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers. BMC Genomics 2023; 24:530. [PMID: 37679681 PMCID: PMC10483869 DOI: 10.1186/s12864-023-09623-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a "generalist" species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive. RESULTS In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events. CONCLUSIONS A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers' gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.
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Affiliation(s)
- Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Xiaomeng Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Fang Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Bo Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Kun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Qianwen Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Guixin Liang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Ruiqi Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Xin'an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
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Heng YC, Menon N, Chen B, Loo BZL, Wong GWJ, Lim ACH, Silvaraju S, Kittelmann S. Ligilactobacillus ubinensis sp. nov., a novel species isolated from the wild ferment of a durian fruit ( Durio zibethinus). Int J Syst Evol Microbiol 2023; 73. [PMID: 36920986 DOI: 10.1099/ijsem.0.005733] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
A Gram-stain-positive, rod-shaped, non-spore-forming, catalase-negative, urease-negative, homofermentative and facultatively anaerobic strain, named WILCCON 0076T, was isolated from a wild ferment of pieces of a 'Kampung' durian fruit collected on the island of Ubin (Pulau Ubin), Singapore. The durian had fallen to the ground from a durian tree (Durio zibethinus), on which a group of long-tailed macaques had been observed picking and eating the fruits. Comparative analyses of 16S rRNA gene sequences indicated that WILCCON 0076T potentially represented a novel species within the genus Ligilactobacillus, with the most closely related type strain being Ligilactobacillus agilis DSM 20509T (16S rRNA gene sequence similarity of 97.2 %). Average nucleotide identity and digital DNA-DNA hybridization prediction values were only 86.0% and 18.9 %, respectively. On the basis of the results of a polyphasic approach that included phylogenomic, chemotaxonomic and morphological analyses, we propose a novel species with the name Ligilactobacillus ubinensis sp. nov. (type strain WILCCON 0076T=DSM 114293T=LMG 32698T).
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Affiliation(s)
- Yu Chyuan Heng
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Nandita Menon
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Binbin Chen
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan Zong Lin Loo
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Garrett Wei Jie Wong
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Amber Ching Han Lim
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Shaktheeshwari Silvaraju
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
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Tohno M, Tanizawa Y, Sawada H, Sakamoto M, Ohkuma M, Kobayashi H. A novel species of lactic acid bacteria, Ligilactobacillus pabuli sp. nov., isolated from alfalfa silage. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we isolated a novel strain of lactic acid bacteria, AF129T, from alfalfa silage prepared locally in Morioka, Iwate, Japan. Polyphasic taxonomy was used to characterize the bacterial strain. The bacterium was rod-shaped, Gram-stain-positive, non-spore-forming and catalase-negative. The strain grew at various temperatures (15–40°C) and pH levels (4.0–8.0). The optimum growth conditions were a temperature of 30°C and a pH of 6.0. AF129T exhibited growth at salt (NaCl) concentrations of up to 6.5 % (w/v). The G+C content of the strain’s genomic DNA was 41.5 %. The major fatty acids were C16 : 0, C18 : 1ω9c, C19 : 0cyclo ω8c and summed feature 8. 16S rRNA gene sequencing revealed that AF129T represents a member of the genus
Ligilactobacillus
and it has higher sequence similarities with
Ligilactobacillus pobuzihii
(98.4 %),
Ligilactobacillus acidipiscis
(97.5 %) and
Ligilactobacillus salitolerans
(97.4 %). The digital DNA–DNA hybridization values for AF129T and phylogenetically related species of the genus
Ligilactobacillus
ranged from 19.8% to 24.1%. The average nucleotide identity of the strain with its closely related taxa was lower than the threshold (95 %–96 %) used for species differentiation. In the light of the above-mentioned physiological, genotypic, chemotaxonomic and phylogenetic evidence, we confirm that AF129T represents a member of the genus
Ligilactobacillus
and constitutes a novel species; we propose the name Ligilactobacillus pabuli sp. nov. for this species. The type strain is AF129T =MAFF 518002T =JCM 34518T=BCRC 81335T.
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Affiliation(s)
- Masanori Tohno
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroyuki Sawada
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
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Stanojković A, Skoupý S, Škaloud P, Dvořák P. High genomic differentiation and limited gene flow indicate recent cryptic speciation within the genus Laspinema (cyanobacteria). Front Microbiol 2022; 13:977454. [PMID: 36160208 PMCID: PMC9500459 DOI: 10.3389/fmicb.2022.977454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
The sympatric occurrence of closely related lineages displaying conserved morphological and ecological traits is often characteristic of free-living microbes. Gene flow, recombination, selection, and mutations govern the genetic variability between these cryptic lineages and drive their differentiation. However, sequencing conservative molecular markers (e.g., 16S rRNA) coupled with insufficient population-level sampling hindered the study of intra-species genetic diversity and speciation in cyanobacteria. We used phylogenomics and a population genomic approach to investigate the extent of local genomic diversity and the mechanisms underlying sympatric speciation of Laspinema thermale. We found two cryptic lineages of Laspinema. The lineages were highly genetically diverse, with recombination occurring more frequently within than between them. That suggests the existence of a barrier to gene flow, which further maintains divergence. Genomic regions of high population differentiation harbored genes associated with possible adaptations to high/low light conditions and stress stimuli, although with a weak diversifying selection. Overall, the diversification of Laspinema species might have been affected by both genomic and ecological processes.
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Affiliation(s)
| | - Svatopluk Skoupý
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
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5
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Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O’Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina del Rio T, DeAngelis KM. Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. Microbiol Spectr 2022; 10:e0234621. [PMID: 35579457 PMCID: PMC9241852 DOI: 10.1128/spectrum.02346-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.
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Affiliation(s)
- Gina Chaput
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Jacob Ford
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Lani DeDiego
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Achala Narayanan
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Wing Yin Tam
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Meghan Whalen
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Marcel Huntemann
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alicia Clum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alex Spunde
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Manoj Pillay
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Neha Varghese
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Mikhailova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - I-Min Chen
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Dimitrios Stamatis
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - T. B. K Reddy
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Ronan O’Malley
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nicole Shapiro
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Ivanova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nikos C. Kyrpides
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Tanja Woyke
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
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Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov. Mol Genet Genomics 2022; 297:213-225. [PMID: 34988605 DOI: 10.1007/s00438-021-01829-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.
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Perez M, Ntemiri A, Tan H, Harris HMB, Roager HM, Ribière C, O’Toole PW. A synthetic consortium of 100 gut commensals modulates the composition and function in a colon model of the microbiome of elderly subjects. Gut Microbes 2021; 13:1-19. [PMID: 33993839 PMCID: PMC8128205 DOI: 10.1080/19490976.2021.1919464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Administration of cultured gut isolates holds promise for modulating the altered composition and function of the microbiota in older subjects, and for promoting their health. From among 692 initial isolates, we selected 100 gut commensal strains (MCC100) based on emulating the gut microbiota of healthy subjects, and retaining strain diversity within selected species. MCC100 susceptibility to seven antibiotics was determined, and their genomes were screened for virulence factor, antimicrobial resistance and bacteriocin genes. Supplementation of healthy and frail elderly microbiota types with the MCC100 in an in vitro colon model increased alpha-diversity, raised relative abundance of taxa including Blautia luti, Bacteroides fragilis, and Sutterella wadsworthensis; and introduced taxa such as Bifidobacterium spp. Microbiota changes correlated with higher levels of branched chain amino acids, which are health-associated in elderly. The study establishes that the MCC100 consortium can modulate older subjects' microbiota composition and associated metabolome in vitro, paving the way for pre-clinical and human trials.
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Affiliation(s)
- Marta Perez
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Alexandra Ntemiri
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Huizi Tan
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hugh M. B. Harris
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Céline Ribière
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul W. O’Toole
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland,CONTACT Paul W. O’Toole School of Microbiology & APC Microbiome Ireland, Food Science Building, University College Cork, CorkT12 YN60, Ireland
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8
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Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in Lactobacillus salivarius. Microorganisms 2021; 9:microorganisms9102038. [PMID: 34683359 PMCID: PMC8539994 DOI: 10.3390/microorganisms9102038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/23/2022] Open
Abstract
Lactobacillus salivarius has drawn attention because of its promising probiotic functions. Tolerance to the gastrointestinal tract condition is crucial for orally administrated probiotics to exert their functions. However, previous studies of L. salivarius have only focused on the bile salt resistance of particular strains, without uncovering the common molecular mechanisms of this species. Therefore, in this study, we expanded our research to 90 L. salivarius strains to explore their common functional genes for bile salt resistance. First, the survival rates of the 90 L. salivarius strains in 0.3% bile salt solutions were determined. Comparative genomics analysis was then performed to screen for the potential functional genes related to bile salt tolerance. Next, real-time polymerase chain reaction and gene knockout experiments were conducted to further verify the tolerance-related functional genes. The results indicated that the strain-dependent bile salt tolerance of L. salivarius was mainly associated with four peptidoglycan synthesis-related genes, seven phosphotransferase system-related genes, and one chaperone-encoding gene involved in the stress response. Among them, the GATase1-encoding gene showed the most significant association with bile salt tolerance. In addition, four genes related to DNA damage repair and substance transport were redundant in the strains with high bile salt tolerance. Besides, cluster analysis showed that bile salt hydrolases did not contribute to the bile salt tolerance of L. salivarius. In this study, we determined the global regulatory genes, including LSL_1568, LSL_1716 and LSL_1709, for bile salt tolerance in L. salivarius and provided a potential method for the rapid screening of bile salt-tolerant L. salivarius strains, based on PCR amplification of functional genes.
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Xiao Y, Yang C, Yu L, Tian F, Wu Y, Zhao J, Zhang H, Yang R, Chen W, Hill C, Cui Y, Zhai Q. Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model. MICROBIOME 2021; 9:180. [PMID: 34470652 PMCID: PMC8411540 DOI: 10.1186/s40168-021-01108-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/02/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear. RESULTS By population genomic analysis of 418 Bifidobacterium longum strains, including 143 newly sequenced in this study, three geographically distinct gene pools/populations, BLAsia1, BLAsia2, and BLothers, were identified. Genes involved in cell wall biosynthesis, particularly peptidoglycan biosynthesis, varied considerably among the core genomes of the different populations, but accessory genes that contributed to the carbohydrate metabolism were significantly distinct. Although active transmission was observed inter-host, inter-country, inter-city, intra-community, and intra-family, a single B. longum clone seemed to reside within each individual. A significant negative association was observed between host age and relative abundance of B. longum, while there was a strong positive association between host age and strain genotype [e.g., single nucleotide polymorphisms in the arginine biosynthesis pathway]. Further animal experiments performed with the B. longum isolates via using a D-galactose-induced aging mouse model supported these associations, in which B. longum strains with different genotypes in arginine biosynthesis pathway showed divergent abilities on protecting against host aging possibly via their different abilities to modify the metabolism of gut microbes. CONCLUSIONS This is the first known example of research on the evolutionary history and transmission of this probiotic species. Our results propose a new mechanistic insight for promoting host longevity via the informed use of specific probiotics or molecules. Video abstract.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- International Joint Research Laboratory for Probiotics At Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004 China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 People’s Republic of China
| | - Colin Hill
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, T12 YN60 Ireland
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- International Joint Research Laboratory for Probiotics At Jiangnan University, Wuxi, 214122 Jiangsu China
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10
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Xiao Y, Zhao J, Zhang H, Zhai Q, Chen W. Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species. Microb Genom 2021; 7:000581. [PMID: 34100697 PMCID: PMC8461469 DOI: 10.1099/mgen.0.000581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- Yangzhou Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, PR China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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11
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Xiao Y, Wang C, Zhao J, Zhang H, Chen W, Zhai Q. Quantitative Detection of Bifidobacterium longum Strains in Feces Using Strain-Specific Primers. Microorganisms 2021; 9:1159. [PMID: 34071208 PMCID: PMC8227663 DOI: 10.3390/microorganisms9061159] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/20/2021] [Indexed: 12/27/2022] Open
Abstract
We adopted a bioinformatics-based technique to identify strain-specific markers, which were then used to quantify the abundances of three distinct B. longum sup. longum strains in fecal samples of humans and mice. A pangenome analysis of 205 B. longum sup. longum genomes revealed the accumulation of considerable strain-specific genes within this species; specifically, 28.7% of the total identified genes were strain-specific. We identified 32, 14, and 49 genes specific to B. longum sup. longum RG4-1, B. longum sup. longum M1-20-R01-3, and B. longum sup. longum FGSZY6M4, respectively. After performing an in silico validation of these strain-specific markers using a nucleotide BLAST against both the B. longum sup. longum genome database and an NR/NT database, RG4-1_01874 (1331 bp), M1-20-R01-3_00324 (1745 bp), and FGSZY6M4_01477 (1691 bp) were chosen as target genes for strain-specific quantification. The specificities of the qPCR primers were validated against 47 non-target microorganisms and fecal baseline microbiota to ensure that they produced no PCR amplification products. The performance of the qPCR primer-based analysis was further assessed using fecal samples. After oral administration, the target B. longum strains appeared to efficiently colonize both the human and mouse guts, with average population levels of >108 CFU/g feces. The bioinformatics pipeline proposed here can be applied to the quantification of various bacterial species.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road No.1800, Binhu District, Wuxi 214122, China; (Y.X.); (C.W.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road No.1800, Binhu District, Wuxi 214122, China; (Y.X.); (C.W.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road No.1800, Binhu District, Wuxi 214122, China; (Y.X.); (C.W.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road No.1800, Binhu District, Wuxi 214122, China; (Y.X.); (C.W.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research, Institute Wuxi Branch, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road No.1800, Binhu District, Wuxi 214122, China; (Y.X.); (C.W.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road No.1800, Binhu District, Wuxi 214122, China; (Y.X.); (C.W.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi 214122, China
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12
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Dec M, Stępień-Pyśniak D, Puchalski A, Hauschild T, Pietras-Ożga D, Ignaciuk S, Urban-Chmiel R. Biodiversity of Ligilactobacillus salivarius Strains from Poultry and Domestic Pigeons. Animals (Basel) 2021; 11:ani11040972. [PMID: 33807321 PMCID: PMC8065712 DOI: 10.3390/ani11040972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/17/2021] [Accepted: 03/24/2021] [Indexed: 01/13/2023] Open
Abstract
Simple Summary Ligilactobcillus salivarius is a Gram-positive bacterium that commonly colonizes the mucous membranes of the digestive tracts of humans and animals, including birds. It belongs to the group of lactic acid bacteria which, by producing lactic acid, acidify the intestinal environment and limit the development of undesirable intestinal microflora. In addition, L. salivarius can produce other antimicrobial substances, such as bacteriocins and hydrogen peroxide. Due to limiting the development of unfavourable microflora and other health-promoting effects, L. salivarius bacteria are considered as potential probiotics that may increase animal health, and thus animal production indicators. In this work, we undertook research on the characteristics of L. salivarius strains from chickens, geese, turkeys and domestic pigeons. We showed great variation in phenotypic and genotypic traits between strains and the evolutionary adaptation of L. salivarius strains to the colonization of a specific host. The results of the study contribute to knowledge of the characteristics of the species L. salivarius and may be useful in the selection of probiotic strains. Abstract Ligilactobacillus salivarius is an important member of the human and animal gut microbiota, and selected strains are promising probiotics, but knowledge of the characteristics of avian isolates is still limited. In this study, we examined selected phenotypic and genotypic traits of 33 L. salivarius strains from geese, chickens, turkeys and pigeons. The strains varied in terms of cell size, colony morphology, broth growth characteristics, biofilm formation, tolerance to bile, hydrophobicity and phenotypic and genotypic antibiotic resistance profiles. Large variation among strains was noted for the utilization of sorbitol, salicin, trehalose, rhamnose, inulin and N-acetyl-D-glucosamine. The presence of genes related to sugar metabolism, i.e., mipB, tktA, rhaB and LSL_1894, was not always correlated with the biochemical phenotypic profile. Correlations were recorded between the host and utilization of certain sugars as well as tolerance to bile. The repA-type megaplasmid and genes coding for Abp118 bacteriocin were detected in 94% and 51.5% of L. salivarius strains, respectively. Phylogeny based on groEL gene sequences was partly correlated with the origin of the strains and revealed an evolutionary distance between L. salivarius strains from humans and birds. The results of the study contribute to knowledge of the characteristics of the species L. salivarius. Intraspecies variations of L. salivarius strains may affect their ability to colonize specific niches and utilize nutrients and reveal potential strain-dependent effects on host health.
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Affiliation(s)
- Marta Dec
- Sub-Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, 20-033 Lublin, Poland; (M.D.); (D.S.-P.); (A.P.)
| | - Dagmara Stępień-Pyśniak
- Sub-Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, 20-033 Lublin, Poland; (M.D.); (D.S.-P.); (A.P.)
| | - Andrzej Puchalski
- Sub-Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, 20-033 Lublin, Poland; (M.D.); (D.S.-P.); (A.P.)
| | - Tomasz Hauschild
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, 15-245 Białystok, Poland;
| | - Dorota Pietras-Ożga
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-612 Lublin, Poland;
| | - Szymon Ignaciuk
- Sub-Department of Mathematics, Department of Applied Mathematics and Computer Science, Faculty of Production Engineering, University of Life Sciences in Lublin, 20-612 Lublin, Poland;
| | - Renata Urban-Chmiel
- Sub-Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, 20-033 Lublin, Poland; (M.D.); (D.S.-P.); (A.P.)
- Correspondence: ; Tel.: +48-814-456-036
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13
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Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum "Campylobacterota". PLoS One 2020; 15:e0241366. [PMID: 33301463 PMCID: PMC7728183 DOI: 10.1371/journal.pone.0241366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class “Campylobacteria”, but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within “Campylobacteria” are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.
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14
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Quilodrán-Vega S, Albarracin L, Mansilla F, Arce L, Zhou B, Islam MA, Tomokiyo M, Al Kassaa I, Suda Y, Kitazawa H, Villena J. Functional and Genomic Characterization of Ligilactobacillus salivarius TUCO-L2 Isolated From Lama glama Milk: A Promising Immunobiotic Strain to Combat Infections. Front Microbiol 2020; 11:608752. [PMID: 33363529 PMCID: PMC7752859 DOI: 10.3389/fmicb.2020.608752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/16/2020] [Indexed: 12/27/2022] Open
Abstract
Potential probiotic or immunobiotic effects of lactic acid bacteria (LAB) isolated from the milk of the South American camelid llama (Lama glama) have not been reported in published studies. The aim of the present work was to isolate beneficial LAB from llama milk that can be used as potential probiotics active against bacterial pathogens. LAB strains were isolated from llama milk samples. In vitro functional characterization of the strains was performed by evaluating the resistance against gastrointestinal conditions and inhibition of the pathogen growth. Additionally, the adhesive and immunomodulatory properties of the strains were assessed. The functional studies were complemented with a comparative genomic evaluation and in vivo studies in mice. Ligilactobacillus salivarius TUCO-L2 showed enhanced probiotic/immunobiotic potential compared to that of other tested strains. The TUCO-L2 strain was resistant to pH and high bile salt concentrations and demonstrated antimicrobial activity against Gram-negative intestinal pathogens and adhesion to mucins and epithelial cells. L. salivarius TUCO-L2 modulated the innate immune response triggered by Toll-like receptor (TLR)-4 activation in intestinal epithelial cells. This effect involved differential regulation of the expression of inflammatory cytokines and chemokines mediated by the modulation of the negative regulators of the TLR signaling pathway. Moreover, the TUCO-L2 strain enhanced the resistance of mice to Salmonella infection. This is the first report on the isolation and characterization of a potential probiotic/immunobiotic strain from llama milk. The in vitro, in vivo, and in silico investigation performed in this study reveals several research directions that are needed to characterize the TUCO-L2 strain in detail to position this strain as a probiotic or immunobiotic that can be used against infections in humans or animals, including llama.
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Affiliation(s)
- Sandra Quilodrán-Vega
- Laboratory of Food Microbiology, Faculty of Veterinary Sciences, University of Concepción, Chillán, Chile
| | - Leonardo Albarracin
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán, Argentina.,Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Laboratory of Computing Science, Faculty of Exact Sciences and Technology, Tucuman University, Tucuman, Argentina
| | - Flavia Mansilla
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán, Argentina.,Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Lorena Arce
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Infection Biology Laboratory, Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET), Tucumán, Argentina
| | - Binghui Zhou
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Md Aminul Islam
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mikado Tomokiyo
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Imad Al Kassaa
- Faculty of Public Health, Lebanese University, Hadath, Lebanon
| | - Yoshihito Suda
- Department of Food, Agriculture and Environment, Miyagi University, Sendai, Japan
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Julio Villena
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán, Argentina.,Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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15
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Zhou B, Albarracin L, Indo Y, Arce L, Masumizu Y, Tomokiyo M, Islam MA, Garcia-Castillo V, Ikeda-Ohtsubo W, Nochi T, Morita H, Takahashi H, Kurata S, Villena J, Kitazawa H. Selection of Immunobiotic Ligilactobacillus salivarius Strains from the Intestinal Tract of Wakame-Fed Pigs: Functional and Genomic Studies. Microorganisms 2020; 8:microorganisms8111659. [PMID: 33114778 PMCID: PMC7716343 DOI: 10.3390/microorganisms8111659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/11/2022] Open
Abstract
In this article, Ligilactobacillus salivarius FFIG strains, isolated from the intestinal tract of wakame-fed pigs, are characterized according to their potential probiotic properties. Strains were evaluated by studying their interaction with porcine intestinal epithelial (PIE) cells in terms of their ability to regulate toll-like receptor (TLR)-3- or TLR4-mediated innate immune responses, as well as by assessing their adhesion capabilities to porcine epithelial cells and mucins. These functional studies were complemented with comparative genomic evaluations using the complete genome sequences of porcine L. salivarius strains selected from subgroups that demonstrated different “immune” and “adhesion” phenotypes. We found that their immunomodulatory and adhesion capabilities are a strain-dependent characteristic. Our analysis indicated that the differential immunomodulatory and adhesive activities of FFIG strains would be dependent on the combination of several surface structures acting simultaneously, which include peptidoglycan, exopolysaccharides, lipoteichoic acid, and adhesins. Of note, our results indicate that there is no correlation between the immunomodulatory capacity of the strains with their adhesion ability to mucins and epithelial cells. Therefore, in the selection of strains destined to colonize the intestinal mucosa and modulate the immunity of the host, both properties must be adequately evaluated. Interestingly, we showed that L. salivarius FFIG58 functionally modulated the innate immune responses triggered by TLR3 and TLR4 activation in PIE cells and efficiently adhered to these cells. Moreover, the FFIG58 strain was capable of reducing rotavirus replication in PIE cells. Therefore, L. salivarius FFIG58 is a good candidate for further in vivo studying the protective effect of lactobacilli against intestinal infections in the porcine host. We also reported and analyzed, for the first time, the complete genome of several L. salivarius strains that were isolated from the intestine of pigs after the selective pressure of feeding the animals with wakame. Further genomic analysis could be of value to reveal the metabolic characteristics and potential of the FFIG strains in general and of the FFIG58 strain, in particular, relating to wakame by-products assimilation.
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Affiliation(s)
- Binghui Zhou
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
| | - Leonardo Albarracin
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucuman 4000, Argentina
- Scientific Computing Laboratory, Computer Science Department, Faculty of Exact Sciences and Technology, National University of Tucuman, Tucuman 4000, Argentina
| | - Yuhki Indo
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
| | - Lorena Arce
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Infection Biology Laboratory, INSIBIO-CONICET, Faculty of Medicine, University of Tucuman, Tucuman 4000, Argentina
| | - Yuki Masumizu
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
| | - Mikado Tomokiyo
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
| | - Md. Aminul Islam
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
- Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Valeria Garcia-Castillo
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucuman 4000, Argentina
| | - Wakako Ikeda-Ohtsubo
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
| | - Tomonori Nochi
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
- Laboratory of Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan;
| | - Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
- Plant Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Shoichiro Kurata
- Laboratory of Molecular Genetics, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8572, Japan;
| | - Julio Villena
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucuman 4000, Argentina
- Correspondence: (J.V.); (H.K.)
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (B.Z.); (L.A.); (Y.I.); (L.A.); (Y.M.); (M.T.); (M.A.I.); (V.G.-C.); (W.I.-O.)
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan;
- Correspondence: (J.V.); (H.K.)
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Draft Genome Sequence of Ligilactobacillus salivarius FFIG58, Isolated from the Intestinal Tract of Wakame-Fed Pig. Microbiol Resour Announc 2020; 9:9/34/e00839-20. [PMID: 32816987 PMCID: PMC7441245 DOI: 10.1128/mra.00839-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Ligilactobacillus salivarius FFIG58 was isolated from the intestine of a wakame-fed pig and sequenced with an Illumina HiSeq system. FFIG58 genome sequencing revealed a genome size of 1,984,180 bp, with 1,994 protein-coding genes and a GC content of 32.9%. This draft genome sequence will contribute to a better understanding of the porcine gut microbiome. Ligilactobacillus salivarius FFIG58 was isolated from the intestine of a wakame-fed pig and sequenced with an Illumina HiSeq system. FFIG58 genome sequencing revealed a genome size of 1,984,180 bp, with 1,994 protein-coding genes and a GC content of 32.9%. This draft genome sequence will contribute to a better understanding of the porcine gut microbiome.
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17
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Huang D, Yang B, Chen Y, Stanton C, Ross RP, Zhao J, Zhang H, Chen W. Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Comparative genomics and gene-trait matching analysis of Bifidobacterium breve from Chinese children. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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19
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Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O'Toole PW, Pot B, Vandamme P, Walter J, Watanabe K, Wuyts S, Felis GE, Gänzle MG, Lebeer S. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782-2858. [PMID: 32293557 DOI: 10.1099/ijsem.0.004107] [Citation(s) in RCA: 1537] [Impact Index Per Article: 384.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
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Affiliation(s)
- Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, PR China
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Elisa Salvetti
- Dept. of Biotechnology, University of Verona, Verona, Italy
| | - Charles M A P Franz
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Kiel, Germany
| | - Hugh M B Harris
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Paola Mattarelli
- University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jens Walter
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Koichi Watanabe
- Food Industry Research and Development Institute, Bioresource Collection and Research Center, Hsinchu, Taiwan, ROC.,National Taiwan University, Dept. of Animal Science and Technology, Taipei, Taiwan, ROC
| | - Sander Wuyts
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | | | - Michael G Gänzle
- Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, PR China.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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20
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Jiang J, Yang B, Ross RP, Stanton C, Zhao J, Zhang H, Chen W. Comparative Genomics of Pediococcus pentosaceus Isolated From Different Niches Reveals Genetic Diversity in Carbohydrate Metabolism and Immune System. Front Microbiol 2020; 11:253. [PMID: 32174896 PMCID: PMC7055311 DOI: 10.3389/fmicb.2020.00253] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/03/2020] [Indexed: 12/13/2022] Open
Abstract
Pediococcus pentosaceus isolated from fermented food and the gastrointestinal tracts of humans and animals have been widely identified, and some strains have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, the genomes of 65 P. pentosaceus strains isolated from human and animal feces and different fermented food were sequenced and comparative genomics analysis was performed on all strains along with nine sequenced representative strains to preliminarily reveal the lifestyle of P. pentosaceus, and investigate the genomic diversity within this species. The results reveal that P. pentosaceus is not host-specific, and shares core genes encoding proteins related to translation, ribosomal structure and biogenesis and signal transduction mechanisms, while its genetic diversity relates mainly to carbohydrate metabolism, and horizontally transferred DNA, especially prophages and bacteriocins encoded on plasmids. Additionally, this is the first report of a type IIA CRISPR/Cas system in P. pentosaceus. This work provides expanded resources of P. pentosaceus genomes, and offers a framework for understanding the biotechnological potential of this species.
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Affiliation(s)
- Jie Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Research Center for Probiotics and Gut Health, Jiangnan University, Wuxi, China
| | - R Paul Ross
- International Joint Research Center for Probiotics and Gut Health, Jiangnan University, Wuxi, China.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- International Joint Research Center for Probiotics and Gut Health, Jiangnan University, Wuxi, China.,Moorepark Teagasc Food Research Centre, Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China
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21
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Zhou X, Yang B, Stanton C, Ross RP, Zhao J, Zhang H, Chen W. Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa. BMC Genomics 2020; 21:119. [PMID: 32013858 PMCID: PMC6998098 DOI: 10.1186/s12864-020-6527-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 01/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. RESULTS In this study, to explore the genomic diversity and mine potential probiotic characteristics of L. gasseri, 92 strains of L. gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. paragasseri (n = 79) and L. gasseri (n = 13), respectively. Their pan/core-genomes were determined, revealing that L. paragasseri had an open pan-genome. Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. paragasseri harboured Type II-A CRISPR-Cas system while 12 strains of L. gasseri contained Type I-E and II-A CRISPR-Cas systems. Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species. CONCLUSIONS This is the first time to study pan/core-genome of L. gasseri and L. paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.
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Affiliation(s)
- Xingya Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China. .,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.
| | - Catherine Stanton
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - R Paul Ross
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China. .,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China. .,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Beijing Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China
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22
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Host-adapted lactobacilli in food fermentations: impact of metabolic traits of host adapted lactobacilli on food quality and human health. Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2020.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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23
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Reis AC, Kolvenbach BA, Chami M, Gales L, Egas C, Corvini PFX, Nunes OC. Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. BMC Genomics 2019; 20:885. [PMID: 31752666 PMCID: PMC6868719 DOI: 10.1186/s12864-019-6206-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/21/2019] [Indexed: 02/01/2023] Open
Abstract
Background Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified. Results Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements. Conclusions Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.
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Affiliation(s)
- Ana C Reis
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.,Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Mohamed Chami
- BioEM lab, C-Cina, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Luís Gales
- Instituto de Investigação e Inovação em Saúde - i3S, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Biologia Molecular e Celular - IBMC, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar - ICBAS, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Faculty of Medicine, Rua Larga, Pólo I, 3004-504, Coimbra, Portugal
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Olga C Nunes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
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24
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Zhang W, Wang J, Zhang D, Liu H, Wang S, Wang Y, Ji H. Complete Genome Sequencing and Comparative Genome Characterization of Lactobacillus johnsonii ZLJ010, a Potential Probiotic With Health-Promoting Properties. Front Genet 2019; 10:812. [PMID: 31552103 PMCID: PMC6746964 DOI: 10.3389/fgene.2019.00812] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/06/2019] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus johnsonii ZLJ010 is a probiotic strain isolated from the feces of a healthy sow and has putative health-promoting properties. To determine the molecular basis underlying the probiotic potential of ZLJ010 and the genes involved in the same, complete genome sequencing and comparative genome analysis with L. johnsonii ZLJ010 were performed. The ZLJ010 genome was found to contain a single circular chromosome of 1,999,879 bp with a guanine-cytosine (GC) content of 34.91% and encoded 18 ribosomal RNA (rRNA) genes and 77 transfer RNA (tRNA) genes. From among the 1,959 protein coding sequences (CDSs), genes known to confer probiotic properties were identified, including genes related to stress adaptation, biosynthesis, metabolism, transport of amino acid, secretion, and the defense machinery. ZLJ010 lacked complete or partial biosynthetic pathways for amino acids but was predicted to compensate for this with an enhanced transport system and some unique amino acid permeases and peptidases that allow it to acquire amino acids and other precursors exogenously. The comparative genomic analysis of L. johnsonii ZLP001 and seven other available L. johnsonii strains, including L. johnsonii NCC533, FI9785, DPC6026, N6.2, BS15, UMNLJ22, and PF01, revealed 2,732 pan-genome orthologous gene clusters and 1,324 core-genome orthologous gene clusters. Phylogenomic analysis based on 1,288 single copy genes showed that ZLJ010 had a closer relationship with the BS15 from yogurt and DPC6026 from the porcine intestinal tract but was located on a relatively standalone branch. The number of clusters of unique, strain-specific genes ranged from 42 to 185. A total of 219 unique genes present in the genome of L. johnsonii ZLJ010 primarily encoded proteins that are putatively involved in replication, recombination and repair, defense mechanisms, transcription, amino acid transport and metabolism, and carbohydrate transport and metabolism. Two unique prophages were predicted in the ZLJ010 genome. The present study helps us understand the ability of L. johnsonii ZLJ010 to better adapt to the gut environment and also its probiotic functionalities.
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Affiliation(s)
- Wei Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jing Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Dongyan Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Sixin Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yamin Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haifeng Ji
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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25
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Abstract
Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods. In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.
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26
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Wuyts S, Allonsius CN, Wittouck S, Thys S, Lievens B, Weckx S, De Vuyst L, Sarah L. Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group. Microb Genom 2019; 5. [PMID: 31368886 PMCID: PMC6807380 DOI: 10.1099/mgen.0.000286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity that is roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group, which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402T, had been described, but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harboured the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on a plasmid in at least two of the strains studied.
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Affiliation(s)
- Sander Wuyts
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.,Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Camille Nina Allonsius
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sofie Thys
- Laboratory of Cell Biology and Histology, Antwerp Centre for Advanced Microscopy (ACAM), University of Antwerp, Antwerp, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lebeer Sarah
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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27
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Bravo M, Combes T, Martinez FO, Cerrato R, Rey J, Garcia-Jimenez W, Fernandez-Llario P, Risco D, Gutierrez-Merino J. Lactobacilli Isolated From Wild Boar ( Sus scrofa) Antagonize Mycobacterium bovis Bacille Calmette-Guerin (BCG) in a Species-Dependent Manner. Front Microbiol 2019; 10:1663. [PMID: 31417502 PMCID: PMC6683848 DOI: 10.3389/fmicb.2019.01663] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 07/04/2019] [Indexed: 01/06/2023] Open
Abstract
Background: Wildlife poses a significant burden for the complete eradication of bovine tuberculosis (bTB). In particular, wild boar (Sus scrofa) is one of the most important reservoirs of Mycobacterium bovis, the causal agent of bTB. Wild boar can display from mild TB lesions, usually found in head lymph nodes, to generalized TB lesions distributed in different anatomical regions; but rarely clinical signs, which complicates the diagnosis of Mycobacterium bovis infection and bTB control. Among the possibilities for this variability in lesion distribution is the influence of the host-beneficial commensal-primed immune barrier. In this respect, beneficial microbes may delay bTB dissemination as a consequence of an antagonistic competition for nutrients and phagocytes. In order to explore this possibility, we have tested whether typical commensals such as lactobacilli have the capacity to reduce the survival rate of the surrogate M. bovis strain Bacillus Calmette-Guerin (BCG); and to modulate its phagocyte intake. Results: Three Lactobacillus species, L. casei, L. plantarum, and L. salivarius, isolated from wild boar feces displayed a pH-dependent inhibitory activity against BCG and influenced its intake by porcine blood phagocytes in a species-dependent manner. All lactobacilli showed a very significant bactericidal effect against BCG at low pH, but only isolates of L. plantarum and L. casei displayed such antimycobacterial activity at neutral pH. The genomes of these isolates revealed the presence of two-peptide bacteriocins whose precursor genes up-regulate in the presence of BCG cells. Furthermore, L. plantarum reduced significantly the BCG phagocytic intake, whereas L. casei had the opposite effect. L. salivarius had no significant influence on the phagocytic response to BCG. Conclusions: Our in vitro results show that lactobacilli isolated from wild boar antagonize BCG as a consequence of their antimycobacterial activity and a competitive phagocytic response. These findings suggest that commensal bacteria could play a beneficial role in influencing the outcome of bTB dissemination. Further work with lactobacilli as a potential competitive pressure to control bTB will need to take into account the complex nature of the commensal microbiome, the specific immunity of the wild boar and the in vivo infection context with pathogenic strains of M. bovis.
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Affiliation(s)
- Maria Bravo
- Innovación en Gestión y Conservación de Ungulados SL, Cáceres, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Theo Combes
- Department of Biochemical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Fernando O Martinez
- Department of Biochemical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Rosario Cerrato
- Innovación en Gestión y Conservación de Ungulados SL, Cáceres, Spain
| | - Joaquín Rey
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | | | - David Risco
- Innovación en Gestión y Conservación de Ungulados SL, Cáceres, Spain
| | - Jorge Gutierrez-Merino
- Department of Nutritional Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
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28
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Moriuchi R, Dohra H, Kanesaki Y, Ogawa N. Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses. Front Microbiol 2019; 10:133. [PMID: 30809202 PMCID: PMC6379261 DOI: 10.3389/fmicb.2019.00133] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/21/2019] [Indexed: 01/05/2023] Open
Abstract
Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain's ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 and 3.4 Mb) and two circular plasmids (427 and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia. As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.
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Affiliation(s)
- Ryota Moriuchi
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.,The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Naoto Ogawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan.,Graduate School of Agriculture, Shizuoka University, Shizuoka, Japan
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29
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Grouzdev DS, Rysina MS, Bryantseva IA, Gorlenko VM, Gaisin VA. Draft genome sequences of ' Candidatus Chloroploca asiatica' and ' Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications. Stand Genomic Sci 2018; 13:24. [PMID: 30338027 PMCID: PMC6180586 DOI: 10.1186/s40793-018-0329-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 09/28/2018] [Indexed: 11/10/2022] Open
Abstract
'Candidatus Chloroploca asiatica' B7-9 and 'Candidatus Viridilinea mediisalina' Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became available in the last few years and only in stable enrichment culture. In this study, we report the draft genomic sequences of 'Ca. Chloroploca asiatica' B7-9 and 'Ca. Viridilinea mediisalina' Kir15-3F, which were assembled from metagenomes of their cultures with a fold coverage 86.3× and 163.8×, respectively. The B7-9 (5.8 Mb) and the Kir15-3F (5.6 Mb) draft genome harbors 4818 and 4595 predicted protein-coding genes, respectively. In this article, we analyzed the phylogeny of representatives of the Chloroflexineae suborder in view of the appearance of new genomic data. These data were used for the revision of earlier published group-specific conserved signature indels and for searching for novel signatures for taxons in the Chloroflexineae suborder.
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Affiliation(s)
- Denis S. Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria S. Rysina
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
| | - Irina A. Bryantseva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir M. Gorlenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vasil A. Gaisin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
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30
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Kazou M, Alexandraki V, Blom J, Pot B, Tsakalidou E, Papadimitriou K. Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade. Front Microbiol 2018; 9:1244. [PMID: 29942291 PMCID: PMC6004923 DOI: 10.3389/fmicb.2018.01244] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/23/2018] [Indexed: 02/05/2023] Open
Abstract
Lactobacillus acidipiscis belongs to the Lactobacillus salivarius clade and it is found in a variety of fermented foods. Strain ACA-DC 1533 was isolated from traditional Greek Kopanisti cheese and among the available L. acidipiscis genomes it is the only one with a fully sequenced chromosome. L. acidipiscis strains exhibited a high degree of conservation at the genome level. Investigation of the distribution of prophages and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) among the three strains suggests the potential existence of lineages within the species. Based on the presence/absence patterns of these genomic traits, strain ACA-DC 1533 seems to be more related to strain JCM 10692T than strain KCTC 13900. Interestingly, strains ACA-DC 1533 and JCM 10692T which lack CRISPRs, carry two similar prophages. In contrast, strain KCTC 13900 seems to have acquired immunity to these prophages according to the sequences of spacers in its CRISPRs. Nonetheless, strain KCTC 13900 has a prophage that is absent from strains ACA-DC 1533 and JCM 10692T. Furthermore, comparative genomic analysis was performed among L. acidipiscis ACA-DC 1533, L. salivarius UCC118 and Lactobacillus ruminis ATCC 27782. The chromosomes of the three species lack long-range synteny. Important differences were also determined in the number of glycobiome related proteins, proteolytic enzymes, transporters, insertion sequences and regulatory proteins. Moreover, no obvious genomic traits supporting a probiotic potential of L. acidipiscis ACA-DC 1533 were detected when compared to the probiotic L. salivarius UCC118. However, the existence of more than one glycine-betaine transporter within the genome of ACA-DC 1533 may explain the ability of L. acidipiscis to grow in fermented foods containing high salt concentrations. Finally, in silico analysis of the L. acidipiscis ACA-DC 1533 genome revealed pathways that could underpin the production of major volatile compounds during the catabolism of amino acids that may contribute to the typical piquant flavors of Kopanisti cheese.
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Affiliation(s)
- Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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31
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Cousin FJ, Lynch DB, Chuat V, Bourin MJB, Casey PG, Dalmasso M, Harris HMB, McCann A, O'Toole PW. A long and abundant non-coding RNA in Lactobacillus salivarius. Microb Genom 2017; 3:e000126. [PMID: 29114404 PMCID: PMC5643018 DOI: 10.1099/mgen.0.000126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/21/2017] [Indexed: 01/12/2023] Open
Abstract
Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq)transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L. salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.
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Affiliation(s)
- Fabien J Cousin
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Denise B Lynch
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Victoria Chuat
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maxence J B Bourin
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Pat G Casey
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marion Dalmasso
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Hugh M B Harris
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Angela McCann
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- 2APC Microbiome Institute, University College Cork, Cork, Ireland.,1School of Microbiology, University College Cork, Cork, Ireland
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