151
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Yang LL, Jiang Z, Li Y, Wang ET, Zhi XY. Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae. Genome Biol Evol 2020; 12:2002-2014. [PMID: 32687170 PMCID: PMC7719263 DOI: 10.1093/gbe/evaa152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 12/17/2022] Open
Abstract
Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.
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Affiliation(s)
- Ling-Ling Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, PR China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City D.F., México
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
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152
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Xu N, Wang M, Yang X, Xu Y, Guo M. In silico analysis of the chemotactic system of Agrobacterium tumefaciens. Microb Genom 2020; 6:mgen000460. [PMID: 33118922 PMCID: PMC7725337 DOI: 10.1099/mgen.0.000460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/06/2020] [Indexed: 01/23/2023] Open
Abstract
Agrobacterium tumefaciens is an efficient tool for creating transgenic host plants. The first step in the genetic transformation process involves A. tumefaciens chemotaxis, which is crucial to the survival of A. tumefaciens in changeable, harsh and even contaminated soil environments. However, a systematic study of its chemotactic signalling pathway is still lacking. In this study, the distribution and classification of chemotactic genes in the model A. tumefaciens C58 and 21 other strains were annotated. Local blast was used for comparative genomics, and hmmer was used for predicting protein domains. Chemotactic phenotypes for knockout mutants of ternary signalling complexes in A. tumefaciens C58 were evaluated using a swim agar plate. A major cluster, in which chemotaxis genes were consistently organized as MCP (methyl-accepting chemotaxis protein), CheS, CheY1, CheA, CheR, CheB, CheY2 and CheD, was found in A. tumefaciens, but two coupling CheW proteins were located outside the 'che' cluster. In the ternary signalling complexes, the absence of MCP atu0514 significantly impaired A. tumefaciens chemotaxis, and the absence of CheA (atu0517) or the deletion of both CheWs abolished chemotaxis. A total of 465 MCPs were found in the 22 strains, and the cytoplasmic domains of these MCPs were composed of 38 heptad repeats. A high homology was observed between the chemotactic systems of the 22 A. tumefaciens strains with individual differences in the gene and receptor protein distributions, possibly related to their ecological niches. This preliminary study demonstrates the chemotactic system of A. tumefaciens, and provides some reference for A. tumefaciens sensing and chemotaxis to exogenous signals.
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Affiliation(s)
- Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, PR China
| | - Mingqi Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xiaojing Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, PR China
| | - Yujuan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, PR China
| | - Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, PR China
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153
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Gupta SR, Gupta E, Ohri A, Shrivastava SK, Kachhwaha S, Sharma V, Mishra RK, Niraj RRK. Comparative Proteome Analysis of Mycobacterium Tuberculosis Strains - H37Ra, H37Rv, CCDC5180, and CAS/NITR204: A Step Forward to Identify Novel Drug Targets. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200531165148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background:
Mycobacterium tuberculosis is a causative agent of tuberculosis. It is a
non-motile, acid-fast, obligatory aerobic bacterium. Finding novel drug targets in Mycobacterium
tuberculosis has become extremely important as the bacterium is evolving into a more dangerous
multi-drug resistant pathogen. The predominant strains in India belong to the Central-Asian, East-
African Indian, and Beijing clad. For the same reason, the whole proteomes of a non-virulent strain
(H37Ra), a virulent (H37Rv) and two clinical strains, a Central-Asian clad (CAS/NITR204) and a
Beijing clad (CCDC5180) have been selected for comparative study. Selecting a phylogenetically
close and majorly studied non-virulent strain is helpful in removing the common and undesired proteins
from the study.
Objective:
The study compares the whole proteome of non-virulent strain with the other three virulent
strains to find a unique protein responsible for virulence in virulent strains. It is expected that
the drugs developed against identified targets will be specific to the virulent strains. Additionally, to
assure minimal toxicity to the host, we also screened the human proteome.
Methods:
Comparative proteome analysis was used for target identification and in silico validation
of identified target protein Rv2466c, identification of the respective ligand of the identified target
protein and binding interaction study using Molecular docking and Molecular Dynamic Simulation
study were used in this study.
Results and Discussion:
Finally, eleven proteins were found to be unique in virulent strain only and
out of which, Rv2466c (PDB-ID: 4ZIL) was found to be an essential protein and identified as a putative
drug target protein for further study. The compound glutathione was found to be a suitable
inhibitor for Rv2466c. In this study, we used a comparative proteomics approach to identify novel
target proteins.
Conclusion:
This study is unique as we are assured that the study will move forward the research in
a new direction to cure the deadly disease (tuberculosis) caused by Mycobacterium tuberculosis.
Rv2466c was identified as a novel drug target and glutathione as a respective ligand of Rv2466c.
Discovery of the novel drug target as well as the drug will provide a solution to drug resistance as
well as the infection caused by Mycobacterium tuberculosis.
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Affiliation(s)
| | - Ekta Gupta
- Dr B. Lal Institute of Biotechnology Jaipur, Jaipur, India
| | - Avnam Ohri
- Dr B. Lal Institute of Biotechnology Jaipur, Jaipur, India
| | | | | | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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154
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Shetty SA, Boeren S, Bui TPN, Smidt H, de Vos WM. Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics. Environ Microbiol 2020; 22:4863-4875. [PMID: 33001550 PMCID: PMC7702098 DOI: 10.1111/1462-2920.15269] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 11/28/2022]
Abstract
The d- and l-forms of lactate are important fermentation metabolites produced by intestinal bacteria but are found to negatively affect mucosal barrier function and human health. Both enantiomers of lactate can be converted with acetate into the presumed beneficial butyrate by a phylogenetically related group of anaerobes, including Anaerobutyricum and Anaerostipes spp. This is a low energy yielding process with a partially unknown pathway in Anaerobutyricum and Anaerostipes spp. and hence, we sought to address this via a comparative genomics, proteomics and physiology approach. We compared growth of Anaerobutyricum soehngenii on lactate with that on sucrose and sorbitol. Comparative proteomics revealed complete pathway of butyrate formation from sucrose, sorbitol and lactate. Notably, a gene cluster, lctABCDEF was abundantly expressed when grown on lactate. This gene cluster encodes a lactate dehydrogenase (lctD), electron transport proteins A and B (lctCB), nickel-dependent racemase (lctE), lactate permease (lctF) and short-chain acyl-CoA dehydrogenase (lctG). Investigation of available genomes of intestinal bacteria revealed this new gene cluster to be highly conserved in only Anaerobutyricum and Anaerostipes spp. Present study demonstrates that A. soehngenii and several related Anaerobutyricum and Anaerostipes spp. are highly adapted for a lifestyle involving lactate plus acetate utilization in the human intestinal tract.
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Affiliation(s)
- Sudarshan A Shetty
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Thi P N Bui
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.,No Caelus Pharmaceuticals, Armsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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155
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Li X, Gan L, Hu M, Wang S, Tian Y, Shi B. Halomonas pellis sp. nov., a moderately halophilic bacterium isolated from wetsalted hides. Int J Syst Evol Microbiol 2020; 70:5417-5424. [DOI: 10.1099/ijsem.0.004426] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A Gram-stain-negative, moderately halophilic strain, designated strain L5T, was isolated from wetsalted hides collected from Chengdu, south-west PR China. The cells were motile, facultative aerobic, short rod-shaped and non-endospore-forming. Growth of strain L5T occurred at pH 6–10 (optimum, pH 8), 10–45 °C (optimum, 30 °C) and in the presence of 1–17 % (w/v) NaCl (optimum, 10 %). Results of phylogenetic analyses based on 16S rRNA, gyrB and rpoD gene sequences and its genome revealed that strain L5T belonged to the genus
Halomonas
. Strain L5T was found to be most closely related to the type strains of
Halomonas saliphila
,
Halomonas lactosivorans
,
Halomonas kenyensis
,
Halomonas daqingensis
and
Halomonas desiderata
(98.8, 98.6, 98.3, 97.9 and 97.4 % 16S rRNA gene sequence similarity, respectively). The draft genome was approximately 4.2 Mb in size with a G+C content of 63.5 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization values among strain L5T and the selected
Halomonas
species were 83.3–88.9 % (ANIm), 71.1–87.3 % (ANIb) and 20.2–34.6 %, which are below the recommended cutoff values. Major fatty acids were C16 : 0, C16 : 1
ω7c, C18 : 1
ω7c and C19 : 0 cyclo ω8c and the predominant ubiquinone was Q-9, with minor ubiquinone Q-8 also present. The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four unidentified aminophospholipids and three unidentified phospholipids. Based on the mentioned polyphasic taxonomic evidence, strain L5T represents a novel species within the genus
Halomonas
, for which Halomonas pellis sp. nov. is proposed. The type strain is L5T (=CGMCC 1.17335T=KCTC 72573T).
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Affiliation(s)
- Xiaoguang Li
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Longzhan Gan
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Mengyao Hu
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Shiting Wang
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Bi Shi
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
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156
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Abstract
This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied. While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera “Candidatus Planktophila” (acI-A) and “Candidatus Nanopelagicus” (acI-B) and the proteobacterial genus “Candidatus Fonsibacter” (LD12). While “Ca. Planktophila” and “Ca. Fonsibacter” had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which “Ca. Planktophila” is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain “Ca. Planktophila” population abundance, the success of “Ca. Nanopelagicus” and “Ca. Fonsibacter” is better explained as a community by-product. Ecotype differentiation of “Ca. Fonsibacter” as a means of escaping predation was supported but not for overcoming auxotrophies. IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.
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157
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Kovács M, Seffer D, Pénzes-Hűvös Á, Juhász Á, Kerepesi I, Csepregi K, Kovács-Valasek A, Fekete C. Structural and functional comparison of Saccharomonospora azurea strains in terms of primycin producing ability. World J Microbiol Biotechnol 2020; 36:160. [PMID: 32989522 PMCID: PMC7522111 DOI: 10.1007/s11274-020-02935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022]
Abstract
Emerging and re-emerging microbial pathogens, together with their rapid evolution and adaptation against antibiotics, highlight the importance not only of screening for new antimicrobial agents, but also for deepening knowledge about existing antibiotics. Primycin is a large 36-membered non-polyene macrolide lactone exclusively produced by Saccharomonospora azurea. This study provides information about strain dependent primycin production ability in conjunction with the structural, functional and comparative genomic examinations. Comparison of high- and low-primycin producer strains, transcriptomic analysis identified a total of 686 differentially expressed genes (DEGs), classified into diverse Cluster of Orthologous Groups. Among them, genes related to fatty acid synthesis, self-resistance, regulation of secondary metabolism and agmatinase encoding gene responsible for catalyze conversion between guanidino/amino forms of primycin were discussed. Based on in silico data mining methods, we were able to identify DEGs whose altered expression provide a good starting point for the optimization of fermentation processes, in order to perform targeted strain improvement and rational drug design.
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Affiliation(s)
- Márk Kovács
- PannonPharma Pharmaceutical Ltd., 7720, Pécsvárad, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, 7624, Pécs, Hungary
| | - Dénes Seffer
- PannonPharma Pharmaceutical Ltd., 7720, Pécsvárad, Hungary
| | | | - Ákos Juhász
- Faculty of Agricultural and Environmental Sciences, Institute of Biological Sciences, Szent István University, 2100, Gödöllő, Hungary
| | - Ildikó Kerepesi
- Faculty of Sciences, Institute of Biology, University of Pécs, 7624, Pécs, Hungary
| | - Kitti Csepregi
- Faculty of Sciences, Institute of Biology, University of Pécs, 7624, Pécs, Hungary
| | | | - Csaba Fekete
- Faculty of Sciences, Institute of Biology, University of Pécs, 7624, Pécs, Hungary.
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158
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Compositional and Functional Adaptations of Intestinal Microbiota and Related Metabolites in CKD Patients Receiving Dietary Protein Restriction. Nutrients 2020; 12:nu12092799. [PMID: 32932711 PMCID: PMC7551076 DOI: 10.3390/nu12092799] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/04/2020] [Accepted: 09/06/2020] [Indexed: 12/13/2022] Open
Abstract
The relationship between change of gut microbiota and host serum metabolomics associated with low protein diet (LPD) has been unraveled incompletely in CKD patients. Fecal 16S rRNA gene sequencing and serum metabolomics profiling were performed. We reported significant changes in the β-diversity of gut microbiota in CKD patients having LPD (CKD-LPD, n = 16). We identified 19 genera and 12 species with significant differences in their relative abundance among CKD-LPD patients compared to patients receiving normal protein diet (CKD-NPD, n = 27) or non-CKD controls (n = 34), respectively. CKD-LPD had a significant decrease in the abundance of many butyrate-producing bacteria (family Lachnospiraceae and Bacteroidaceae) associated with enrichment of functional module of butanoate metabolism, leading to concomitant reduction in serum levels of SCFA (acetic, heptanoic and nonanoic acid). A secondary bile acid, glyco λ-muricholic acid, was significantly increased in CKD-LPD patients. Serum levels of indoxyl sulfate and p-cresyl sulfate did not differ among groups. The relationship between abundances of microbes and metabolites remained significant in subset of resampling subjects of comparable characteristics. Enrichment of bacterial gene markers related to D-alanine, ketone bodies and glutathione metabolism was noted in CKD-LPD patients. Our analyses reveal signatures and functions of gut microbiota to adapt dietary protein restriction in renal patients.
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159
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Lastovetsky OA, Krasnovsky LD, Qin X, Gaspar ML, Gryganskyi AP, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Pawlowska TE. Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism. mBio 2020; 11:e02088-20. [PMID: 32900811 PMCID: PMC7482071 DOI: 10.1128/mbio.02088-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 01/06/2023] Open
Abstract
Fungal-bacterial symbioses range from antagonisms to mutualisms and remain one of the least understood interdomain interactions despite their ubiquity as well as ecological and medical importance. To build a predictive conceptual framework for understanding interactions between fungi and bacteria in different types of symbioses, we surveyed fungal and bacterial transcriptional responses in the mutualism between Rhizopus microsporus (Rm) (ATCC 52813, host) and its Mycetohabitans (formerly Burkholderia) endobacteria versus the antagonism between a nonhost Rm (ATCC 11559) and Mycetohabitans isolated from the host, at two time points, before and after partner physical contact. We found that bacteria and fungi sensed each other before contact and altered gene expression patterns accordingly. Mycetohabitans did not discriminate between the host and nonhost and engaged a common set of genes encoding known as well as novel symbiosis factors. In contrast, responses of the host versus nonhost to endobacteria were dramatically different, converging on the altered expression of genes involved in cell wall biosynthesis and reactive oxygen species (ROS) metabolism. On the basis of the observed patterns, we formulated a set of hypotheses describing fungal-bacterial interactions and tested some of them. By conducting ROS measurements, we confirmed that nonhost fungi increased production of ROS in response to endobacteria, whereas host fungi quenched their ROS output, suggesting that ROS metabolism contributes to the nonhost resistance to bacterial infection and the host ability to form a mutualism. Overall, our study offers a testable framework of predictions describing interactions of early divergent Mucoromycotina fungi with bacteria.IMPORTANCE Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.
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Affiliation(s)
- Olga A Lastovetsky
- Graduate Field of Microbiology, Cornell University, Ithaca, New York, USA
| | - Lev D Krasnovsky
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Xiaotian Qin
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Maria L Gaspar
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | | | - Marcel Huntemann
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Manoj Pillay
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Neha Varghese
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Mikhailova
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Dimitrios Stamatis
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - T B K Reddy
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nicole Shapiro
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Ivanova
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nikos Kyrpides
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
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160
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Mobeen F, Sharma V, Prakash T. Comparative gut microbiome analysis of the Prakriti and Sasang systems reveals functional level similarities in constitutionally similar classes. 3 Biotech 2020; 10:379. [PMID: 32802721 PMCID: PMC7413973 DOI: 10.1007/s13205-020-02376-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
The traditional medicinal systems (TMS) of India (Prakriti) and Korea (Sasang) classify human individuals based on their constitution determined by the physiological and psychological traits of individuals. Similarities in the constitutions are already found between the classes of Prakriti (Vata, Pitta, and Kapha) and Sasang (TE: Taeeumin, SE: Soeumin, and SY: Soyangin) systems. Gut health is an important aspect of this constitution based classification in TMS. To determine the role of gut microbes in such classifications, we have analyzed the gut microbiome (taxa and imputed functions) in the constitutionally similar Prakriti and Sasang classes. An enrichment of Bacteroides and Prevotella enterotypes is observed in the Sasang and Prakriti samples, respectively. The impact of the constitution is found to be more prominent with respect to the taxa and predicted-functions within the Prakriti classes. Gut microbiome functional-level similarities are found to correlate well with the host phenotypes of the constitutionally similar Prakriti and Sasang classes. An enrichment of carbohydrate and amino-acid metabolism is observed in the Vata and SE classes which may be responsible for meeting with their high energy demands and lean phenotype. The Pitta and SY classes exhibit the high capacity to metabolize toxins. An enrichment of functions responsible for predisposition to obesity and high drug metabolism is observed in the Kapha and TE classes. The contribution of gut adaptive functions is found to correlate with the constitution-based classification in both Prakriti and Sasang systems. The TE class harboured the highest number of biofilm-forming and stress-tolerant microbes thus exhibiting the maximum tolerance of environmental stress. Similarities in the gut microbiota and the resulting disease predisposition patterns are found to exist between the constitutionally matching Prakriti and Sasang classes.
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Affiliation(s)
- Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005 India
| | - Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005 India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005 India
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Rhizobium leguminosarum bv. trifolii NodD2 Enhances Competitive Nodule Colonization in the Clover-Rhizobium Symbiosis. Appl Environ Microbiol 2020; 86:AEM.01268-20. [PMID: 32651206 DOI: 10.1128/aem.01268-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
Establishment of the symbiotic relationship that develops between rhizobia and their legume hosts is contingent upon an interkingdom signal exchange. In response to host legume flavonoids, NodD proteins from compatible rhizobia activate expression of nodulation genes that produce lipochitin oligosaccharide signaling molecules known as Nod factors. Root nodule formation commences upon legume recognition of compatible Nod factor. Rhizobium leguminosarum was previously considered to contain one copy of nodD; here, we show that some strains of the Trifolium (clover) microsymbiont R. leguminosarum bv. trifolii contain a second copy designated nodD2. nodD2 genes were present in 8 out of 13 strains of R. leguminosarum bv. trifolii, but were absent from the genomes of 16 R. leguminosarum bv. viciae strains. Analysis of single and double nodD1 and nodD2 mutants in R. leguminosarum bv. trifolii strain TA1 revealed that NodD2 was functional and enhanced nodule colonization competitiveness. However, NodD1 showed significantly greater capacity to induce nod gene expression and infection thread formation. Clover species are either annual or perennial and this phenological distinction is rarely crossed by individual R. leguminosarum bv. trifolii microsymbionts for effective symbiosis. Of 13 strains with genome sequences available, 7 of the 8 effective microsymbionts of perennial hosts contained nodD2, whereas the 3 microsymbionts of annual hosts did not. We hypothesize that NodD2 inducer recognition differs from NodD1, and NodD2 functions to enhance competition and effective symbiosis, which may discriminate in favor of perennial hosts.IMPORTANCE Establishment of the rhizobium-legume symbiosis requires a highly specific and complex signal exchange between both participants. Rhizobia perceive legume flavonoid compounds through LysR-type NodD regulators. Often, rhizobia encode multiple copies of nodD, which is one determinant of host specificity. In some species of rhizobia, the presence of multiple copies of NodD extends their symbiotic host-range. Here, we identified and characterized a second copy of nodD present in some strains of the clover microsymbiont Rhizobium leguminosarum bv. trifolii. The second nodD gene contributed to the competitive ability of the strain on white clover, an important forage legume. A screen for strains containing nodD2 could be utilized as one criterion to select strains with enhanced competitive ability for use as inoculants for pasture production.
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Nguyen NK, Deehan EC, Zhang Z, Jin M, Baskota N, Perez-Muñoz ME, Cole J, Tuncil YE, Seethaler B, Wang T, Laville M, Delzenne NM, Bischoff SC, Hamaker BR, Martínez I, Knights D, Bakal JA, Prado CM, Walter J. Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate. MICROBIOME 2020; 8:118. [PMID: 32814582 PMCID: PMC7439537 DOI: 10.1186/s40168-020-00887-w] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 06/30/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Variability in the health effects of dietary fiber might arise from inter-individual differences in the gut microbiota's ability to ferment these substrates into beneficial metabolites. Our understanding of what drives this individuality is vastly incomplete and will require an ecological perspective as microbiomes function as complex inter-connected communities. Here, we performed a parallel two-arm, exploratory randomized controlled trial in 31 adults with overweight and class-I obesity to characterize the effects of long-chain, complex arabinoxylan (n = 15) at high supplementation doses (female: 25 g/day; male: 35 g/day) on gut microbiota composition and short-chain fatty acid production as compared to microcrystalline cellulose (n = 16, non-fermentable control), and integrated the findings using an ecological framework. RESULTS Arabinoxylan resulted in a global shift in fecal bacterial community composition, reduced α-diversity, and the promotion of specific taxa, including operational taxonomic units related to Bifidobacterium longum, Blautia obeum, and Prevotella copri. Arabinoxylan further increased fecal propionate concentrations (p = 0.012, Friedman's test), an effect that showed two distinct groupings of temporal responses in participants. The two groups showed differences in compositional shifts of the microbiota (p ≤ 0.025, PERMANOVA), and multiple linear regression (MLR) analyses revealed that the propionate response was predictable through shifts and, to a lesser degree, baseline composition of the microbiota. Principal components (PCs) derived from community data were better predictors in MLR models as compared to single taxa, indicating that arabinoxylan fermentation is the result of multi-species interactions within microbiomes. CONCLUSION This study showed that long-chain arabinoxylan modulates both microbiota composition and the output of health-relevant SCFAs, providing information for a more targeted application of this fiber. Variation in propionate production was linked to both compositional shifts and baseline composition, with PCs derived from shifts of the global microbial community showing the strongest associations. These findings constitute a proof-of-concept for the merit of an ecological framework that considers features of the wider gut microbial community for the prediction of metabolic outcomes of dietary fiber fermentation. This provides a basis to personalize the use of dietary fiber in nutritional application and to stratify human populations by relevant gut microbiota features to account for the inconsistent health effects in human intervention studies. TRIAL REGISTRATION Clinicaltrials.gov, NCT02322112 , registered on July 3, 2015. Video Abstract.
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Affiliation(s)
- Nguyen K. Nguyen
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Edward C. Deehan
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Zhengxiao Zhang
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Mingliang Jin
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
- School of Life Science, Northwestern Polytechnical University, Xi’an, 710072 People’s Republic of China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Nami Baskota
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Janis Cole
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Yunus E. Tuncil
- Food Engineering Department, Ordu University, 52200 Ordu, Turkey
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN 47907 USA
| | - Benjamin Seethaler
- Institute of Nutritional Medicine, University of Hohenheim, 70593 Stuttgart, Germany
| | - Ting Wang
- Patient Health Outcomes Research and Clinical Effectiveness Unit, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Martine Laville
- Centre de Recherche en Nutrition Humaine Rhône-Alpes and Centre Européen Nutrition Santé, 69310 Pierre Bénite, France
| | - Nathalie M. Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, 1200 Brussels, Belgium
| | - Stephan C. Bischoff
- Institute of Nutritional Medicine, University of Hohenheim, 70593 Stuttgart, Germany
| | - Bruce R. Hamaker
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN 47907 USA
| | - Inés Martínez
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455 USA
- BioTechnology Institute, University of Minnesota, Saint Paul, MN 55455 USA
| | - Jeffrey A. Bakal
- Patient Health Outcomes Research and Clinical Effectiveness Unit, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Carla M. Prado
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Jens Walter
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada
- School of Microbiology, Department of Medicine, and APC Microbiome Institute, University College Cork–National University of Ireland, Cork, T12 YT20 Ireland
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Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown. Nat Commun 2020; 11:4017. [PMID: 32782292 PMCID: PMC7419316 DOI: 10.1038/s41467-020-17847-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/21/2020] [Indexed: 12/22/2022] Open
Abstract
The thick mucus layer of the gut provides a barrier to infiltration of the underlying epithelia by both the normal microbiota and enteric pathogens. Some members of the microbiota utilise mucin glycoproteins as a nutrient source, but a detailed understanding of the mechanisms used to breakdown these complex macromolecules is lacking. Here we describe the discovery and characterisation of endo-acting enzymes from prominent mucin-degrading bacteria that target the polyLacNAc structures within oligosaccharide side chains of both animal and human mucins. These O-glycanases are part of the large and diverse glycoside hydrolase 16 (GH16) family and are often lipoproteins, indicating that they are surface located and thus likely involved in the initial step in mucin breakdown. These data provide a significant advance in our knowledge of the mechanism of mucin breakdown by the normal microbiota. Furthermore, we also demonstrate the potential use of these enzymes as tools to explore changes in O-glycan structure in a number of intestinal disease states. Epithelial cells that line the gut secrete complex glycoproteins that form a mucus layer to protect the gut wall from enteric pathogens. Here, the authors provide a comprehensive characterisation of endo-acting glycoside hydrolases expressed by mucin-degrading members of the microbiome that are able to cleave the O-glycan chains of a range of different animal and human mucins.
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164
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Harrington LB, Ma E, Chen JS, Witte IP, Gertz D, Paez-Espino D, Al-Shayeb B, Kyrpides NC, Burstein D, Banfield JF, Doudna JA. A scoutRNA Is Required for Some Type V CRISPR-Cas Systems. Mol Cell 2020; 79:416-424.e5. [PMID: 32645367 PMCID: PMC8196889 DOI: 10.1016/j.molcel.2020.06.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/02/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12c/d proteins share limited homology with Cas12a and Cas9 bacterial CRISPR RNA (crRNA)-guided nucleases used widely for genome editing and DNA detection. However, Cas12c (C2c3)- and Cas12d (CasY)-catalyzed DNA cleavage and genome editing activities have not been directly observed. We show here that a short-complementarity untranslated RNA (scoutRNA), together with crRNA, is required for Cas12d-catalyzed DNA cutting. The scoutRNA differs in secondary structure from previously described tracrRNAs used by CRISPR-Cas9 and some Cas12 enzymes, and in Cas12d-containing systems, scoutRNA includes a conserved five-nucleotide sequence that is essential for activity. In addition to supporting crRNA-directed DNA recognition, biochemical and cell-based experiments establish scoutRNA as an essential cofactor for Cas12c-catalyzed pre-crRNA maturation. These results define scoutRNA as a third type of transcript encoded by a subset of CRISPR-Cas genomic loci and explain how Cas12c/d systems avoid requirements for host factors including ribonuclease III for bacterial RNA-mediated adaptive immunity.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/immunology
- Bacteria/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/immunology
- Escherichia coli/metabolism
- Genome, Bacterial/immunology
- Nucleic Acid Conformation
- Phylogeny
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- Sequence Alignment
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Janice S Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Isaac P Witte
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dov Gertz
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - David Paez-Espino
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nikos C Kyrpides
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94114, USA.
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165
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Singh R, Ranaivoarisoa TO, Gupta D, Bai W, Bose A. Genetic Redundancy in Iron and Manganese Transport in the Metabolically Versatile Bacterium Rhodopseudomonas palustris TIE-1. Appl Environ Microbiol 2020; 86:e01057-20. [PMID: 32503905 PMCID: PMC7414945 DOI: 10.1128/aem.01057-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 05/31/2020] [Indexed: 12/24/2022] Open
Abstract
The purple nonsulfur bacterium Rhodopseudomonas palustris TIE-1 can produce useful biochemicals such as bioplastics and biobutanol. Production of such biochemicals requires intracellular electron availability, which is governed by the availability and the transport of essential metals such as iron (Fe). Because of the distinct chemical properties of ferrous [Fe(II)] and ferric iron [Fe(III)], different systems are required for their transport and storage in bacteria. Although Fe(III) transport systems are well characterized, we know much less about Fe(II) transport systems except for the FeoAB system. Iron transporters can also import manganese (Mn). We studied Fe and Mn transport by five putative Fe transporters in TIE-1 under metal-replete, metal-depleted, oxic, and anoxic conditions. We observed that by overexpressing feoAB, efeU, and nramp1AB, the intracellular concentrations of Fe and Mn can be enhanced in TIE-1 under oxic and anoxic conditions, respectively. The deletion of a single gene/operon does not attenuate Fe or Mn uptake in TIE-1 regardless of the growth conditions used. This indicates that genetically dissimilar yet functionally redundant Fe transporters in TIE-1 can complement each other. Relative gene expression analysis shows that feoAB and efeU are expressed during Fe and Mn depletion under both oxic and anoxic conditions. The promoters of these transporter genes contain a combination of Fur and Fnr boxes, suggesting that their expression is regulated by both Fe and oxygen availability. The findings from this study will help us modulate intracellular Fe and Mn concentrations, ultimately improving TIE-1's ability to produce desirable biomolecules.IMPORTANCERhodopseudomonas palustris TIE-1 is a metabolically versatile bacterium that can use various electron donors, including Fe(II) and poised electrodes, for photoautotrophic growth. TIE-1 can produce useful biomolecules, such as biofuels and bioplastics, under various growth conditions. Production of such reduced biomolecules is controlled by intracellular electron availability, which, in turn, is mediated by various iron-containing proteins in the cell. Several putative Fe transporters exist in TIE-1's genome. Some of these transporters can also transport Mn, part of several important cellular enzymes. Therefore, understanding the ability to transport and respond to various levels of Fe and Mn under different conditions is important to improve TIE-1's ability to produce useful biomolecules. Our data suggest that by overexpressing Fe transporter genes via plasmid-based expression, we can increase the import of Fe and Mn in TIE-1. Future work will leverage these data to improve TIE-1 as an attractive microbial chassis and future biotechnological workhorse.
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Affiliation(s)
- Rajesh Singh
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Dinesh Gupta
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wei Bai
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Arpita Bose
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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Saint-Vincent PMB, Ridout M, Engle NL, Lawrence TJ, Yeary ML, Tschaplinski TJ, Newcombe G, Pelletier DA. Isolation, Characterization, and Pathogenicity of Two Pseudomonas syringae Pathovars from Populus trichocarpa Seeds. Microorganisms 2020; 8:microorganisms8081137. [PMID: 32731357 PMCID: PMC7465253 DOI: 10.3390/microorganisms8081137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas syringae is a ubiquitous plant pathogen, infecting both woody and herbaceous plants and resulting in devastating agricultural crop losses. Characterized by a remarkable specificity for plant hosts, P. syringae pathovars utilize a number of virulence factors including the type III secretion system and effector proteins to elicit disease in a particular host species. Here, two Pseudomonas syringae strains were isolated from diseased Populustrichocarpa seeds. The pathovars were capable of inhibiting poplar seed germination and were selective for the Populus genus. Sequencing of the newly described organisms revealed similarity to phylogroup II pathogens and genomic regions associated with woody host-associated plant pathogens, as well as genes for specific virulence factors. The host response to infection, as revealed through metabolomics, is the induction of the stress response through the accumulation of higher-order salicylates. Combined with necrosis on leaf surfaces, the plant appears to quickly respond by isolating infected tissues and mounting an anti-inflammatory defense. This study improves our understanding of the initial host response to epiphytic pathogens in Populus and provides a new model system for studying the effects of a bacterial pathogen on a woody host plant in which both organisms are fully genetically sequenced.
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Affiliation(s)
- Patricia MB Saint-Vincent
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
- Geologic and Environmental Systems Directorate, National Energy Technology Laboratory, Pittsburgh, PA 15236, USA
| | - Mary Ridout
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, ID 83844, USA; (M.R.); (G.N.)
| | - Nancy L. Engle
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
| | - Travis J. Lawrence
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
| | - Meredith L. Yeary
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
| | - Timothy J. Tschaplinski
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
| | - George Newcombe
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, ID 83844, USA; (M.R.); (G.N.)
| | - Dale A. Pelletier
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (P.M.S.-V.); (N.L.E.); (T.J.L.); (M.L.Y.); (T.J.T.)
- Correspondence:
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167
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Zuniga EG, Boateng KKA, Bui NU, Kurnfuli S, Muthana SM, Risser DD. Identification of a hormogonium polysaccharide-specific gene set conserved in filamentous cyanobacteria. Mol Microbiol 2020; 114:597-608. [PMID: 32614458 DOI: 10.1111/mmi.14566] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/23/2020] [Indexed: 01/09/2023]
Abstract
Cyanobacteria comprise a phylum defined by the capacity for oxygenic photosynthesis. Members of this phylum are frequently motile as well. Strains that display gliding or twitching motility across semisolid surfaces are powered by a conserved type IV pilus system (T4P). Among the filamentous, heterocyst-forming cyanobacteria, motility is usually confined to specialized filaments known as hormogonia, and requires the deposition of an associated hormogonium polysaccharide (HPS). The genes involved in assembly and export of HPS are largely undefined, and it has been hypothesized that HPS exits the outer membrane via an atypical T4P-driven mechanism. Here, several novel hps loci, primarily encoding glycosyl transferases, are identified. Mutational analysis demonstrates that the majority of these genes are essential for both motility and production of HPS. Notably, most mutant strains accumulate wild-type cellular levels of the major pilin PilA, but not extracellular PilA, indicating dysregulation of the T4P motors, and, therefore, a regulatory interaction between HPS assembly and T4P activity. A co-occurrence analysis of Hps orthologs among cyanobacteria identified an extended set of putative Hps proteins comprising most components of a Wzx/Wzy-type polysaccharide synthesis and export system. This implies that HPS may be secreted through a more canonical pathway, rather than a T4P-mediated mechanism.
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Affiliation(s)
| | | | - Nhi U Bui
- Department of Biology, University of the Pacific, Stockton, CA, USA
| | - Shadi Kurnfuli
- Department of Biology, University of the Pacific, Stockton, CA, USA
| | - Sawsan M Muthana
- Department of Biology, University of the Pacific, Stockton, CA, USA
| | - Douglas D Risser
- Department of Biology, University of the Pacific, Stockton, CA, USA
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168
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Rozadilla G, Clemente JM, McCarthy CB. HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets. Bio Protoc 2020; 10:e3679. [PMID: 33659350 PMCID: PMC7842381 DOI: 10.21769/bioprotoc.3679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 11/02/2022] Open
Abstract
Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy. When using taxonomy-dependent alignment-based methods to classify and label reads, the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are usually compared to various databases (nucleotide and protein) using local sequence aligners such as BLASTN and BLASTX. Nevertheless, the analysis and integration of these results can be problematic because the outputs from these searches usually show inconsistencies, which can be notorious when working with RNA-seq. Moreover, and to the best of our knowledge, existing tools do not criss-cross and integrate information from the different homology searches, but provide the results of each analysis separately. We developed the HoSeIn workflow to intersect the information from these homology searches, and then determine the taxonomic and functional profile of the sample using this integrated information. The workflow is based on the assumption that the sequences that correspond to a certain taxon are composed of: sequences that were assigned to the same taxon by both homology searches; sequences that were assigned to that taxon by one of the homology searches but returned no hits in the other one.
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Affiliation(s)
- Gaston Rozadilla
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Jorgelina Moreiras Clemente
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Christina B. McCarthy
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- Departamento de Informática y Tecnología, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Buenos Aires, Argentina
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169
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Co-Expression Networks for Causal Gene Identification Based on RNA-Seq Data of Corynebacterium pseudotuberculosis. Genes (Basel) 2020; 11:genes11070794. [PMID: 32674507 PMCID: PMC7397307 DOI: 10.3390/genes11070794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/19/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a Gram-positive bacterium that causes caseous lymphadenitis, a disease that predominantly affects sheep, goat, cattle, buffalo, and horses, but has also been recognized in other animals. This bacterium generates a severe economic impact on countries producing meat. Gene expression studies using RNA-Seq are one of the most commonly used techniques to perform transcriptional experiments. Computational analysis of such data through reverse-engineering algorithms leads to a better understanding of the genome-wide complexity of gene interactomes, enabling the identification of genes having the most significant functions inferred by the activated stress response pathways. In this study, we identified the influential or causal genes from four RNA-Seq datasets from different stress conditions (high iron, low iron, acid, osmosis, and PH) in C. pseudotuberculosis, using a consensus-based network inference algorithm called miRsigand next identified the causal genes in the network using the miRinfluence tool, which is based on the influence diffusion model. We found that over 50% of the genes identified as influential had some essential cellular functions in the genomes. In the strains analyzed, most of the causal genes had crucial roles or participated in processes associated with the response to extracellular stresses, pathogenicity, membrane components, and essential genes. This research brings new insight into the understanding of virulence and infection by C. pseudotuberculosis.
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Mnguni FC, Padayachee T, Chen W, Gront D, Yu JH, Nelson DR, Syed K. More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium. Int J Mol Sci 2020; 21:ijms21134814. [PMID: 32646068 PMCID: PMC7369989 DOI: 10.3390/ijms21134814] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/18/2022] Open
Abstract
Unraveling the role of cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins present in living and non-living entities, in secondary metabolite synthesis is gaining momentum. In this direction, in this study, we analyzed the genomes of 203 Streptomyces species for P450s and unraveled their association with secondary metabolism. Our analyses revealed the presence of 5460 P450s, grouped into 253 families and 698 subfamilies. The CYP107 family was found to be conserved and highly populated in Streptomyces and Bacillus species, indicating its key role in the synthesis of secondary metabolites. Streptomyces species had a higher number of P450s than Bacillus and cyanobacterial species. The average number of secondary metabolite biosynthetic gene clusters (BGCs) and the number of P450s located in BGCs were higher in Streptomyces species than in Bacillus, mycobacterial, and cyanobacterial species, corroborating the superior capacity of Streptomyces species for generating diverse secondary metabolites. Functional analysis via data mining confirmed that many Streptomyces P450s are involved in the biosynthesis of secondary metabolites. This study was the first of its kind to conduct a comparative analysis of P450s in such a large number (203) of Streptomyces species, revealing the P450s’ association with secondary metabolite synthesis in Streptomyces species. Future studies should include the selection of Streptomyces species with a higher number of P450s and BGCs and explore the biotechnological value of secondary metabolites they produce.
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Affiliation(s)
- Fanele Cabangile Mnguni
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA;
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: (D.R.N.); (K.S.)
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
- Correspondence: (D.R.N.); (K.S.)
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171
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Azaroff A, Goñi Urriza M, Gassie C, Monperrus M, Guyoneaud R. Marine mercury-methylating microbial communities from coastal to Capbreton Canyon sediments (North Atlantic Ocean). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114333. [PMID: 32443198 DOI: 10.1016/j.envpol.2020.114333] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Microbial mercury (Hg) methylation transforms inorganic mercury to neurotoxic methylmercury (MeHg) mainly in aquatic anoxic environments. Sampling challenges in marine ecosystems, particularly in submarine canyons, leads to a lack of knowledge about the Hg methylating microbia in marine sediments. A previous study showed an enrichment of mercury species in sediments from the Capbreton Canyon where both geochemical parameters and microbial activities constrained the net MeHg production. In order to characterize Hg-methylating microbial communities from coastal to deeper sediments, we analysed the diversity of microorganisms' (16S rDNA-based sequencing) and Hg methylators (hgcA based cloning and sequencing). Both, 16S rDNA and hgcA gene analysis demonstrated that the putative Hg-methylating prokaryotes were likely within the Deltaproteobacteria, dominated by sulfur-compounds based reducing bacteria (mainly sulfate reducers). Additionally, others clades were also identified as carrying HgcA gene, such as, Chloroflexi, Spirochaetes, Elusimicrobia, PVC superphylum (Plantomycetes, Verrucomicrobia and Chlamydiae) and Euryarchaea. Nevertheless, 61% of the hgcA sequences were not assigned to specific clade, indicating that further studies are needed to understand the implication of new microorganisms carrying hgcA in the Hg methylation in marine environments. These first results suggest that sulfur cycle drives the Hg-methylation in marine ecosystem.
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Affiliation(s)
- Alyssa Azaroff
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM-MIRA, UMR 5254, 64600 Anglet, France
| | - Marisol Goñi Urriza
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM-MIRA Environmental Microbiology, UMR 5254, 64000, Pau, France
| | - Claire Gassie
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM-MIRA Environmental Microbiology, UMR 5254, 64000, Pau, France
| | - Mathilde Monperrus
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM-MIRA, UMR 5254, 64600 Anglet, France
| | - Rémy Guyoneaud
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM-MIRA Environmental Microbiology, UMR 5254, 64000, Pau, France.
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172
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Vick SHW, Greenfield P, Willows RD, Tetu SG, Midgley DJ, Paulsen IT. Subsurface Stappia: Success Through Defence, Specialisation and Putative Pressure-Dependent Carbon Fixation. MICROBIAL ECOLOGY 2020; 80:34-46. [PMID: 31828390 DOI: 10.1007/s00248-019-01471-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Diverse microbial communities living in subsurface coal seams are responsible for important geochemical processes including the movement of carbon between the geosphere, biosphere and atmosphere. Microbial conversion of the organic matter in coal to methane involves a complex assemblage of bacteria and archaea working in syntrophic relationships. Despite the importance and value of this microbial process, very few of the microbial taxa have defined metabolic or ecological roles in these environments. Additionally, the genomic features mediating life in this chemically reduced, energy poor, deep subsurface environment are not well characterised. Here we describe the isolation and genomic and catabolic characterisation of three alphaproteobacterial Stappia indica species from three coal basins across Australia. S. indica genomes from coal seams were compared with those from closely related S. indica isolated from diverse surface waters, revealing a coal seam-specific suite of genes associated with life in the subsurface. These genes are linked to processes including viral defence, secondary metabolite production, polyamine metabolism, polypeptide uptake membrane transporters and putative energy neutral pressure-dependent CO2 fixation. This indicates that subsurface Stappia have diverse metabolisms for biomass recycling and pressure-dependent CO2 fixation and require a suite of defensive and competitive strategies relative to their surface-dwelling relatives.
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Affiliation(s)
- Silas H W Vick
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia.
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia.
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia
| | - Robert D Willows
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia
| | - Sasha G Tetu
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia
| | - David J Midgley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia
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173
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Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli. J Bacteriol 2020; 202:JB.00133-20. [PMID: 32341074 DOI: 10.1128/jb.00133-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/21/2020] [Indexed: 01/24/2023] Open
Abstract
Bacteria synthesize inorganic polyphosphate (polyP) in response to a variety of different stress conditions. polyP protects bacteria by acting as a protein-stabilizing chaperone, metal chelator, or regulator of protein function, among other mechanisms. However, little is known about how stress signals are transmitted in the cell to lead to increased polyP accumulation. Previous work in the model enterobacterium Escherichia coli has indicated that the RNA polymerase-binding regulatory protein DksA is required for polyP synthesis in response to nutrient limitation stress. In this work, I set out to characterize the role of DksA in polyP regulation in more detail. I found that overexpression of DksA increases cellular polyP content (explaining the long-mysterious phenotype of dksA overexpression rescuing growth of a dnaK mutant at high temperatures) and characterized the roles of known functional residues of DksA in this process, finding that binding to RNA polymerase is required but that none of the other functions of DksA appear to be necessary. Transcriptomics revealed genome-wide transcriptional changes upon nutrient limitation, many of which were affected by DksA, and follow-up experiments identified complex interactions between DksA and the stress-sensing alternative sigma factors FliA, RpoN, and RpoE that impact polyP production, indicating that regulation of polyP synthesis is deeply entwined in the multifactorial stress response network of E. coli IMPORTANCE Inorganic polyphosphate (polyP) is an evolutionarily ancient, widely conserved biopolymer required for stress resistance and pathogenesis in diverse bacteria, but we do not understand how its synthesis is regulated. In this work, I gained new insights into this process by characterizing the role of the transcriptional regulator DksA in polyP regulation in Escherichia coli and identifying previously unknown links between polyP synthesis and the stress-responsive alternative sigma factors FliA, RpoN, and RpoE.
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174
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Marynowska M, Goux X, Sillam-Dussès D, Rouland-Lefèvre C, Halder R, Wilmes P, Gawron P, Roisin Y, Delfosse P, Calusinska M. Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites. MICROBIOME 2020; 8:96. [PMID: 32576253 PMCID: PMC7313118 DOI: 10.1186/s40168-020-00872-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/20/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humification. Lignocellulose is often a principal component of such plant diet, and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While lower termites and their gut flagellates were given larger scientific attention in the past, the gut lignocellulolytic bacteria of higher termites remain less explored. Therefore, in this study, we investigated the structure and function of gut prokaryotic microbiomes from 11 higher termite genera representative of Syntermitinae, Apicotermitinae, Termitidae and Nasutitermitinae subfamilies, broadly grouped into plant fibre- and soil-feeding termite categories. RESULTS Despite the different compositional structures of the studied termite gut microbiomes, reflecting well the diet and host lineage, we observed a surprisingly high functional congruency between gut metatranscriptomes from both feeding groups. The abundance of transcripts encoding for carbohydrate active enzymes as well as expression and diversity profiles of assigned glycoside hydrolase families were also similar between plant fibre- and soil-feeding termites. Yet, dietary imprints highlighted subtle metabolic differences specific to each feeding category. Roughly, 0.18% of de novo re-constructed gene transcripts were shared between the different termite gut microbiomes, making each termite gut a unique reservoir of genes encoding for potentially industrially applicable enzymes, e.g. relevant to biomass degradation. Taken together, we demonstrated the functional equivalence in microbial populations across different termite hosts. CONCLUSIONS Our results provide valuable insight into the bacterial component of the termite gut system and significantly expand the inventory of termite prokaryotic genes participating in the deconstruction of plant biomass. Video Abstract.
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Affiliation(s)
- Martyna Marynowska
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
- Université Libre de Bruxelles, 50 avenue F.D. Roosevelt, B-1050, Brussels, Belgium
| | - Xavier Goux
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - David Sillam-Dussès
- Université Paris 13-Sorbonne Paris Cité, LEEC, EA 4443, Villetaneuse, France
| | - Corinne Rouland-Lefèvre
- iEES-Paris, Institute of Research for Development, Sorbonne Universités, U 242, Bondy, France
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Yves Roisin
- Université Libre de Bruxelles, 50 avenue F.D. Roosevelt, B-1050, Brussels, Belgium
| | - Philippe Delfosse
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
- University of Luxembourg, 2 avenue de l'Université, L-4365, Esch-sur-Alzette, Luxembourg
| | - Magdalena Calusinska
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg.
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175
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Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria. ISME JOURNAL 2020; 14:2347-2357. [PMID: 32514119 PMCID: PMC7608860 DOI: 10.1038/s41396-020-0696-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 01/23/2023]
Abstract
While horizontal gene transfer is prevalent across the biosphere, the regulatory features that enable expression and functionalization of foreign DNA remain poorly understood. Here, we combine high-throughput promoter activity measurements and large-scale genomic analysis of regulatory regions to investigate the cross-compatibility of regulatory elements (REs) in bacteria. Functional characterization of thousands of natural REs in three distinct bacterial species revealed distinct expression patterns according to RE and recipient phylogeny. Host capacity to activate foreign promoters was proportional to their genomic GC content, while many low GC regulatory elements were both broadly active and had more transcription start sites across hosts. The difference in expression capabilities could be explained by the influence of the host GC content on the stringency of the AT-rich canonical σ70 motif necessary for transcription initiation. We further confirm the generalizability of this model and find widespread GC content adaptation of the σ70 motif in a set of 1,545 genomes from all major bacterial phyla. Our analysis identifies a key mechanism by which the strength of the AT-rich σ70 motif relative to a host's genomic GC content governs the capacity for expression of acquired DNA. These findings shed light on regulatory adaptation in the context of evolving genomic composition.
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176
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Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago , Antarctica. Mar Drugs 2020; 18:md18060298. [PMID: 32498449 PMCID: PMC7345734 DOI: 10.3390/md18060298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 01/04/2023] Open
Abstract
Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.
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177
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Männle D, McKinnie SMK, Mantri SS, Steinke K, Lu Z, Moore BS, Ziemert N, Kaysser L. Comparative Genomics and Metabolomics in the Genus Nocardia. mSystems 2020; 5:e00125-20. [PMID: 32487740 PMCID: PMC7413640 DOI: 10.1128/msystems.00125-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/13/2020] [Indexed: 01/22/2023] Open
Abstract
Using automated genome analysis tools, it is often unclear to what degree genetic variability in homologous biosynthetic pathways relates to structural variation. This hampers strain prioritization and compound identification and can lead to overinterpretation of chemical diversity. Here, we assessed the metabolic potential of Nocardia, an underinvestigated actinobacterial genus that is known to comprise opportunistic human pathogens. Our analysis revealed a plethora of putative biosynthetic gene clusters of various classes, including polyketide, nonribosomal peptide, and terpenoid pathways. Furthermore, we used the highly conserved biosynthetic pathway for nocobactin-like siderophores to investigate how gene cluster differences correlate to structural differences in the produced compounds. Sequence similarity networks generated by BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) showed the presence of several distinct gene cluster families. Metabolic profiling of selected Nocardia strains using liquid chromatography-mass spectrometry (LC-MS) metabolomics data, nuclear magnetic resonance (NMR) spectroscopy, and GNPS (Global Natural Product Social molecular networking) revealed that nocobactin-like biosynthetic gene cluster (BGC) families above a BiG-SCAPE threshold of 70% can be assigned to distinct structural types of nocobactin-like siderophores.IMPORTANCE Our work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug discovery campaigns.
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Affiliation(s)
- Daniel Männle
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Shaun M K McKinnie
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA
| | - Shrikant S Mantri
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Katharina Steinke
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Zeyin Lu
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California, San Diego, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
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178
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Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 2020; 38:685-688. [PMID: 32483366 PMCID: PMC7365738 DOI: 10.1038/s41587-020-0548-6] [Citation(s) in RCA: 2329] [Impact Index Per Article: 582.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Vincent J Maffei
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Jesse R Zaneveld
- Division of Biological Sciences, School of STEM, University of Washington Bothell, Bothell, WA, USA
| | - Svetlana N Yurgel
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, Nova Scotia, Canada
| | - James R Brown
- Computational Biology, GlaxoSmithKline R&D, Collegeville, PA, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Curtis Huttenhower
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
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179
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Global distribution of a chlorophyll f cyanobacterial marker. ISME JOURNAL 2020; 14:2275-2287. [PMID: 32457503 PMCID: PMC7608106 DOI: 10.1038/s41396-020-0670-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/16/2020] [Accepted: 04/28/2020] [Indexed: 02/04/2023]
Abstract
Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype’s distribution.
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180
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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181
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Hammers DS, Donaghy CM, Heiss SL, Harris LM, Gordon JM, Stevens JW, Murray LP, Schwab AD, Hester BC, Culpepper MA. Identification and Characterization of a DmoB Flavin Oxidoreductase from a Putative Two-Component DMS C-Monooxygenase. ACS OMEGA 2020; 5:9830-9838. [PMID: 32391470 PMCID: PMC7203701 DOI: 10.1021/acsomega.9b04489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/05/2020] [Indexed: 06/11/2023]
Abstract
The compound dimethyl sulfide (DMS) links terrestrial and oceanic sulfur with the atmosphere because of its volatility. Atmospheric DMS is responsible for cloud formation and radiation backscattering and has been implicated in climate control mitigation. The enzyme DMS C-monooxygenase degrades DMS and has been classified as a two-component FMNH2-dependent monooxygenase. This enzyme requires a flavin reductase B subunit to supply electrons to the monooxygenase A subunit where DMS conversion occurs. One form of the enzyme from Hyphomicrobium sulfonivorans has been isolated and characterized. In this work, a putative DMS C-monooxygenase has been identified with bioinformatics in Arthrobacter globiformis. We report the expression, purification, and characterization of the DmoB flavin reductase subunit, termed DmoB, from A. globiformis. Data support DmoB preference and optimal activity for the cosubstrates flavin mononucleotide (FMN) and NADH. FMN binds at a 1:1 stoichiometry with high affinity (K d = 1.11 μM). The reductase is able to generate product with the A subunit from H. sulfonivorans expressed in Escherichia coli, albeit at a lower turnover than the natively expressed enzyme. No static protein-protein interactions were observed under the conditions tested between the two subunits. These results provide new details in the classification of enzymes involved in the sulfur cycling pathway and emerging forms of the enzyme DMS monooxygenase.
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Affiliation(s)
- D. Scott Hammers
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Caroline M. Donaghy
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Sarah L. Heiss
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Lydia M. Harris
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Jackson M. Gordon
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - John W. Stevens
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Lucian P. Murray
- Department
of Physics and Astronomy, Appalachian State
University, Boone, North Carolina 28608, United States
| | - Alexander D. Schwab
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Brooke C. Hester
- Department
of Physics and Astronomy, Appalachian State
University, Boone, North Carolina 28608, United States
| | - Megen A. Culpepper
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
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182
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Transcriptomic Study of Substrate-Specific Transport Mechanisms for Iron and Carbon in the Marine Copiotroph Alteromonas macleodii. mSystems 2020; 5:5/2/e00070-20. [PMID: 32345736 PMCID: PMC7190382 DOI: 10.1128/msystems.00070-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
As the major facilitators of the turnover of organic matter in the marine environment, the ability of heterotrophic bacteria to acquire specific compounds within the diverse range of dissolved organic matter will affect the regeneration of essential nutrients such as iron and carbon. TonB-dependent transporters are a prevalent cellular tool in Gram-negative bacteria that allow a relatively high-molecular-weight fraction of organic matter to be directly accessed. However, these transporters are not well characterized in marine bacteria, limiting our understanding of the flow of specific substrates through the marine microbial loop. Here, we characterize the TonB-dependent transporters responsible for iron and carbon acquisition in a representative marine copiotroph and examine their distribution across the genus Alteromonas. We provide evidence that substrate-specific bioavailability is niche specific, particularly for iron complexes, indicating that transport capacity may serve as a significant control on microbial community dynamics and the resultant cycling of organic matter. Iron is an essential micronutrient for all microbial growth in the marine environment, and in heterotrophic bacteria, iron is tightly linked to carbon metabolism due to its central role as a cofactor in enzymes of the respiratory chain. Here, we present the iron- and carbon-regulated transcriptomes of a representative marine copiotroph, Alteromonas macleodii ATCC 27126, and characterize its cellular transport mechanisms. ATCC 27126 has distinct metabolic responses to iron and carbon limitation and, accordingly, uses distinct sets of TonB-dependent transporters for the acquisition of iron and carbon. These distinct sets of TonB-dependent transporters were of a similar number, indicating that the diversity of carbon and iron substrates available to ATCC 27126 is of a similar scale. For the first time in a marine bacterium, we have also identified six characteristic inner membrane permeases for the transport of siderophores via an ATPase-independent mechanism. An examination of the distribution of specific TonB-dependent transporters in 31 genomes across the genus Alteromonas points to niche specialization in transport capacity, particularly for iron. We conclude that the substrate-specific bioavailability of both iron and carbon in the marine environment will likely be a key control on the processing of organic matter through the microbial loop. IMPORTANCE As the major facilitators of the turnover of organic matter in the marine environment, the ability of heterotrophic bacteria to acquire specific compounds within the diverse range of dissolved organic matter will affect the regeneration of essential nutrients such as iron and carbon. TonB-dependent transporters are a prevalent cellular tool in Gram-negative bacteria that allow a relatively high-molecular-weight fraction of organic matter to be directly accessed. However, these transporters are not well characterized in marine bacteria, limiting our understanding of the flow of specific substrates through the marine microbial loop. Here, we characterize the TonB-dependent transporters responsible for iron and carbon acquisition in a representative marine copiotroph and examine their distribution across the genus Alteromonas. We provide evidence that substrate-specific bioavailability is niche specific, particularly for iron complexes, indicating that transport capacity may serve as a significant control on microbial community dynamics and the resultant cycling of organic matter.
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183
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Jang BS, Chang JH, Chie EK, Kim K, Park JW, Kim MJ, Song EJ, Nam YD, Kang SW, Jeong SY, Kim HJ. Gut Microbiome Composition Is Associated with a Pathologic Response After Preoperative Chemoradiation in Patients with Rectal Cancer. Int J Radiat Oncol Biol Phys 2020; 107:736-746. [PMID: 32315676 DOI: 10.1016/j.ijrobp.2020.04.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE There are ongoing investigations to find promising biomarkers for predicting a complete response (CR) after concurrent chemoradiation (CCRT) in rectal cancer. We aimed to find the predictive value in the gut microbiome in terms of response after preoperative CCRT. METHODS AND MATERIALS We collected a total of 45 fecal samples from patients with rectal cancer before CCRT. Tumor response after CCRT was assessed according to the American Joint Committee on Cancer tumor regression grading system. Analysis of linear discriminant analysis effect size and MetaCyc pathway abundance predictions were performed to compare composition and metabolic function of microbiome between patients with and without CR. We also established a Bayesian network model to identify microbial networks and species to be related with CCRT response. RESULTS Seven patients (15.6%) demonstrated pathologically CR, and 38 patients (84.4%) showed non-CR after preoperative CCRT. Between CR and non-CR patients, there was a significant difference in terms of β-diversity (P = .028), but no difference in α-diversity was found. Bacteroidales (Bacteroidaceae, Rikenellaceae, Bacteroides) were relatively more abundant in patients with non-CR than those with CR. Pathways related to anabolic function predominated in CR patients. According to Bayesian network analysis, Duodenibacillus massiliensis was linked with the improved CR rate. CONCLUSIONS From the fecal microbiome using samples obtained before preoperative CCRT, differences in microbial community composition and functions were observed between patients with and without CR in rectal cancer. However, the finding that a specific taxon may be linked with the improved therapeutic response should be verified in a prospective setting.
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Affiliation(s)
- Bum-Sup Jang
- Department of Radiation Oncology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Ji Hyun Chang
- Department of Radiation Oncology, Seoul National University Hospital, Seoul, Korea
| | - Eui Kyu Chie
- Department of Radiation Oncology, Seoul National University Hospital, Seoul, Korea; Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea
| | - Kyubo Kim
- Department of Radiation Oncology, Ewha Womans University College of Medicine, Seoul, Korea
| | - Ji Won Park
- Department of Surgery, Seoul National University Hospital, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Min Jung Kim
- Department of Surgery, Seoul National University Hospital, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Eun-Ji Song
- Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, Korea; Research Group of Healthcare, Korea Food Research Institute, Wanju, Korea
| | - Young-Do Nam
- Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, Korea; Research Group of Healthcare, Korea Food Research Institute, Wanju, Korea
| | - Seung Wan Kang
- Department of Nursing, Seoul National University College of Nursing, Seoul, Korea
| | - Seung-Yong Jeong
- Department of Surgery, Seoul National University Hospital, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hak Jae Kim
- Department of Radiation Oncology, Seoul National University Hospital, Seoul, Korea; Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.
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184
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Berckx F, Wibberg D, Kalinowski J, Pawlowski K. The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type. Genes (Basel) 2020; 11:genes11040432. [PMID: 32316316 PMCID: PMC7231273 DOI: 10.3390/genes11040432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 11/16/2022] Open
Abstract
Nitrogen-fixing Actinobacteria of the genus Frankia can be subdivided into four phylogenetically distinct clades; members of clusters one to three engage in nitrogen-fixing root nodule symbioses with actinorhizal plants. Mur enzymes are responsible for the biosynthesis of the peptidoglycan layer of bacteria. The four Mur ligases,MurC, MurD, MurE, and MurF, catalyse the addition of a short polypeptide to UDP-N-acetylmuramic acid. Frankia strains of cluster-2 and cluster-3 contain two copies of murC, while the strains of cluster-1 and cluster-4 contain only one. Phylogenetically, the protein encoded by the murC gene shared only by cluster-2 and cluster-3, termed MurC1, groups with MurC proteins of other Actinobacteria. The protein encoded by the murC gene found in all Frankia strains, MurC2, shows a higher similarity to the MurC proteins of plants than of Actinobacteria. MurC2 could have been either acquired via horizontal gene transfer or via gene duplication and convergent evolution, while murC1 was subsequently lost in the cluster-1 and cluster-4 strains. In the nodules induced by the cluster-2 strains, the expression levels of murC2 were significantly higher than those of murC1. Thus, there is clear sequence divergence between both types of Frankia MurC, and Frankia murC1 is in the process of being replaced by murC2, indicating selection in favour of murC2. Nevertheless, protein modelling showed no major structural differences between the MurCs from any phylogenetic group examined.
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Affiliation(s)
- Fede Berckx
- Department of Ecology, Environment, and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden;
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
| | - Katharina Pawlowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
- Correspondence: ; Tel.: +46-8-16-3772; Fax: +46-8-16-5525
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185
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Sampedro I, Pérez-Mendoza D, Toral L, Palacios E, Arriagada C, Llamas I. Effects of Halophyte Root Exudates and Their Components on Chemotaxis, Biofilm Formation and Colonization of the Halophilic Bacterium Halomonas Anticariensis FP35 T. Microorganisms 2020; 8:E575. [PMID: 32316222 PMCID: PMC7232322 DOI: 10.3390/microorganisms8040575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/25/2022] Open
Abstract
Increase in soil salinity poses an enormous problem for agriculture and highlights the need for sustainable crop production solutions. Plant growth-promoting bacteria can be used to boost the growth of halophytes in saline soils. Salicornia is considered to be a promising salt-accumulating halophyte for capturing large amounts of carbon from the atmosphere. In addition, colonization and chemotaxis could play an important role in Salicornia-microbe interactions. In this study, the role of chemotaxis in the colonization of the halophilic siredophore-producing bacteria, Halomonas anticariensis FP35T, on Salicornia hispanica plants was investigated. The chemotactic response of FP35T to Salicornia root exudates showed optimum dependence at a salt concentration of 5 % NaCl (w/v). Oleanolic acid, the predominant compound in the exudates detected by HPLC and identified by UPLC-HRMS Q-TOF, acts as a chemoattractant. In vitro experiments demonstrated the enhanced positive effects of wild-type H. anticariensis strain FP35T on root length, shoot length, germination and the vigour index of S. hispanica. Furthermore, these positive effects partially depend on an active chemotaxis system, as the chemotaxis mutant H. anticariensis FP35 ΔcheA showed reduced plant growth promotion for all the parameters tested. Overall, our results suggest that chemotaxis responses to root exudates play an important role in interactions between Salicornia and halophilic bacteria, enhance their colonization and boost plant growth promotion. Preliminary results also indicate that root exudates have a positive impact on H. anticariensis FP35T biofilm formation under saline conditions, an effect which totally depends on the presence of the cheA gene.
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Affiliation(s)
- Inmaculada Sampedro
- Department of Microbiology, Pharmacy Faculty, Campus de Cartuja s/n, 18071 Granada, Spain; (D.P.-M.); (E.P.); (I.L.)
- Biomedical Research Center (CIBM), Biotechnology Institute, Avda del Conocimiento s/n, 18100 Armilla, Granada, Spain
| | - Daniel Pérez-Mendoza
- Department of Microbiology, Pharmacy Faculty, Campus de Cartuja s/n, 18071 Granada, Spain; (D.P.-M.); (E.P.); (I.L.)
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Laura Toral
- Xtrem Biotech S.L., European Business Innovation Center, Avenida de la Innovación, 1, 18016 Armilla, Granada, Spain;
| | - Esther Palacios
- Department of Microbiology, Pharmacy Faculty, Campus de Cartuja s/n, 18071 Granada, Spain; (D.P.-M.); (E.P.); (I.L.)
- Biomedical Research Center (CIBM), Biotechnology Institute, Avda del Conocimiento s/n, 18100 Armilla, Granada, Spain
| | - César Arriagada
- Department of Forestry Science, Bioremediation Laboratory, Faculty of Agricultural and Forestry Science, University of La Frontera, 01145 Temuco, Chile;
| | - Inmaculada Llamas
- Department of Microbiology, Pharmacy Faculty, Campus de Cartuja s/n, 18071 Granada, Spain; (D.P.-M.); (E.P.); (I.L.)
- Biomedical Research Center (CIBM), Biotechnology Institute, Avda del Conocimiento s/n, 18100 Armilla, Granada, Spain
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186
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Dovrolis N, Kolios G, Spyrou GM, Maroulakou I. Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders. Brief Bioinform 2020; 20:825-841. [PMID: 29186317 DOI: 10.1093/bib/bbx154] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/17/2017] [Indexed: 12/14/2022] Open
Abstract
Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. The definitive mechanisms of this last bidirectional interaction will be our main focus because it presents researchers with a new conundrum. In this review, we prospect current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications. We will present bioinformatics tools used in exploring these synergies that help build and interpret microbial 16S ribosomal RNA data sets, produced by shotgun and high-throughput sequencing of healthy and neurological disorder samples stored in biological databases. These approaches provide alternative means for researchers to form hypotheses to their inquests faster, cheaper and swith precision. The goal of these studies relies on the integration of combined metagenomics and metabolomics assessments. An accurate characterization of the microbiome and its functionality can support new diagnostic, prognostic and therapeutic strategies for neurological disorders, customized for each individual host.
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187
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Structural basis and designing of peptide vaccine using PE-PGRS family protein of Mycobacterium ulcerans—An integrated vaccinomics approach. Mol Immunol 2020; 120:146-163. [DOI: 10.1016/j.molimm.2020.02.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/16/2020] [Accepted: 02/12/2020] [Indexed: 12/29/2022]
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188
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Abstract
Here, we present a search-based strategy for disease detection and classification, which detects diseased samples via their outlier novelty versus a database of samples from healthy subjects and then compares them to databases of samples from patients. This approach enables the identification of microbiome states associated with disease even in the presence of different cohorts, multiple sequencing platforms, or significant contamination. Microbiome-based disease classification depends on well-validated disease-specific models or a priori organismal markers. These are lacking for many diseases. Here, we present an alternative, search-based strategy for disease detection and classification, which detects diseased samples via their outlier novelty versus a database of samples from healthy subjects and then compares these to databases of samples from patients. Our strategy’s precision, sensitivity, and speed outperform model-based approaches. In addition, it is more robust to platform heterogeneity and to contamination in 16S rRNA gene amplicon data sets. This search-based strategy shows promise as an important first step in microbiome big-data-based diagnosis. IMPORTANCE Here, we present a search-based strategy for disease detection and classification, which detects diseased samples via their outlier novelty versus a database of samples from healthy subjects and then compares them to databases of samples from patients. This approach enables the identification of microbiome states associated with disease even in the presence of different cohorts, multiple sequencing platforms, or significant contamination.
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189
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Kang SM, Asaf S, Khan AL, Lubna, Khan A, Mun BG, Khan MA, Gul H, Lee IJ. Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions. Microorganisms 2020; 8:E382. [PMID: 32182882 PMCID: PMC7142416 DOI: 10.3390/microorganisms8030382] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 12/02/2022] Open
Abstract
In the current study, we aimed to elucidate the plant growth-promoting characteristics of Pseudomonas psychrotolerans CS51 under heavy metal stress conditions (Zn, Cu, and Cd) and determine the genetic makeup of the CS51 genome using the single-molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that inoculation with CS51 induced endogenous indole-3-acetic acid (IAA) and gibberellins (GAs), which significantly enhanced cucumber growth (root shoot length) and increased the heavy metal tolerance of cucumber plants. Moreover, genomic analysis revealed that the CS51 genome consisted of a circular chromosome of 5,364,174 base pairs with an average G+C content of 64.71%. There were around 4774 predicted protein-coding sequences (CDSs) in 4859 genes, 15 rRNA genes, and 67 tRNA genes. Around 3950 protein-coding genes with function prediction and 733 genes without function prediction were identified. Furthermore, functional analyses predicted that the CS51 genome could encode genes required for auxin biosynthesis, nitrate and nitrite ammonification, the phosphate-specific transport system, and the sulfate transport system, which are beneficial for plant growth promotion. The heavy metal resistance of CS51 was confirmed by the presence of genes responsible for cobalt-zinc-cadmium resistance, nickel transport, and copper homeostasis in the CS51 genome. The extrapolation of the curve showed that the core genome contained a minimum of 2122 genes (95% confidence interval = 2034.24 to 2080.215). Our findings indicated that the genome sequence of CS51 may be used as an eco-friendly bioresource to promote plant growth in heavy metal-contaminated areas.
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Affiliation(s)
- Sang-Mo Kang
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.-M.K.); (B.-G.M.); (M.A.K.)
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (S.A.); (A.L.K.); (A.K.)
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (S.A.); (A.L.K.); (A.K.)
| | - Lubna
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; (L.); (H.G.)
| | - Adil Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (S.A.); (A.L.K.); (A.K.)
| | - Bong-Gyu Mun
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.-M.K.); (B.-G.M.); (M.A.K.)
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.-M.K.); (B.-G.M.); (M.A.K.)
| | - Humaira Gul
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; (L.); (H.G.)
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.-M.K.); (B.-G.M.); (M.A.K.)
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190
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Zhang M, Chen H, Liu L, Xu L, Wang X, Chang L, Chang Q, Lu G, Jiang J, Zhu L. The Changes in the Frog Gut Microbiome and Its Putative Oxygen-Related Phenotypes Accompanying the Development of Gastrointestinal Complexity and Dietary Shift. Front Microbiol 2020; 11:162. [PMID: 32194513 PMCID: PMC7062639 DOI: 10.3389/fmicb.2020.00162] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 01/22/2020] [Indexed: 12/05/2022] Open
Abstract
There are many examples of symbiotic and reciprocal relationships in ecological systems; animal gut microbiome-host interactions are one such kind of bidirectional and complex relationship. Here, we utilized several approaches (16S rRNA gene sequencing, metagenomics, and transcriptomics) to explore potential gut microbiome-host interactions accompanying the development of gastrointestinal complexity and a dietary shift from metamorphosis to maturity in ornamented pygmy frogs (Microhyla fissipes). We identified the possible coevolution between a particular gut microbial group (increased putative fat-digesting Erysipelotrichaceae and chitin-digesting Bacteroides and Ruminococcaceae) and the host dietary shift [from herbivore to insectivore (high proportion of dietary chitin and fat)] during metamorphosis. We also found that the remodeling and complexity of the gastrointestinal system during metamorphosis might have a profound effect on the gut microbial community (decreasing facultative anaerobic Proteobacteria and increasing anaerobic Firmicutes) and its putative oxygen-related phenotypes. Moreover, a high proportion of chitin-digesting bacteria and increased carbohydrate metabolism by gut microbiomes at the climax of metamorphosis would help the frog's nutrition and energy needs during metamorphosis and development. Considering the increased expression of particular host genes (e.g., chitinase) in juvenile frogs, we speculate that host plays an important role in amphibian metamorphosis, and their symbiotic gut microbiome may help in this process by providing the nutrition and energy needs. We provide this basic information for the amphibian conservation and managements.
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Affiliation(s)
- Mengjie Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hua Chen
- Hangzhou Legenomics Bio-Pham Technology Co., Ltd., Hangzhou, China
| | - Lusha Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Liangliang Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xungang Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Liming Chang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qing Chang
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guoqing Lu
- Department of Biology, University of Nebraska Omaha, Omaha, NE, United States
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lifeng Zhu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
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191
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Maggiori C, Stromberg J, Blanco Y, Goordial J, Cloutis E, García-Villadangos M, Parro V, Whyte L. The Limits, Capabilities, and Potential for Life Detection with MinION Sequencing in a Paleochannel Mars Analog. ASTROBIOLOGY 2020; 20:375-393. [PMID: 31976742 DOI: 10.1089/ast.2018.1964] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
No instrument capable of direct life detection has been included on a mission payload to Mars since NASA's Viking missions in the 1970s. This prevents us from discovering whether life is or ever was present on Mars. DNA is an ideal target biosignature since it is unambiguous, nonspecific, and readily detectable with nanopore sequencing. Here, we present a proof-of-concept utilization of the Oxford Nanopore Technologies (ONT) MinION sequencer for direct life detection and show how it can complement results from established space mission instruments. We used nanopore sequencing data from the MinION to detect and characterize the microbial life in a set of paleochannels near Hanksville, UT, with supporting data from X-ray diffraction, reflectance spectroscopy, Raman spectroscopy, and Life Detector Chip (LDChip) microarray immunoassay analyses. These paleochannels are analogs to martian sinuous ridges. The MinION-generated metagenomes reveal a rich microbial community dominated by bacteria and containing radioresistant, psychrophilic, and halophilic taxa. With spectral data and LDChip immunoassays, these metagenomes were linked to the surrounding Mars analog environment and potential metabolisms (e.g., methane production and perchlorate reduction). This shows a high degree of synergy between these techniques for detecting and characterizing biosignatures. We also resolved a prospective lower limit of ∼0.001 ng of DNA required for successful sequencing. This work represents the first determination of the MinION's DNA detection limits beyond ONT recommendations and the first whole metagenome analysis of a sinuous ridge analog.
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Affiliation(s)
- Catherine Maggiori
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
| | | | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Jacqueline Goordial
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine
| | - Edward Cloutis
- Department of Geography, Faculty of Science, University of Winnipeg, Winnipeg, Canada
| | | | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Lyle Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
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Planococcus lenghuensis sp. nov., an oil-degrading bacterium isolated from petroleum-contaminated soil. Antonie van Leeuwenhoek 2020; 113:839-850. [PMID: 32114684 DOI: 10.1007/s10482-020-01394-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
Abstract
A Gram-staining-positive and aerobic coccus with the ability to degrade petroleum bacterium, designated Y42T, was isolated from the Lenghu oil field located in the northern margin of the Qaidam Basin. Phylogenetic and signature nucleotides analyses revealed that strain Y42T belongs to the genus Planococcus. The multiple sequence alignments of 16S rRNA and housekeeping genes showed that strain Y42T formed a distinct lineage with the other Planococcus clade. The average nucleotide identity (ANI) and DNA-DNA hybridization values (DDH) between strain Y42T and the reference strains were 69.5-70.1 and 19.4-21.7%, respectively, which values were below the threshold for species delineation. The major fatty acids of strain Y42T were anteiso-C15:0. The respiratory quinone was MK-7 (71.8%) as the predominant menaquinone followed the MK-6 (28.2%) and the cell-wall hydrolysates contained LL-diaminopimelic acid. The polar lipid was composed of diphosphatidyl glycerol, phosphatidyl glycerol, phosphoglycolipid, aminophospholipid and four unidentified lipids. The peptidoglycan type was A4α (L-Lys-D-Glu). The strain Y42T possessed larger genome (approximately 4 MB) and revealed obvious differences for the abundance of the COG categories compared with the other Planococcus bacteria. Also, the strain Y42T also possessed more unique orthologous proteins. The structural characteristics of the strain Y42T genome provided a competitive advantage for better survival in petroleum-polluted environments. Combined with the 16S rRNA gene and genome sequence, phenotypic as well as chemotaxonomic characterisations, strain Y42T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus lenghuensis sp. nov. be proposed. The type strain is Y42T (= CGMCC 1.15921T = JCM 32719T).
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Patel V, Chevignon G, Manzano-Marín A, Brandt JW, Strand MR, Russell JA, Oliver KM. Cultivation-Assisted Genome of Candidatus Fukatsuia symbiotica; the Enigmatic "X-Type" Symbiont of Aphids. Genome Biol Evol 2020; 11:3510-3522. [PMID: 31725149 PMCID: PMC7145644 DOI: 10.1093/gbe/evz252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2019] [Indexed: 12/19/2022] Open
Abstract
Heritable symbionts are common in terrestrial arthropods and often provide beneficial services to hosts. Unlike obligate, nutritional symbionts that largely persist under strict host control within specialized host cells, heritable facultative symbionts exhibit large variation in within-host lifestyles and services rendered with many retaining the capacity to transition among roles. One enigmatic symbiont, Candidatus Fukatsuia symbiotica, frequently infects aphids with reported roles ranging from pathogen, defensive symbiont, mutualism exploiter, and nutritional co-obligate symbiont. Here, we used an in vitro culture-assisted protocol to sequence the genome of a facultative strain of Fukatsuia from pea aphids (Acyrthosiphon pisum). Phylogenetic and genomic comparisons indicate that Fukatsuia is an aerobic heterotroph, which together with Regiella insecticola and Hamiltonella defensa form a clade of heritable facultative symbionts within the Yersiniaceae (Enterobacteriales). These three heritable facultative symbionts largely share overlapping inventories of genes associated with housekeeping functions, metabolism, and nutrient acquisition, while varying in complements of mobile DNA. One unusual feature of Fukatsuia is its strong tendency to occur as a coinfection with H. defensa. However, the overall similarity of gene inventories among aphid heritable facultative symbionts suggests that metabolic complementarity is not the basis for coinfection, unless playing out on a H. defensa strain-specific basis. We also compared the pea aphid Fukatsuia with a strain from the aphid Cinara confinis (Lachninae) where it is reported to have transitioned to co-obligate status to support decaying Buchnera function. Overall, the two genomes are very similar with no clear genomic signatures consistent with such a transition, which suggests co-obligate status in C. confinis was a recent event.
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Affiliation(s)
- Vilas Patel
- Department of Entomology, University of Georgia
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Abstract
SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes. The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear. IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.
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195
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Guo B, Zhang Y, Zhang L, Zhou Y, Liu Y. RNA-based spatial community analysis revealed intra-reactor variation and expanded collection of direct interspecies electron transfer microorganisms in anaerobic digestion. BIORESOURCE TECHNOLOGY 2020; 298:122534. [PMID: 31835200 DOI: 10.1016/j.biortech.2019.122534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Granular activated carbon (GAC) has been shown to mediate direct interspecies electron transfer (DIET) in anaerobic digestion. Adding GAC to up-flow anaerobic sludge bed reactor increased the total biomass slightly from 20.0 to 26.6 gVSS/reactor, and maximum organic removal capacity remarkably from 285 to 1660 mgCOD/L/d. Since GAC occupied 7% of reactor volume (denser than suspended sludge, settled to the reactor bottom), we used a spatial sampling strategy (sludge bed top/mid/bottom layers, and tightly attached GAC-biofilm) and DNA- and RNA-based community analyses. RNA-based analysis demonstrated significant community differences between the non-GAC and GAC-amended reactors (p < 0.05) based on ANOSIM statistical analysis. In comparison, DNA-based analysis showed little community difference between these reactors (p > 0.05). RNA-based analysis revealed active enrichments in GAC-biofilm, including bacteria Geobacter, Syntrophus, Desulfovibrio and Blvii28, and archaea Methanosaeta and Methanospirillum. These are potential electro-active syntrophic microorganisms related with DIET, which expand the previously defined list of DIET microorganisms.
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Affiliation(s)
- Bing Guo
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada
| | - Yingdi Zhang
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada
| | - Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada
| | - Yun Zhou
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, T6G 1H9 Edmonton, Canada.
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Valk LC, Diender M, Stouten GR, Petersen JF, Nielsen PH, Dueholm MS, Pronk JT, van Loosdrecht MCM. " Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex. Front Microbiol 2020; 11:63. [PMID: 32063897 PMCID: PMC7000372 DOI: 10.3389/fmicb.2020.00063] [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: 09/26/2019] [Accepted: 01/13/2020] [Indexed: 11/24/2022] Open
Abstract
Acetogens have the ability to fixate carbon during fermentation by employing the Wood-Ljungdahl pathway (WLP), which is highly conserved across Bacteria and Archaea. In a previous study, product stoichometries in galacturonate-limited, anaerobic enrichment cultures of “Candidatus Galacturonibacter soehngenii,” from a novel genus within the Lachnospiraceae, suggested the simultaneous operation of a modified Entner-Doudoroff pathway for galacturonate fermentation and a WLP for acetogenesis. However, a draft metagenome-assembled genome (MAG) based on short reads did not reveal homologs of genes encoding a canonical WLP carbon-monoxide-dehydrogenase/acetyl-Coenzyme A synthase (CODH/ACS) complex. In this study, NaH13CO3 fed to chemostat-grown, galacturonate-limited enrichment cultures of “Ca. G. soehngenii” was shown to be incorporated into acetate. Preferential labeling of the carboxyl group of acetate was consistent with acetogenesis via a WLP in which the methyl group of acetate was predominately derived from formate. This interpretation was further supported by high transcript levels of a putative pyruvate-formate lyase gene and very low transcript levels of a candidate gene for formate dehydrogenase. Reassembly of the “Ca. G. soehngenii” MAG with support from long-read nanopore sequencing data produced a single-scaffold MAG, which confirmed the absence of canonical CODH/ACS-complex genes homologs. However, high CO-dehydrogenase activities were measured in cell extracts of “Ca. G. soehngenii” enrichment cultures, contradicting the absence of corresponding homologs in the MAG. Based on the highly conserved amino-acid motif associated with anaerobic Ni-CO dehydrogenase proteins, a novel candidate was identified which could be responsible for the observed activities. These results demonstrate operation of an acetogenic pathway, most probably as a yet unresolved variant of the Wood-Ljungdahl pathway, in anaerobic, galacturonate-limited cultures of “Ca. G. soehngenii.”
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Affiliation(s)
- Laura C Valk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Gerben R Stouten
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jette F Petersen
- Department of Chemistry and Bioscience, Centre for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Department of Chemistry and Bioscience, Centre for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Morten S Dueholm
- Department of Chemistry and Bioscience, Centre for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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Sanderson H, Ortega-Polo R, Zaheer R, Goji N, Amoako KK, Brown RS, Majury A, Liss SN, McAllister TA. Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants. BMC Microbiol 2020; 20:20. [PMID: 31980014 PMCID: PMC6982392 DOI: 10.1186/s12866-019-1683-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/12/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Enterococcus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. RESULTS VRE isolates, including E. faecalis (n = 24), E. faecium (n = 11), E. casseliflavus (n = 2) and E. gallinarum (n = 2) were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium (p < 0.001) and E. faecalis (p < 0.001) and with the number of AMR genes in E. faecium (p = 0.005). Genes conferring vancomycin resistance, including vanA and vanM (E. faecium), vanG (E. faecalis), and vanC (E. casseliflavus/E. gallinarum), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium, E. faecalis, E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium, than E. casseliflavus and E. gallinarum. A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium. Phylogenetic analysis demonstrated differential clustering of isolates based on original source but not WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. CONCLUSIONS There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp.
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Affiliation(s)
- Haley Sanderson
- Agriculture and AgriFood Canada, Lethbridge Research and Development Center, 5403 1 Avenue South, PO Box 3000, Lethbridge, T1J 4B1 Canada
- School of Environmental Studies, Queen’s University, Kingston, K7L 3N6 Canada
| | - Rodrigo Ortega-Polo
- Agriculture and AgriFood Canada, Lethbridge Research and Development Center, 5403 1 Avenue South, PO Box 3000, Lethbridge, T1J 4B1 Canada
| | - Rahat Zaheer
- Agriculture and AgriFood Canada, Lethbridge Research and Development Center, 5403 1 Avenue South, PO Box 3000, Lethbridge, T1J 4B1 Canada
| | - Noriko Goji
- Canadian Food Inspection Agency, National Centre for Animal Disease, Lethbridge Laboratory, Lethbridge, T1J 3Z4 Canada
| | - Kingsley K. Amoako
- Canadian Food Inspection Agency, National Centre for Animal Disease, Lethbridge Laboratory, Lethbridge, T1J 3Z4 Canada
| | - R. Stephen Brown
- School of Environmental Studies, Queen’s University, Kingston, K7L 3N6 Canada
- Department of Chemistry, Queen’s University, Kingston, K7L 3N6 Canada
| | - Anna Majury
- School of Environmental Studies, Queen’s University, Kingston, K7L 3N6 Canada
- Public Health Ontario, Kingston, K7L 3K3 Canada
| | - Steven N. Liss
- School of Environmental Studies, Queen’s University, Kingston, K7L 3N6 Canada
- Department of Biology, Ryerson University, Toronto, M5B 2K3 Canada
| | - Tim A. McAllister
- Agriculture and AgriFood Canada, Lethbridge Research and Development Center, 5403 1 Avenue South, PO Box 3000, Lethbridge, T1J 4B1 Canada
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Comparative Genomics Guides Elucidation of Vitamin B 12 Biosynthesis in Novel Human-Associated Akkermansia Strains. Appl Environ Microbiol 2020; 86:AEM.02117-19. [PMID: 31757822 PMCID: PMC6974653 DOI: 10.1128/aem.02117-19] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila. However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B12. The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health. Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a “next-generation probiotic.” However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B12) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B12 production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome. IMPORTANCE There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila. However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B12. The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.
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199
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Wang Q, Zhao L, Han L, Fu G, Tuo X, Ma S, Li Q, Wang Y, Liang D, Tang M, Sun C, Wang Q, Song Q, Li Q. The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ. J Ovarian Res 2020; 13:8. [PMID: 31954395 PMCID: PMC6969417 DOI: 10.1186/s13048-019-0603-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 12/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background With the improvement of bacterial detection, the theory of the sterile female upper reproductive tract has been frequently challenged in recent years. However, thus far, no researchers have used ovaries as study targets. Methods Six women who were diagnosed with ovarian cancer were included in the cancer group, and ten women who were diagnosed with a noncancerous ovarian condition (including three patients with uterine myoma and seven patients with uterine adenomyosis) were included in the control group. Immunohistochemistry staining using an antibacterial lipopolysaccharide (LPS) antibody was used to confirm the presence of bacteria in the ovarian tissues. In addition, 16S rRNA sequencing was used to compare the differences in the bacteria between ovarian cancer tissues and noncancerous ovarian tissues. BugBase and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to predict the functional composition of the bacteria. Results Bacterial LPS was present in ovarian cancer tissue and noncancerous ovarian tissue, which implied the presence of bacteria in ovarian tissue. When compared to the noncancerous ovarian bacteria at the phylum level, the cancerous ovarian bacteria were composed of increased Aquificae and Planctomycetes and decreased Crenarchaeota. When predicting metagenomes, gene functions associated with the potentially pathogenic and the oxidative stress-tolerant phenotype were enriched in the ovaries of the cancer group. Forty-six significantly different KEGG pathways existed in the ovarian bacteria of the cancer group compared to that of the control group. Conclusions Different bacteria compositions were present in cancerous and noncancerous ovarian tissues. Trial registration Chines Clinical Trail Registry, CHiCTR1800020018, Registered 11 September 2018, http://www.chictr.org.cn/
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Affiliation(s)
- Qi Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Gynecological Oncology, Shaanxi Provincial Cancer Hospital, Xi'an, Shaanxi, China
| | - Lanbo Zhao
- Guipei 77, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lu Han
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Guoxing Fu
- Omega Bioservices Inc, Norcross, GA, USA
| | - Xiaoqian Tuo
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Sijia Ma
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qing Li
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yiran Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Dongxin Liang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Miaomiao Tang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chao Sun
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qing Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qing Song
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, USA.
| | - Qiling Li
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus. PLoS One 2020; 15:e0223033. [PMID: 31935215 PMCID: PMC6959600 DOI: 10.1371/journal.pone.0223033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/17/2019] [Indexed: 01/18/2023] Open
Abstract
Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence.
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