151
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Zhang R, Debeljak P, Blain S, Obernosterer I. Seasonal shifts in Fe-acquisition strategies in Southern Ocean microbial communities revealed by metagenomics and autonomous sampling. Environ Microbiol 2023; 25:1816-1829. [PMID: 37157891 DOI: 10.1111/1462-2920.16397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Iron (Fe) governs the cycling of organic carbon in large parts of the Southern Ocean. The strategies of diverse microbes to acquire the different chemical forms of Fe under seasonally changing organic carbon regimes remain, however, poorly understood. Here, we report high-resolution seasonal metagenomic observations from the region off Kerguelen Island (Indian Sector of the Southern Ocean) where natural Fe-fertilization induces consecutive spring and summer phytoplankton blooms. Our data illustrate pronounced, but distinct seasonal patterns in the abundance of genes implicated in the transport of different forms of Fe and organic substrates, of siderophore biosynthesis and carbohydrate-active enzymes. The seasonal dynamics suggest a temporal decoupling in the prokaryotic requirements of Fe and organic carbon during the spring phytoplankton bloom and a concerted access to these resources after the summer bloom. Taxonomic assignments revealed differences in the prokaryotic groups harbouring genes of a given Fe-related category and pronounced seasonal successions were observed. Using MAGs we could decipher the respective Fe- and organic substrate-related genes of individual taxa assigned to abundant groups. The ecological strategies related to Fe-acquisition provide insights on how this element could shape microbial community composition with potential implications on organic matter transformations in the Southern Ocean.
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Affiliation(s)
- Rui Zhang
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
| | - Pavla Debeljak
- Sorbonne Université, Muséum National d'Histoire, Naturelle, CNRS, EPHE, Université des Antilles, Institut de Systématique, Evolution, Biodiversité (ISYEB), Paris, France
- SupBiotech, Villejuif, France
| | - Stephane Blain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
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152
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Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B. Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes. THE ISME JOURNAL 2023; 17:1660-1670. [PMID: 37452097 PMCID: PMC10504331 DOI: 10.1038/s41396-023-01466-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.
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Affiliation(s)
| | | | - Ashley G Bell
- School of Biosciences, University of Exeter, Exeter, UK
| | | | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
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153
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Trinh P, Clausen DS, Willis AD. happi: a hierarchical approach to pangenomics inference. Genome Biol 2023; 24:214. [PMID: 37773075 PMCID: PMC10540326 DOI: 10.1186/s13059-023-03040-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms. However, metagenome-assembled genomes vary in quality and may contain omissions and contamination. These errors present challenges for detecting genes and comparing gene enrichment across sample types. To address this, we propose happi, an approach to testing hypotheses about gene enrichment that accounts for genome quality. We illustrate the advantages of happi over existing approaches using published Saccharibacteria MAGs, Streptococcus thermophilus MAGs, and via simulation.
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Affiliation(s)
- Pauline Trinh
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - David S Clausen
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
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154
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Zehnle H, Otersen C, Benito Merino D, Wegener G. Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin. Front Microbiol 2023; 14:1279865. [PMID: 37840718 PMCID: PMC10570749 DOI: 10.3389/fmicb.2023.1279865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.
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Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Carolin Otersen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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155
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Dhulappa A, Rao MPN, Wang H, Rekadwad BN, Kang YQ. Proposal to transfer Bacillus massiliigorillae to the genus Peribacillus as Peribacillus massiliigorillae comb. nov., and Bacillus sinesaloumensis to the genus Ferdinandcohnia as Ferdinandcohnia sinesaloumensis comb. nov. Arch Microbiol 2023; 205:343. [PMID: 37755612 DOI: 10.1007/s00203-023-03675-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/19/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
The present study was carried out to clarify the taxonomic position of Bacillus massiliigorillae and Bacillus sinesaloumensis. The 16S rRNA gene sequences extracted from the Bacillus sinesaloumensis Marseille-P3516T (FTOX00000000) and Bacillus massiliigorillae G2T (CAVL000000000) genomes showed 98.5 and 99.1% similarity with the type strains of Ferdinandcohnia humi and Peribacillus endoradicis, respectively. The amino acid identity (AAI) values of Bacillus sinesaloumensis Marseille-P3516T were higher with Ferdinandcohnia members, while Bacillus massiliigorillae G2T with Peribacillus members. In phylogenomic and phylogenetic trees, Bacillus sinesaloumensis Marseille-P3516T and Bacillus massiliigorillae G2T clade with members of the genera Ferdinandcohnia and Peribacillus, respectively. Based on the above results, we propose to transfer Bacillus massiliigorillae to the genus Peribacillus as Peribacillus massiliigorillae comb. nov., and Bacillus sinesaloumensis to the genus Ferdinandcohnia as Ferdinandcohnia sinesaloumensis comb. nov.
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Affiliation(s)
- Awalagaway Dhulappa
- Department of Microbiology, Maharani's Science College for Women, Bangalore, 560001, India
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, 3460000, Talca, Chile
| | - Haijie Wang
- Department of Clinical Laboratory, Affiliated Jinyang Hospital of Guizhou Medical University, Guiyang, Guizhou, 550081, China
| | - Bhagwan Narayan Rekadwad
- Department of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, Karnataka, India
| | - Ying-Qian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Talent Base of Microbiology and Human Health of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, GuiyangGuizhou, 550025, China.
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156
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Wegner CE, Stahl R, Velsko I, Hübner A, Fagernäs Z, Warinner C, Lehmann R, Ritschel T, Totsche KU, Küsel K. A glimpse of the paleome in endolithic microbial communities. MICROBIOME 2023; 11:210. [PMID: 37749660 PMCID: PMC10518947 DOI: 10.1186/s40168-023-01647-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/09/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards. RESULTS By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past. CONCLUSIONS Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.
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Affiliation(s)
- Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Irina Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Alex Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Thomas Ritschel
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
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157
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Bodle KB, Mueller RC, Pernat MR, Kirkland CM. Treatment performance and microbial community structure in an aerobic granular sludge sequencing batch reactor amended with diclofenac, erythromycin, and gemfibrozil. FRONTIERS IN MICROBIOMES 2023; 2:1242895. [PMID: 38076031 PMCID: PMC10705044 DOI: 10.3389/frmbi.2023.1242895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
This study characterizes the effects of three commonly detected pharmaceuticals-diclofenac, erythromycin, and gemfibrozil-on aerobic granular sludge. Approximately 150 μg/L of each pharmaceutical was fed in the influent to a sequencing batch reactor for 80 days, and the performance of the test reactor was compared with that of a control reactor. Wastewater treatment efficacy in the test reactor dropped by approximately 30-40%, and ammonia oxidation was particularly inhibited. The relative abundance of active Rhodocyclaceae, Nitrosomonadaceae, and Nitrospiraceae families declined throughout exposure, likely explaining reductions in wastewater treatment performance. Pharmaceuticals were temporarily removed in the first 12 days of the test via both sorption and degradation; both removal processes declined sharply thereafter. This study demonstrates that aerobic granular sludge may successfully remove pharmaceuticals in the short term, but long-term tests are necessary to confirm if pharmaceutical removal is sustainable.
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Affiliation(s)
- Kylie B. Bodle
- Department of Civil Engineering, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Rebecca C. Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- United States Department of Agriculture (USDA) Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Madeline R. Pernat
- Department of Civil Engineering, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Catherine M. Kirkland
- Department of Civil Engineering, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
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158
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Seong HJ, Kim JJ, Sul WJ. ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool. Brief Bioinform 2023; 24:bbad381. [PMID: 37889119 DOI: 10.1093/bib/bbad381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/16/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional Clustering Refiner (ACR) to enhance high-purity prokaryotic and eukaryotic metagenome-assembled genome (MAGs) recovery. ACR refines low-quality MAGs by subjecting them to iterative k-means clustering predicated on contig abundance and increasing bin purity through validated universal marker genes. Synthetic and real-world metagenomic datasets, including short- and long-read sequences, evaluated ACR's effectiveness. The results demonstrated improved MAG purity and a significant increase in high- and medium-quality MAG recovery rates. In addition, ACR seamlessly integrates with various binning algorithms, augmenting their strengths without modifying core features. Furthermore, its multiple sequencing technology compatibilities expand its applicability. By efficiently recovering high-quality prokaryotic and eukaryotic genomes, ACR is a promising tool for deepening our understanding of microbial communities through genome-centric metagenomics.
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Affiliation(s)
- Hoon Je Seong
- Korean Medicine Data Division, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
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159
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Yao T, Deemer DG, Chen MH, Reuhs BL, Hamaker BR, Lindemann SR. Differences in fine arabinoxylan structures govern microbial selection and competition among human gut microbiota. Carbohydr Polym 2023; 316:121039. [PMID: 37321733 DOI: 10.1016/j.carbpol.2023.121039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/27/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023]
Abstract
Dietary fibers are known to modulate microbiome composition, but it is unclear to what extent minor fiber structural differences impact community assembly, microbial division of labor, and organismal metabolic responses. To test the hypothesis that fine linkage variations afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fecal fermentation with four fecal inocula and measured responses using an integrated multi-omics approach. Two sorghum arabinoxylans (SAXs) were fermented, with one (RSAX) having slightly more complex branch linkages than the other (WSAX). Although there were minor glycoysl linkage differences, consortia on RSAX retained much higher species diversity (42 members) than on WSAX (18-23 members) with distinct species-level genomes and metabolic outcomes (e.g., higher short chain fatty acid production from RSAX and more lactic acid produced from WSAX). The major SAX-selected members were from genera of Bacteroides and Bifidobacterium and family Lachnospiraceae. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials among key members; however, CAZyme genes enriched in different consortia displayed various catabolic domain fusions with diverse accessory motifs that differ among the two SAX types. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia.
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Affiliation(s)
- Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Dane G Deemer
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Ming-Hsu Chen
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA; Institute of Food Science and Technology of National Taiwan University. No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Bradley L Reuhs
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
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160
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Ershov AP, Babich TL, Grouzdev DS, Sokolova DS, Semenova EM, Avtukh AN, Poltaraus AB, Ianutsevich EA, Nazina TN. Genome Analysis and Potential Ecological Functions of Members of the Genus Ensifer from Subsurface Environments and Description of Ensifer oleiphilus sp. nov. Microorganisms 2023; 11:2314. [PMID: 37764159 PMCID: PMC10538136 DOI: 10.3390/microorganisms11092314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
The current work deals with genomic analysis, possible ecological functions, and biotechnological potential of two bacterial strains, HO-A22T and SHC 2-14, isolated from unique subsurface environments, the Cheremukhovskoe oil field (Tatarstan, Russia) and nitrate- and radionuclide-contaminated groundwater (Tomsk region, Russia), respectively. New isolates were characterized using polyphasic taxonomy approaches and genomic analysis. The genomes of the strains HO-A22T and SHC 2-14 contain the genes involved in nitrate reduction, hydrocarbon degradation, extracellular polysaccharide synthesis, and heavy metal detoxification, confirming the potential for their application in various environmental biotechnologies. Genomic data were confirmed by cultivation studies. Both strains were found to be neutrophilic, chemoorganotrophic, facultatively anaerobic bacteria, growing at 15-33 °C and 0-1.6% NaCl (w/v). The 16S rRNA gene sequences of the strains were similar to those of the type strains of the genus Ensifer (99.0-100.0%). Nevertheless, genomic characteristics of strain HO-A22T were below the thresholds for species delineation: the calculated average nucleotide identity (ANI) values were 83.7-92.4% (<95%), and digital DNA-DNA hybridization (dDDH) values were within the range of 25.4-45.9% (<70%), which supported our conclusion that HO-A22T (=VKM B-3646T = KCTC 92427T) represented a novel species of the genus Ensifer, with the proposed name Ensifer oleiphilus sp. nov. Strain SHC 2-14 was assigned to the species 'Ensifer canadensis', which has not been validly published. This study expanded the knowledge about the phenotypic diversity among members of the genus Ensifer and its potential for the biotechnologies of oil recovery and radionuclide pollution treatment.
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Affiliation(s)
- Alexey P. Ershov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Tamara L. Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | | | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Ekaterina M. Semenova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Alexander N. Avtukh
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Elena A. Ianutsevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
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161
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Magnuson E, Altshuler I, Freyria NJ, Leveille RJ, Whyte LG. Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring. MICROBIOME 2023; 11:203. [PMID: 37697305 PMCID: PMC10494364 DOI: 10.1186/s40168-023-01628-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/19/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7-8% salinity), anoxic (~ 0.04 ppm O2), and highly reducing (~ - 430 mV) brines rich in sulfate (2.2 g.L-1) and sulfide (9.5 ppm), making Gypsum Hill an analog to putative sulfate-rich briny habitats on extraterrestrial bodies such as Mars. RESULTS Genome-resolved metagenomics and metatranscriptomics were utilized to describe an active microbial community containing novel metagenome-assembled genomes and dominated by sulfur-cycling Desulfobacterota and Gammaproteobacteria. Sulfate reduction was dominated by hydrogen-oxidizing chemolithoautotrophic Desulfovibrionaceae sp. and was identified in phyla not typically associated with sulfate reduction in novel lineages of Spirochaetota and Bacteroidota. Highly abundant and active sulfur-reducing Desulfuromusa sp. highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. Despite low oxygen availability, sulfide oxidation was primarily attributed to aerobic chemolithoautotrophic Halothiobacillaceae. Low abundance and transcription of photoautotrophs indicated sulfur-based chemolithoautotrophy drives primary productivity even during periods of constant illumination. CONCLUSIONS We identified a rare surficial chemolithoautotrophic, sulfur-cycling microbial community active in a unique anoxic, cold, hypersaline Arctic spring. We detected Mars-relevant metabolisms including hydrogenotrophic sulfate reduction, sulfur reduction, and sulfide oxidation, which indicate the potential for microbial life in analogous S-rich brines on past and present Mars. Video Abstract.
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Affiliation(s)
- Elisse Magnuson
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
| | - Ianina Altshuler
- MACE Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nastasia J. Freyria
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
| | - Richard J. Leveille
- Department of Earth and Planetary Sciences, McGill University, Montreal, QC Canada
- Geosciences Department, John Abbott College, Ste-Anne-de-Bellevue, QC Canada
| | - Lyle G. Whyte
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
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162
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Zhang K, Narsing Rao MP, Banerjee A, Wang J, Ning SY, Zi J, Wang Y, Wan Y. Description of Tellurirhabdus bombi sp. nov., Isolated from Bumblebee. Curr Microbiol 2023; 80:337. [PMID: 37668731 DOI: 10.1007/s00284-023-03440-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/06/2023] [Indexed: 09/06/2023]
Abstract
A Gram-stain-negative, aerobic, non-motile, and rod-shaped bacterium, designated IE-0392T, was isolated from a bumblebee. The 16S rRNA gene sequence (highest 16S rRNA gene sequence similarity with the type strain of Tellurirhabdus rosea (90.0%) and phylogenetic analysis suggest that strain IE-0392T was a member of the genus Tellurirhabdus. Strain IE-0392T optimally grew at 25 ℃ and pH 7.0. Menaquinone 7 (MK-7) was the only isoprenoid quinone present in strain IE-0392T. The major fatty acids (> 10%) of strain IE-0392T were iso-C15:0, C16:1 ω5c, and iso-C17:0 3-OH. The polar lipids of strain IE-0392T were phosphatidylethanolamine, phosphatidylserine, unidentified aminophospholipids, unidentified aminolipid, unidentified phospholipid, and unidentified lipids. The genomic DNA G + C content of strain IE-0392T was 48.8%. The amino acid identity (AAI) and the average nucleotide identity (ANI) values suggest that strain IE-0392T is a novel member of the genus Tellurirhabdus. The results suggest that strain IE-0392T represents a novel species of the genus Tellurirhabdus, for which the name Tellurirhabdus bombi sp. nov., is proposed. The type strain is IE-0392T (= GDMCC 1.2794T = JCM 35040T).
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Affiliation(s)
- Kun Zhang
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, 3460000, Talca, Chile
| | - Aparna Banerjee
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, 3460000, Talca, Chile
| | - Jun Wang
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | | | - Jing Zi
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Yan Wang
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Yi Wan
- Shaanxi Institute of Microbiology, Xi'an, 710043, China.
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163
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Ettinger CL, Ostovar T, Yacoub M, Ahrendt S, Hice RH, Federici BA, Stajich JE. Genomes and transcriptomes help unravel the complex life cycle of the blastoclad fungus, Coelomomyces lativittatus, an obligate parasite of mosquitoes and microcrustaceans. Mycologia 2023; 115:630-647. [PMID: 37494633 DOI: 10.1080/00275514.2023.2228182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023]
Abstract
Species of the phylum Blastocladiomycota, early-diverging zoosporic (flagellated) lineages of fungi, are vastly understudied. This phylum includes the genus Coelomomyces, which consists of more than 80 fungal species that are obligate parasites of arthropods. Known Coelomomyces species lack a complete asexual life cycle, instead surviving through an obligate heterecious alternation of generations life cycle. Despite their global distribution and interesting life cycle, little is known about the genomics of any Coelomomyces species. To address this, we generated three draft-level genomes and annotations for C. lativittatus representing its haploid meiospore, orange gamete, and amber gamete life stages. These draft genome assemblies ranged in size from 5002 to 5799 contigs, with a total length of 19.8-22.8 Mb and a mean of 7416 protein-coding genes. We then demonstrated the utility of these genomes by combining the draft annotations as a reference for analysis of C. lativittatus transcriptomes. We analyzed transcriptomes from across host-associated life stages, including infected larvae and excised mature sporangia from the mosquito Anopheles quadrimaculatus. We identified differentially expressed genes and enriched GO terms both across and within life stages and used these to make hypotheses about C. lativittatus biology. Generally, we found the C. lativittatus transcriptome to be a complex and dynamic expression landscape; GO terms related to metabolism and transport processes were enriched during infection and terms related to dispersal were enriched during sporulation. We further identified five high mobility group (HMG)-box genes in C. lativittatus, three belonging to clades with mating type (MAT) loci from other fungi, as well as four ortholog expansions in C. lativittatus compared with other fungi. The C. lativittatus genomes and transcriptomes reported here are a valuable resource and may be leveraged toward furthering understanding of the biology of these and other early-diverging fungal lineages.
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Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
| | - Talieh Ostovar
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
- UCR/SDSU Joint Doctoral Program in Evolutionary Biology, San Diego State University, San Diego, California 92182
| | - Mark Yacoub
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
| | - Steven Ahrendt
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
| | - Robert H Hice
- Department of Entomology, University of California, Riverside, Riverside, California 92521
| | - Brian A Federici
- Department of Entomology, University of California, Riverside, Riverside, California 92521
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521
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Choi BI, Ene A, Du J, Johnson G, Putonti C, Schouw CH, Dargis R, Senneby E, Christensen JJ, Wolfe AJ. Taxonomic considerations on Aerococcus urinae with proposal of subdivision into Aerococcus urinae, Aerococcus tenax sp. nov., Aerococcus mictus sp. nov., and Aerococcus loyolae sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755156 DOI: 10.1099/ijsem.0.006066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Average nucleotide identity analysis, based on whole genome sequences of 115 strains previously identified as Aerococcus urinae, an emerging uropathogen, discriminates at least six unique genomic taxa. The whole genome analysis affords clearer species boundaries over 16S rRNA gene sequencing and traditional phenotypic approaches for the identification and phylogenetic organization of Aerococcus species. The newly described species can be differentiated by matrix-assisted laser desorption ionization time-of-flight analysis of protein signatures. We propose the emendation of the description of A. urinae (type strain ATCC 51268T = CCUG 34223T=NCFB 2893) and the names of Aerococcus tenax sp. nov. (ATCC TSD-302T = DSM 115700T = CCUG 76531T=NR-58630T), Aerococcus mictus sp. nov. (ATCC TSD-301T = DSM 115699T = CCUG 76532T=NR-58629T), and Aerococcus loyolae sp. nov. (ATCC TSD-300T = DSM 115698T = CCUG 76533T=NR-58628T) for three of the newly identified genomic taxa.
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Affiliation(s)
- Brian I Choi
- Loyola University Chicago, Department of Microbiology & Immunology, Maywood IL, USA
| | - Adriana Ene
- Loyola University Chicago, Bioinformatics Program, Chicago IL, USA
| | - Jingjie Du
- Loyola University Chicago, Department of Microbiology & Immunology, Maywood IL, USA
| | | | - Catherine Putonti
- Loyola University Chicago, Department of Microbiology & Immunology, Maywood IL, USA
- Loyola University Chicago, Bioinformatics Program, Chicago IL, USA
- Loyola University Chicago, Department of Biology, Chicago IL, USA
| | - Christian H Schouw
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
| | - Rimtas Dargis
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
| | - Erik Senneby
- Lund University, Clinical Microbiology, Department of Translational Medicine, Lund, Sweden
| | - Jens J Christensen
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Alan J Wolfe
- Loyola University Chicago, Department of Microbiology & Immunology, Maywood IL, USA
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165
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Nguyen M, Elmore Z, Ihle C, Moen FS, Slater AD, Turner BN, Parrello B, Best AA, Davis JJ. Predicting variable gene content in Escherichia coli using conserved genes. mSystems 2023; 8:e0005823. [PMID: 37314210 PMCID: PMC10469788 DOI: 10.1128/msystems.00058-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/25/2023] [Indexed: 06/15/2023] Open
Abstract
Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%-90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943-0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including "hypothetical proteins" was accurately predicted (F1 = 0.902 [0.898-0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876-0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data. IMPORTANCE Having the ability to predict the protein-encoding gene content of a genome is important for assessing genome quality, binning genomes from shotgun metagenomic assemblies, and assessing risk due to the presence of antimicrobial resistance and other virulence genes. In this study, we built a set of binary classifiers for predicting the presence or absence of variable genes occurring in 10%-90% of all publicly available E. coli genomes. Overall, the results show that a large portion of the E. coli variable gene content can be predicted with high accuracy, including genes with functions relating to horizontal gene transfer. This study offers a strategy for predicting gene content using limited input sequence data.
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Affiliation(s)
- Marcus Nguyen
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
| | - Zachary Elmore
- Biology Department, Hope College, Holland, Michigan, USA
| | - Clay Ihle
- Biology Department, Hope College, Holland, Michigan, USA
| | | | - Adam D. Slater
- Biology Department, Hope College, Holland, Michigan, USA
| | | | - Bruce Parrello
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, USA
| | - Aaron A. Best
- Biology Department, Hope College, Holland, Michigan, USA
| | - James J. Davis
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
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166
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Ghaly TM, Focardi A, Elbourne LDH, Sutcliffe B, Humphreys W, Paulsen IT, Tetu SG. Stratified microbial communities in Australia's only anchialine cave are taxonomically novel and drive chemotrophic energy production via coupled nitrogen-sulphur cycling. MICROBIOME 2023; 11:190. [PMID: 37626351 PMCID: PMC10463829 DOI: 10.1186/s40168-023-01633-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Anchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood. RESULTS Here, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling. CONCLUSION These findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments. Video Abstract.
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Affiliation(s)
- Timothy M Ghaly
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Amaranta Focardi
- Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia
| | - Liam D H Elbourne
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | | | - William Humphreys
- School of Biological Sciences, University of Western Australia, Perth, Australia
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, Sydney, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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167
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Zhang Z, Zhang J, Chen Q, He J, Li X, Wang Y, Lu Y. Complete De Novo Assembly of Wolbachia Endosymbiont of Frankliniella intonsa. Int J Mol Sci 2023; 24:13245. [PMID: 37686049 PMCID: PMC10487741 DOI: 10.3390/ijms241713245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
As an endosymbiont, Wolbachia exerts significant effects on the host, including on reproduction, immunity, and metabolism. However, the study of Wolbachia in Thysanopteran insects, such as flower thrips Frankliniella intonsa, remains limited. Here, we assembled a gap-free looped genome assembly of Wolbachia strain wFI in a length of 1,463,884 bp (GC content 33.80%), using Nanopore long reads and Illumina short reads. The annotation of wFI identified a total of 1838 protein-coding genes (including 85 pseudogenes), 3 ribosomal RNAs (rRNAs), 35 transfer RNAs (tRNAs), and 1 transfer-messenger RNA (tmRNA). Beyond this basic description, we identified mobile genetic elements, such as prophage and insertion sequences (ISs), which make up 17% of the entire wFI genome, as well as genes involved in riboflavin and biotin synthesis and metabolism. This research lays the foundation for understanding the nutritional mutualism between Wolbachia and flower thrips. It also serves as a valuable resource for future studies delving into the intricate interactions between Wolbachia and its host.
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Affiliation(s)
- Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
| | - Jiahui Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Qizhang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
| | - Jianyun He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
| | - Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
| | - Yunsheng Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.Z.); (Q.C.); (J.H.); (X.L.); (Y.L.)
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168
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Sun K, Yu M, Zhu XY, Xue CX, Zhang Y, Chen X, Yao P, Chen L, Fu L, Yang Z, Zhang XH. Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole. Microbiol Spectr 2023; 11:e0114923. [PMID: 37623326 PMCID: PMC10580873 DOI: 10.1128/spectrum.01149-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.
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Affiliation(s)
- Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Lin Chen
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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169
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Ene A, Banerjee S, Wolfe AJ, Putonti C. Exploring the genotypic and phenotypic differences distinguishing Lactobacillus jensenii and Lactobacillus mulieris. mSphere 2023; 8:e0056222. [PMID: 37366621 PMCID: PMC10449518 DOI: 10.1128/msphere.00562-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/10/2023] [Indexed: 06/28/2023] Open
Abstract
Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are dominant species of the urogenital microbiota. Prior studies suggest that these Lactobacillus species play a significant role in the urobiome of healthy females. In our prior genomic analysis of all publicly available L. jensenii and Lactobacillus mulieris genomes at the time (n = 43), we identified genes unique to these two closely related species. This motivated our further exploration here into their genotypic differences as well as into their phenotypic differences. First, we expanded genome sequence representatives of both species to 61 strains, including publicly available strains and nine new strains sequenced here. Genomic analyses conducted include phylogenetics of the core genome as well as biosynthetic gene cluster analysis and metabolic pathway analyses. Urinary strains of both species were assayed for their ability to utilize four simple carbohydrates. We found that L. jensenii strains can efficiently catabolize maltose, trehalose, and glucose, but not ribose, and L. mulieris strains can utilize maltose and glucose, but not trehalose and ribose. Metabolic pathway analysis clearly shows the lack of treB within L. mulieris strains, indicative of its inability to catabolize external sources of trehalose. While genotypic and phenotypic observations provide insight into the differences between these two species, we did not find any association with urinary symptom status. Through this genomic and phenotypic investigation, we identify markers that can be leveraged to clearly distinguish these two species in investigations of the female urogenital microbiota. IMPORTANCE We have expanded upon our prior genomic analysis of L. jensenii and L. mulieris strains, including nine new genome sequences. Our bioinformatic analysis finds that L. jensenii and L. mulieris cannot be distinguished by short-read 16S rRNA gene sequencing alone. Thus, to discriminate between these two species, future studies of the female urogenital microbiome should employ metagenomic sequencing and/or sequence species-specific genes, such as those identified here. Our bioinformatic examination also confirmed our prior observations of differences between the two species related to genes associated with carbohydrate utilization, which we tested here. We found that the transport and utilization of trehalose are key distinguishing traits of L. jensenii, which is further supported by our metabolic pathway analysis. In contrast with other urinary Lactobacillus species, we did not find strong evidence for either species, nor particular genotypes, to be associated with lower urinary tract symptoms (or the lack thereof).
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Affiliation(s)
- Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Swarnali Banerjee
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
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170
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Aguirre-Sánchez JR, Quiñones B, Ortiz-Muñoz JA, Prieto-Alvarado R, Vega-López IF, Martínez-Urtaza J, Lee BG, Chaidez C. Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen. Microorganisms 2023; 11:2114. [PMID: 37630674 PMCID: PMC10457828 DOI: 10.3390/microorganisms11082114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes' presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.
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Affiliation(s)
- José R. Aguirre-Sánchez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Culiacan 80110, Mexico;
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA; (B.Q.); (B.G.L.)
| | - José A. Ortiz-Muñoz
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Rogelio Prieto-Alvarado
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Inés F. Vega-López
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Jaime Martínez-Urtaza
- Departament de Genètica i de Microbiologia, Universitat Autờnoma de Barcelona, 08193 Bellaterra, Spain;
| | - Bertram G. Lee
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA; (B.Q.); (B.G.L.)
| | - Cristóbal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Culiacan 80110, Mexico;
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171
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Debeljak P, Bayer B, Sun Y, Herndl GJ, Obernosterer I. Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean. MICROBIOME 2023; 11:187. [PMID: 37596690 PMCID: PMC10439609 DOI: 10.1186/s40168-023-01600-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/16/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer. RESULTS Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae. CONCLUSION The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C- and Fe-related metabolic capabilities of microbial taxa provide new insights into their potential role in the cycling of C and Fe under varying nutrient regimes in the Southern Ocean. Video Abstract.
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Affiliation(s)
- Pavla Debeljak
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France.
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria.
- SupBiotech, Villejuif, France.
| | - Barbara Bayer
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
| | - Ying Sun
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ (Royal Netherlands Institute for Sea Research), Den Burg, 1790 AB, The Netherlands
- Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
| | - Ingrid Obernosterer
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France
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172
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Pavia MJ, Chede A, Wu Z, Cadillo-Quiroz H, Zhu Q. BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes. MICROBIOME 2023; 11:186. [PMID: 37596696 PMCID: PMC10439608 DOI: 10.1186/s40168-023-01625-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/16/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Exploring metagenomic contigs and "binning" them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. RESULTS We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena's usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. CONCLUSIONS BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena , together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. Video Abstract.
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Affiliation(s)
- Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA
| | - Abhinav Chede
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Zijun Wu
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA.
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA.
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA.
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173
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Mincer TJ, Bos RP, Zettler ER, Zhao S, Asbun AA, Orsi WD, Guzzetta VS, Amaral-Zettler LA. Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat. WATER RESEARCH 2023; 242:120033. [PMID: 37244770 DOI: 10.1016/j.watres.2023.120033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/25/2023] [Accepted: 05/01/2023] [Indexed: 05/29/2023]
Abstract
We fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris (PMD), the pelagic brown macroalga Sargassum, and seawater samples collected from the Caribbean and Sargasso Seas of the North Atlantic Ocean. Annotation and mapping of these 16 bacterial genome sequences to a PMD-derived Vibrio metagenome-assembled genome created for this study showcased vertebrate pathogen genes closely-related to cholera and non-cholera pathovars. Phenotype testing of cultivars confirmed rapid biofilm formation, hemolytic, and lipophospholytic activities, consistent with pathogenic potential. Our study illustrates that open ocean vibrios represent a heretofore undescribed group of microbes, some representing potential new species, possessing an amalgam of pathogenic and low nutrient acquisition genes, reflecting their pelagic habitat and the substrates and hosts they colonize.
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Affiliation(s)
- Tracy J Mincer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA; Department of Biology, Wilkes Honors College, Florida Atlantic University, Jupiter, FL, USA.
| | - Ryan P Bos
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Erik R Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - Shiye Zhao
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushimacho, Yokosuka 237-0061, Japan
| | - Alejandro A Asbun
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology,Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | | | - Linda A Amaral-Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands; Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands; Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
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174
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Hatrongjit R, Boueroy P, Jenjaroenpun P, Wongsurawat T, Meekhanon N, Chopjitt P, Zheng H, Fittipaldi N, Chareonsudjai S, Segura M, Gottschalk M, Kerdsin A. Genomic characterization and virulence of Streptococcus suis serotype 4 clonal complex 94 recovered from human and swine samples. PLoS One 2023; 18:e0288840. [PMID: 37498866 PMCID: PMC10374156 DOI: 10.1371/journal.pone.0288840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/05/2023] [Indexed: 07/29/2023] Open
Abstract
Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Herein, we performed genomic analysis of seven S. suis serotype 4 strains belonging to clonal complex (CC) 94 that were recovered from a human patient or from diseased and clinically healthy pigs. Genomic exploration and comparisons, as well as in vitro cytotoxicity tests, indicated that S. suis CC94 serotype 4 strains are potentially virulent. Genomic analysis revealed that all seven strains clustered within minimum core genome group 3 (MCG-3) and had a high number of virulence-associated genes similar to those of virulent serotype 2 strains. Cytotoxicity assays showed that both the human lung adenocarcinoma cell line and HeLa cells rapidly lost viability following incubation for 4 h with the strains at a concentration of 106 bacterial cells. The human serotype 4 strain (ID36054) decreased cell viability profoundly and similarly to the control serotype 2 strain P1/7. In addition, strain ST1689 (ID34572), isolated from a clinically healthy pig, presented similar behaviour in an adenocarcinoma cell line and HeLa cells. The antimicrobial resistance genes tet(O) and ermB that confer resistance to tetracyclines, macrolides, and lincosamides were commonly found in the strains. However, aminoglycoside and streptothricin resistance genes were found only in certain strains in this study. Our results indicate that S. suis CC94 serotype 4 strains are potentially pathogenic and virulent and should be monitored.
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Affiliation(s)
- Rujirat Hatrongjit
- Faculty of Science and Engineering, Department of General Sciences, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Piroon Jenjaroenpun
- Faculty of Medicine Siriraj Hospital, Department of Research and Development, Division of Bioinformatics and Data Management for Research, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Faculty of Medicine Siriraj Hospital, Department of Research and Development, Division of Bioinformatics and Data Management for Research, Mahidol University, Bangkok, Thailand
| | - Nattakan Meekhanon
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Han Zheng
- National Institute for Communicable Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Nahuel Fittipaldi
- Faculty of Veterinary Medicine, Research Group on Infectious Diseases in Production Animals (GREMIP), University of Montreal, Quebec, Canada
| | - Sorujsiri Chareonsudjai
- Faculty of Medicine, Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Mariela Segura
- Faculty of Veterinary Medicine, Research Group on Infectious Diseases in Production Animals (GREMIP), University of Montreal, Quebec, Canada
| | - Marcelo Gottschalk
- Faculty of Veterinary Medicine, Research Group on Infectious Diseases in Production Animals (GREMIP), University of Montreal, Quebec, Canada
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
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Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Lee STM. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Anim Microbiome 2023; 5:35. [PMID: 37461084 DOI: 10.1186/s42523-023-00256-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. RESULTS We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.
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Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
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176
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Thompson J, Barr C, Babcock-Adams L, Bird L, La Cava E, Garber A, Hongoh Y, Liu M, Nealson KH, Okamoto A, Repeta D, Suzuki S, Tacto C, Tashjian M, Merino N. Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system. Front Microbiol 2023; 14:1179857. [PMID: 37520355 PMCID: PMC10373932 DOI: 10.3389/fmicb.2023.1179857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/23/2023] [Indexed: 08/01/2023] Open
Abstract
The terrestrial serpentinite-hosted ecosystem known as "The Cedars" is home to a diverse microbial community persisting under highly alkaline (pH ~ 12) and reducing (Eh < -550 mV) conditions. This extreme environment presents particular difficulties for microbial life, and efforts to isolate microorganisms from The Cedars over the past decade have remained challenging. Herein, we report the initial physiological assessment and/or full genomic characterization of three isolates: Paenibacillus sp. Cedars ('Paeni-Cedars'), Alishewanella sp. BS5-314 ('Ali-BS5-314'), and Anaerobacillus sp. CMMVII ('Anaero-CMMVII'). Paeni-Cedars is a Gram-positive, rod-shaped, mesophilic facultative anaerobe that grows between pH 7-10 (minimum pH tested was 7), temperatures 20-40°C, and 0-3% NaCl concentration. The addition of 10-20 mM CaCl2 enhanced growth, and iron reduction was observed in the following order, 2-line ferrihydrite > magnetite > serpentinite ~ chromite ~ hematite. Genome analysis identified genes for flavin-mediated iron reduction and synthesis of a bacillibactin-like, catechol-type siderophore. Ali-BS5-314 is a Gram-negative, rod-shaped, mesophilic, facultative anaerobic alkaliphile that grows between pH 10-12 and temperatures 10-40°C, with limited growth observed 1-5% NaCl. Nitrate is used as a terminal electron acceptor under anaerobic conditions, which was corroborated by genome analysis. The Ali-BS5-314 genome also includes genes for benzoate-like compound metabolism. Anaero-CMMVII remained difficult to cultivate for physiological studies; however, growth was observed between pH 9-12, with the addition of 0.01-1% yeast extract. Anaero-CMMVII is a probable oxygen-tolerant anaerobic alkaliphile with hydrogenotrophic respiration coupled with nitrate reduction, as determined by genome analysis. Based on single-copy genes, ANI, AAI and dDDH analyses, Paeni-Cedars and Ali-BS5-314 are related to other species (P. glucanolyticus and A. aestuarii, respectively), and Anaero-CMMVII represents a new species. The characterization of these three isolates demonstrate the range of ecophysiological adaptations and metabolisms present in serpentinite-hosted ecosystems, including mineral reduction, alkaliphily, and siderophore production.
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Affiliation(s)
- Jaclyn Thompson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Lydia Babcock-Adams
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Lina Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Eugenio La Cava
- National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Arkadiy Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Mark Liu
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Daniel Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Shino Suzuki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, Sagamihara, Kanagawa, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Clarissa Tacto
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michelle Tashjian
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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177
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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178
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Thieringer PH, Boyd ES, Templeton AS, Spear JR. Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman. Front Microbiol 2023; 14:1205558. [PMID: 37465028 PMCID: PMC10350532 DOI: 10.3389/fmicb.2023.1205558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H2 and CH4. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO2, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.
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Affiliation(s)
- Patrick H. Thieringer
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
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179
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Chicco D, Cumbo F, Angione C. Ten quick tips for avoiding pitfalls in multi-omics data integration analyses. PLoS Comput Biol 2023; 19:e1011224. [PMID: 37410704 DOI: 10.1371/journal.pcbi.1011224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Abstract
Data are the most important elements of bioinformatics: Computational analysis of bioinformatics data, in fact, can help researchers infer new knowledge about biology, chemistry, biophysics, and sometimes even medicine, influencing treatments and therapies for patients. Bioinformatics and high-throughput biological data coming from different sources can even be more helpful, because each of these different data chunks can provide alternative, complementary information about a specific biological phenomenon, similar to multiple photos of the same subject taken from different angles. In this context, the integration of bioinformatics and high-throughput biological data gets a pivotal role in running a successful bioinformatics study. In the last decades, data originating from proteomics, metabolomics, metagenomics, phenomics, transcriptomics, and epigenomics have been labelled -omics data, as a unique name to refer to them, and the integration of these omics data has gained importance in all biological areas. Even if this omics data integration is useful and relevant, due to its heterogeneity, it is not uncommon to make mistakes during the integration phases. We therefore decided to present these ten quick tips to perform an omics data integration correctly, avoiding common mistakes we experienced or noticed in published studies in the past. Even if we designed our ten guidelines for beginners, by using a simple language that (we hope) can be understood by anyone, we believe our ten recommendations should be taken into account by all the bioinformaticians performing omics data integration, including experts.
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Affiliation(s)
- Davide Chicco
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Fabio Cumbo
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Claudio Angione
- School of Computing Engineering and Digital Technologies, Teesside University, Middlesbrough, United Kingdom
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180
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Narsing Rao MP, Banerjee A, Liu GH, Thamchaipenet A. Genome-based reclassification of Bacillus acidicola, Bacillus pervagus and the genera Heyndrickxia, Margalitia and Weizmannia. Int J Syst Evol Microbiol 2023; 73. [PMID: 37462355 DOI: 10.1099/ijsem.0.005961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
In the present study, the taxonomic positions of Bacillus acidicola, Bacillus pervagus and members of the genera Heyndrickxia, Margalitia and Weizmannia were evaluated. The 16S rRNA gene sequence similarity between Bacillus acidicola DSM 14745T, Bacillus pervagus DSM 23947T and members of the genera Heyndrickxia and Margalitia were above the cut-off level (>95 %) for genus delineation. Amino acid identity (AAI) values and the results of phylogenomic analysis suggested that B. acidicola and the members of the genera Heyndrickxia, Margalitia and Weizmannia belong to the same genus. Furthermore, the AAI and phylogenomic results also differentiate B. pervagus from B. acidicola and the members of the genera Heyndrickxia, Margalitia and Weizmannia. Based on the results, we propose to transfer Bacillus acidicola, Margalitia and Weizmannia to the genus Heyndrickxia. We also propose the reclassification of B. pervagus into a new genus Oikeobacillus gen. nov., with the type species Oikeobacillus pervagus comb. nov.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Aparna Banerjee
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca 3460000, Chile
| | - Guo-Hong Liu
- Agricultural Bio‑ Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, Fujian, PR China
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University, Bangkok 10900, Thailand
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181
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Yancey CE, Kiledal EA, Chaganti SR, Denef VJ, Errera RM, Evans JT, Hart LN, Isailovic D, James WS, Kharbush JJ, Kimbrel JA, Li W, Mayali X, Nitschky H, Polik CA, Powers MA, Premathilaka SH, Rappuhn NA, Reitz LA, Rivera SR, Zwiers CC, Dick GJ. The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome. HARMFUL ALGAE 2023; 126:102440. [PMID: 37290887 DOI: 10.1016/j.hal.2023.102440] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/10/2023]
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L⁻¹) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.
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Affiliation(s)
- Colleen E Yancey
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - E Anders Kiledal
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Vincent J Denef
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Reagan M Errera
- National Oceanic and Atmospheric Administration (NOAA), Great Lakes Environmental Research Laboratory (GLERL), 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Jacob T Evans
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Lauren N Hart
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, United States of America; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - William S James
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jenan J Kharbush
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Wei Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Helena Nitschky
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Catherine A Polik
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - McKenzie A Powers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sanduni H Premathilaka
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - Nicole A Rappuhn
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Laura A Reitz
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sara R Rivera
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Claire C Zwiers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Gregory J Dick
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America.
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182
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Buzzanca D, Kerkhof PJ, Alessandria V, Rantsiou K, Houf K. Arcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness. Heliyon 2023; 9:e17652. [PMID: 37449094 PMCID: PMC10336517 DOI: 10.1016/j.heliyon.2023.e17652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/30/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
The Arcobacteraceae family groups Gram-negative bacterial species previously included in the family Campylobacteraceae. These species of which some are considered foodborne pathogens, have been isolated from different environmental niches and hosts. They have been isolated from various types of foods, though predominantly from food of animal origin, as well as from stool of humans with enteritis. Their different abilities to survive in different hosts and environments suggest an evolutionary pressure with consequent variation in their genome content. Moreover, their different physiological and genomic characteristics led to the recent proposal to create new genera within this family, which is however criticized due to the lack of discriminatory features and biological and clinical relevance. Aims of the present study were to assess the Arcobacteraceae pangenome, and to characterize existing similarities and differences in 20 validly described species. For this, analysis has been conducted on the genomes of the corresponding type strains obtained by Illumina sequencing, applying several bioinformatic tools. Results of the present study do not support the proposed division into different genera and revealed the presence of pangenome partitions with numbers comparable to other Gram-negative bacteria genera, such as Campylobacter. Different gene class compositions in animal and human-associated species are present, including a higher percentage of virulence-related gene classes such as cell motility genes. The adaptation to environmental and/or host conditions of some species was identified by the presence of specific genes. Furthermore, a division into pathogenic and non-pathogenic species is suggested, which can support future research on food safety and public health.
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Affiliation(s)
- Davide Buzzanca
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Pieter-Jan Kerkhof
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium
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183
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Brüwer JD, Orellana LH, Sidhu C, Klip HCL, Meunier CL, Boersma M, Wiltshire KH, Amann R, Fuchs BM. In situ cell division and mortality rates of SAR11, SAR86, Bacteroidetes, and Aurantivirga during phytoplankton blooms reveal differences in population controls. mSystems 2023; 8:e0128722. [PMID: 37195198 PMCID: PMC10308942 DOI: 10.1128/msystems.01287-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/21/2023] [Indexed: 05/18/2023] Open
Abstract
Net growth of microbial populations, that is, changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, and the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8/day and Aurantivirga of up to 1.9/day differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9/day, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5/day) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within 1 day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls. IMPORTANCE The growth of a microbial population is often calculated from their numerical abundance over time. However, this does not take cell division and mortality rates into account, which are important for deriving ecological processes like bottom-up and top-down control. In this study, we determined growth by numerical abundance and calibrated microscopy-based methods to determine the frequency of dividing cells and subsequently calculate taxon-specific cell division rates in situ. The cell division and mortality rates of two oligotrophic (SAR11 and SAR86) and two copiotrophic (Bacteroidetes and Aurantivirga) taxa during two spring phytoplankton blooms showed a tight coupling for all four taxa throughout the blooms without any temporal offset. Unexpectedly, SAR11 showed high cell division rates days before the bloom while cell abundances remained constant, which is indicative of strong top-down control. Microscopy remains the method of choice to understand ecological processes like top-down and bottom-up control on a cellular level.
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Affiliation(s)
- Jan D. Brüwer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Helena C. L. Klip
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Cédric L. Meunier
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Maarten Boersma
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
- University of Bremen, Bremen, Germany
| | - Karen H. Wiltshire
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Wattenmeerstation, List auf Sylt, Bremerhaven, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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184
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Gilroy R, Adam ME, Kumar B, Pallen MJ. An initial genomic blueprint of the healthy human oesophageal microbiome. Access Microbiol 2023; 5:acmi000558.v3. [PMID: 37424544 PMCID: PMC10323806 DOI: 10.1099/acmi.0.000558.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/15/2023] [Indexed: 07/11/2023] Open
Abstract
Background The oesophageal microbiome is thought to contribute to the pathogenesis of oesophageal cancer. However, investigations using culture and molecular barcodes have provided only a low-resolution view of this important microbial community. We therefore explored the potential of culturomics and metagenomic binning to generate a catalogue of reference genomes from the healthy human oesophageal microbiome, alongside a comparison set from saliva. Results Twenty-two distinct colonial morphotypes from healthy oesophageal samples were genome-sequenced. These fell into twelve species clusters, eleven of which represented previously defined species. Two isolates belonged to a novel species, which we have named Rothia gullae. We performed metagenomic binning of reads generated from UK samples from this study alongside reads generated from Australian samples in a recent study. Metagenomic binning generated 136 medium or high-quality metagenome-assembled genomes (MAGs). MAGs were assigned to 56 species clusters, eight representing novel Candidatus species, which we have named Ca. Granulicatella gullae, Ca. Streptococcus gullae, Ca. Nanosynbacter quadramensis, Ca. Nanosynbacter gullae, Ca. Nanosynbacter colneyensis, Ca. Nanosynbacter norwichensis, Ca. Nanosynococcus oralis and Ca. Haemophilus gullae. Five of these novel species belong to the recently described phylum Patescibacteria . Although members of the Patescibacteria are known to inhabit the oral cavity, this is the first report of their presence in the oesophagus. Eighteen of the metagenomic species were, until recently, identified only by hard-to-remember alphanumeric placeholder designations. Here we illustrate the utility of a set of recently published arbitrary Latinate species names in providing user-friendly taxonomic labels for microbiome analyses.Our non-redundant species catalogue contained 63 species derived from cultured isolates or MAGs. Mapping revealed that these species account for around half of the sequences in the oesophageal and saliva metagenomes. Although no species was present in all oesophageal samples, 60 species occurred in at least one oesophageal metagenome from either study, with 50 identified in both cohorts. Conclusions Recovery of genomes and discovery of new species represents an important step forward in our understanding of the oesophageal microbiome. The genes and genomes that we have released into the public domain will provide a base line for future comparative, mechanistic and intervention studies.
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Affiliation(s)
- Rachel Gilroy
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mina E. Adam
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Bhaskar Kumar
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
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185
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Lin X, Qiao B, Chang R, Li Y, Zheng W, He Z, Tian Y. Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome. MICROBIOME 2023; 11:139. [PMID: 37355612 PMCID: PMC10290299 DOI: 10.1186/s40168-023-01583-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/23/2023] [Indexed: 06/26/2023]
Abstract
BACKGROUND Keystone taxa are drivers of microbiome structure and functioning, which may play critical roles in microbiome-level responses to recalcitrant pollution and are a key to bioremediation. However, the characterization and manipulation of such taxa is a major challenge due to the complexity of microbial communities and rapid turnover in both time and space. Here, microcosms were set up with benzo[a]-pyrene (BaP) and/or nitrate based on C-rich, S-rich, and N-limited mangrove sediments as reductive experimental models to trigger and track the turnover of keystone taxa to address this challenge. RESULTS Based on microbial co-occurrence network analysis, two keystone taxa, Sulfurovum and Sulfurimonas, were found to exhibit significant role transitions in different microcosms, where these two taxa played nonkeystone roles with neutral relationships in in situ mangrove sediments. However, Sulfurimonas transitioned to be keystone taxa in nitrate-replenished microcosms and formed a keystone guild with Thioalkalispira. Sulfurovum stood out in BaP-added microcosms and mutualized in a densely polycyclic aromatic hydrocarbon (PAH)-degrader-centric keystone guild with Novosphingobium and Robiginitalea, where 63.25% of added BaP was removed. Under the occurrence of nitrate and BaP, they simultaneously played roles as keystone taxa in their respective guilds but exhibited significant competition. Comparative genomics and metagenome-assembled genome (MAG) analysis was then performed to reveal the metabolic potential of those keystone taxa and to empirically deduce their functional role in keystone guilds. Sulfurimonas possesses a better sense system and motility, indicative of its aggressive role in nitrate acquisition and conversion; Sulfurovum exhibited a better ability for oxidation resistance and transporting nutrients and electrons. High-efficiency thermal asymmetric interlaced polymerase reaction (hiTAIL-PCR) and enhanced green fluorescent protein (eGFP)-labeling approaches were employed to capture and label the BaP key degrader to further experimentally verify the roles of keystone taxa Sulfurovum in the keystone guilds. Observations of the enhancement in reactive oxygen species (ROS) removal, cell growth, and degradation efficiency by co-culture of isolated keystone taxa strains experimentally demonstrated that Sulfurovum contributes to the BaP degradative microbiome against BaP toxicity. CONCLUSIONS Our findings suggest that the combined use of co-occurrence network analysis, comparative genomics, and co-culture of captured keystone taxa (3C-strategy) in microbial communities whose structure is strongly shaped by changing environmental factors can characterize keystone taxa roles in keystone guilds and may provide targets for manipulation to improve the function of the microbiome. Video Abstract.
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Affiliation(s)
- Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Baoyi Qiao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Ruirui Chang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Yixin Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Wei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
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186
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Torres-Morales J, Mark Welch JL, Dewhirst FE, Borisy GG. Site-specialization of human oral Gemella species. J Oral Microbiol 2023; 15:2225261. [PMID: 37361319 PMCID: PMC10288933 DOI: 10.1080/20002297.2023.2225261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
Gemella species are core members of the human oral microbiome in healthy subjects and are regarded as commensals, although they can cause opportunistic infections. Our objective was to evaluate the site-specialization of Gemella species among various habitats within the mouth by combining pangenomics and metagenomics. With pangenomics, we identified genome relationships and categorized genes as core and accessory to each species. With metagenomics, we identified the primary oral habitat of individual genomes. Our results establish that the genomes of three species, G. haemolysans, G. sanguinis and G. morbillorum, are abundant and prevalent in human mouths at different oral sites: G. haemolysans on buccal mucosa and keratinized gingiva; G. sanguinis on tongue dorsum, throat, and tonsils; and G. morbillorum in dental plaque. The gene-level basis of site-specificity was investigated by identifying genes that were core to Gemella genomes at a specific oral site but absent from other Gemella genomes. The riboflavin biosynthesis pathway was present in G. haemolysans genomes associated with buccal mucosa but absent from the rest of the genomes. Overall, metapangenomics show that Gemella species have clear ecological preferences in the oral cavity of healthy humans and provides an approach to identifying gene-level drivers of site specificity.
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Affiliation(s)
| | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, MA, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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187
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Zepeda-Rivera MA, Eisele Y, Baryiames A, Wu H, LaCourse KD, Jones DS, Hauner H, Dewhirst FE, Minot SS, Johnston CD, Bullman S. Fusobacterium sphaericum sp. nov. , isolated from a human colon tumor, is prevalent in various human body sites and induces IL-8 secretion from colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545380. [PMID: 37398369 PMCID: PMC10312772 DOI: 10.1101/2023.06.16.545380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. ( Fs ), isolated from primary colon adenocarcinoma tissue. We acquire the complete, closed genome of this organism and phylogenetically confirm its classification into the Fusobacterium genus. Phenotypic and genomic analysis of Fs reveal that this novel organism is of coccoid shape, rare for Fusobacterium members, and has species-distinct gene content. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in ∼1,750 human metagenomic samples shows that it is a moderately prevalent member of the human oral cavity and stool. Intriguingly, analysis of ∼1,270 specimens from patients with colorectal cancer demonstrate that Fs is significantly enriched in colonic and tumor tissue as compared to mucosa or feces. Our study sheds light on a novel bacterial species that is prevalent within the human intestinal microbiota and whose role in human health and disease requires further investigation.
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188
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Simpson AC, Eedara VVR, Singh NK, Damle N, Parker CW, Karouia F, Mason CE, Venkateswaran K. Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station. Front Microbiol 2023; 14:1166013. [PMID: 37396358 PMCID: PMC10308117 DOI: 10.3389/fmicb.2023.1166013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1T. The 16S sequence of the F6_2S_P_1T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1T are anteiso-C15:0 (51.7%), iso-C16:0 (23.1%), and iso-C15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1T (=NRRL B-65657T and DSMZ 115098T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1T, C. rhizosphaerae, and C. ginsengisoli, along with two uncharacterized Cohnella strains, possess a shared set of 332 gene clusters which are not shared with any other WGS of Cohnella species, and form a distinct clade branching off from C. nanjingensis. Functional traits were predicted for the genomes of strain F6_2S_P_1T and other members of this clade.
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Affiliation(s)
- Anna C. Simpson
- California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States
| | - V. V. Ramprasad Eedara
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Nitin K. Singh
- California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States
| | - Namita Damle
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Ceth W. Parker
- California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States
| | | | - Christopher E. Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States
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189
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Wirth R, Bagi Z, Shetty P, Szuhaj M, Cheung TTS, Kovács KL, Maróti G. Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants. THE ISME JOURNAL 2023:10.1038/s41396-023-01448-3. [PMID: 37286740 DOI: 10.1038/s41396-023-01448-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H2/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.
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Affiliation(s)
- Roland Wirth
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.
- Faculty of Water Sciences, University of Public Service, Baja, Hungary.
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190
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Hochart C, Paoli L, Ruscheweyh HJ, Salazar G, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Ziegler M, Porro B, Armstrong EJ, Hume BCC, Aury JM, Pogoreutz C, Paz-García DA, Nugues MM, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Wincker P, Zoccola D, Allemand D, Planes S, Thurber RV, Voolstra CR, Sunagawa S, Galand PE. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean. Nat Commun 2023; 14:3037. [PMID: 37264015 DOI: 10.1038/s41467-023-38502-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.
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Affiliation(s)
- Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | | | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany
| | - Barbara Porro
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric J Armstrong
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Claudia Pogoreutz
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maggy M Nugues
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, 04469, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Paola Furla
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric Gilson
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Department of Medical Genetics, CHU Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
- Institut Universitaire de France, 75231, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, 8 rue de Prague, 75012, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
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191
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Bornemann TLV, Esser SP, Stach TL, Burg T, Probst AJ. uBin: A manual refining tool for genomes from metagenomes. Environ Microbiol 2023; 25:1077-1083. [PMID: 36764661 DOI: 10.1111/1462-2920.16351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
Resolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth's biomes yet producing high-quality genomes from assembled fragments has been an ever-standing problem. While automated binning software and their combination produce prokaryotic bins in high throughput, their manual refinement has been slow, sometimes difficult or missing entirely facilitating error propagation in public databases. Here, we present uBin, a GUI-based, standalone bin refiner that runs on all major operating platforms and was additionally designed for educational purposes. When applied to the public CAMI dataset, refinement of bins using GC content, coverage and taxonomy was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near-complete genomes, whose replication indices indicate the active proliferation of microbes in Earth's lower orbit. uBin is an easy to instal software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software and its helper scripts are open source and available under https://github.com/ProbstLab/uBin.
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Affiliation(s)
- Till L V Bornemann
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Sarah P Esser
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Tom L Stach
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Tim Burg
- Independent Researcher, Im Acker 59, Koblenz, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Germany
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192
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Zehnle H, Laso-Pérez R, Lipp J, Riedel D, Benito Merino D, Teske A, Wegener G. Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes. Nat Microbiol 2023:10.1038/s41564-023-01400-3. [PMID: 37264141 DOI: 10.1038/s41564-023-01400-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.
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Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
- Faculty of Geosciences, University of Bremen, Bremen, Germany.
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Julius Lipp
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Dietmar Riedel
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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193
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Lu DC, Wang FQ, Amann RI, Teeling H, Du ZJ. Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae. MICROBIOME 2023; 11:126. [PMID: 37264413 PMCID: PMC10233909 DOI: 10.1186/s40168-023-01559-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species. RESULTS We sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera. CONCLUSIONS Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome. Video Abstract.
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Affiliation(s)
- De-Chen Lu
- Marine College, Shandong University, No. 180, Wenhua Xilu, Weihai, Shandong Province 264209 China
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Rudolf I. Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, 28359 Germany
| | - Zong-Jun Du
- Marine College, Shandong University, No. 180, Wenhua Xilu, Weihai, Shandong Province 264209 China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
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Tournay RJ, Firrincieli A, Parikh SS, Sivitilli DM, Doty SL. Effect of Arsenic on EPS Synthesis, Biofilm Formation, and Plant Growth-Promoting Abilities of the Endophytes Pseudomonas PD9R and Rahnella laticis PD12R. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37256822 DOI: 10.1021/acs.est.2c08586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Phytoremediation, a cost-effective, eco-friendly alternative to conventional remediation, could expand efforts to remediate arsenic-contaminated soils. As with other pollutants, the plant microbiome may improve phytoremediation outcomes for arsenic-contaminated sites. We used in vitro and in silico methods to compare the arsenic resistance mechanisms, synthesis of extracellular polymeric substances (EPS), biofilm formation, and plant growth-promoting abilities of the endophytes Pseudomonas sp. PD9R and Rahnella laticis PD12R. PD12R, which tolerates arsenate (As(V)) and arsenite (As(III)) to concentrations fivefold greater than PD9R, synthesizes high volumes of EPS in response to arsenic, and sequesters arsenic in the capsular EPS and cells. While arsenic exposure induced EPS synthesis in both strains, only PD12R continued to form biofilms at high As(III) and As(V) concentrations. The effects of endophyte inoculation on Arabidopsis growth varied by strain and As(V) concentration, and PD9R had positive effect on plants exposed to low levels of arsenic. Comparative genomic analyses exploring the EPS synthesis and arsenic resistance mechanisms against other Pseudomonas and Rahnella strains suggest that both strains possess atypical arsenic resistance mechanisms from other plant-associated strains, while the configuration of the EPS synthesis systems appeared to be more broadly distributed among plant- and non-plant-associated strains.
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Affiliation(s)
- Robert J Tournay
- School of Environmental and Forest Sciences, Anderson Hall, Box 352100, University of Washington, Seattle, Washington 98195, United States
| | - Andrea Firrincieli
- School of Environmental and Forest Sciences, Anderson Hall, Box 352100, University of Washington, Seattle, Washington 98195, United States
| | - Shruti S Parikh
- School of Environmental and Forest Sciences, Anderson Hall, Box 352100, University of Washington, Seattle, Washington 98195, United States
| | - Dominic M Sivitilli
- School of Environmental and Forest Sciences, Anderson Hall, Box 352100, University of Washington, Seattle, Washington 98195, United States
| | - Sharon L Doty
- School of Environmental and Forest Sciences, Anderson Hall, Box 352100, University of Washington, Seattle, Washington 98195, United States
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195
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Yancey CE, Yu F, Tripathi A, Sherman DH, Dick GJ. Expression of Microcystis Biosynthetic Gene Clusters in Natural Populations Suggests Temporally Dynamic Synthesis of Novel and Known Secondary Metabolites in Western Lake Erie. Appl Environ Microbiol 2023; 89:e0209222. [PMID: 37070981 PMCID: PMC10231183 DOI: 10.1128/aem.02092-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 04/19/2023] Open
Abstract
Microcystis spp. produce diverse secondary metabolites within freshwater cyanobacterial harmful algal blooms (cyanoHABs) around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, Microcystis genomes harbor numerous BGCs of unknown function, indicating a poorly understood chemical repertoire. While recent studies show that Microcystis produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of Microcystis BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. The results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate, and phosphorus concentrations and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but often unmonitored. It also indicates the prospects for identifying pharmaceutical-like molecules from cyanoHAB-derived BGCs. IMPORTANCE Microcystis spp. dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been studied, the broader suite of secondary metabolites produced by Microcystis remains poorly understood, leaving gaps in our understanding of their impacts on human and ecosystem health. We used community DNA and RNA sequences to track the diversity of genes encoding synthesis of secondary metabolites in natural Microcystis populations and assess patterns of transcription in western Lake Erie cyanoHABs. Our results reveal the presence of both known gene clusters that encode toxic secondary metabolites as well as novel ones that may encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.
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Affiliation(s)
- Colleen E. Yancey
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Natural Products Discovery Core, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, Michigan, USA
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196
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Peters EE, Cahn JKB, Lotti A, Gavriilidou A, Steffens UAE, Loureiro C, Schorn MA, Cárdenas P, Vickneswaran N, Crews P, Sipkema D, Piel J. Distribution and diversity of 'Tectomicrobia', a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites. ISME COMMUNICATIONS 2023; 3:50. [PMID: 37248312 PMCID: PMC10227082 DOI: 10.1038/s43705-023-00259-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
Genomic and functional analyses of bacterial sponge symbionts belonging to the uncultivated candidate genus 'Entotheonella' has revealed them as the prolific producers of bioactive compounds previously identified from their invertebrate hosts. These studies also suggested 'Entotheonella' as the first members of a new candidate phylum, 'Tectomicrobia'. Here we analyzed the phylogenetic structure and environmental distribution of this as-yet sparsely populated phylum-like lineage. The data show that 'Entotheonella' and other 'Tectomicrobia' are not restricted to marine habitats but widely distributed among terrestrial locations. The inferred phylogenetic trees suggest several intra-phylum lineages with diverse lifestyles. Of these, the previously described 'Entotheonella' lineage can be more accurately divided into at least three different candidate genera with the terrestrial 'Candidatus Prasianella', the largely terrestrial 'Candidatus Allonella', the 'Candidatus Thalassonella' comprising sponge-associated members, and the more widely distributed 'Candidatus Entotheonella'. Genomic characterization of 'Thalassonella' members from a range of sponge hosts did not suggest a role as providers of natural products, despite high genomic similarity to 'Entotheonella' regarding primary metabolism and implied lifestyle. In contrast, the analysis revealed a correlation between the revised 'Entotheonella' 16S rRNA gene phylogeny and a specific association with sponges and their natural products. This feature might serve as a discovery method to accelerate the identification of new chemically rich 'Entotheonella' variants, and led to the identification of the first 'Entotheonella' symbiont in a non-tetractinellid sponge, Psammocinia sp., indicating a wide host distribution of 'Entotheonella'-based chemical symbiosis.
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Affiliation(s)
- Eike E Peters
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Jackson K B Cahn
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Alessandro Lotti
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Ursula A E Steffens
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Paco Cárdenas
- Pharmacognosy, Department of Pharmaceutical Biosciences, BioMedical Center, Uppsala University, Husargatan 3, 75124, Uppsala, Sweden
| | - Nilani Vickneswaran
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.
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197
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Anstett J, Plominsky AM, DeLong EF, Kiesser A, Jürgens K, Morgan-Lang C, Stepanauskas R, Stewart FJ, Ulloa O, Woyke T, Malmstrom R, Hallam SJ. A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters. Sci Data 2023; 10:332. [PMID: 37244914 DOI: 10.1038/s41597-023-02222-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.
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Affiliation(s)
- Julia Anstett
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Alvaro M Plominsky
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Alyse Kiesser
- School of Engineering, The University of British Columbia, Kelowna, BC, Canada
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, 4070386, Concepción, Chile
- Instituto Milenio de Oceanografía, Casilla 1313, 4070386, Concepción, Chile
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven J Hallam
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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198
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541916. [PMID: 37292924 PMCID: PMC10245883 DOI: 10.1101/2023.05.23.541916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2 % of the genera found when we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder E. coli isolates and 387 gut E. coli isolates supports the hypothesis that phylogroup distribution and functions of E. coli strains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Baylie R. Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
- Department of Biology, Loyola University Chicago, Chicago, IL 60660
| | - Alan J. Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
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199
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Awori RM, Waturu CN, Pidot SJ, Amugune NO, Bode HB. Draft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil-dwelling nematodes in Kenya. Access Microbiol 2023; 5:acmi000531.v4. [PMID: 37323942 PMCID: PMC10267655 DOI: 10.1099/acmi.0.000531.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/27/2023] [Indexed: 06/17/2023] Open
Abstract
As a proven source of potent and selective antimicrobials, Xenorhabdus bacteria are important to an age plagued with difficult-to-treat microbial infections. Yet, only 27 species have been described to date. In this study, a novel Xenorhabdus species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and Steinernema isolates VH1 and BG5 were recovered from red volcanic loam soils from cultivated land in Vihiga and clay soils from riverine land in Bungoma respectively. From the two nematode isolates, Xenorhabdus sp. BG5 and Xenorhabdus sp. VH1 were isolated. The genomes of these two, plus that of X. griffiniae XN45 - this was previously isolated from Steinernema sp. scarpo that also originated from Kenyan soils - were sequenced and assembled. Nascent genome assemblies of the three isolates were of good quality with over 70 % of their proteome having known functions. These three isolates formed the X. griffiniae clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, Xenorhabdus sp. BG5, X. griffiniae VH1 and X. griffiniae XN45. A pangenome analysis of this clade revealed that over 70 % of species-specific genes encoded unknown functions. Transposases were linked to genomic islands in Xenorhabdus sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new Xenorhabdus isolates from Kenya, both of which were closely related to X. griffiniae . The functions encoded by most species-specific genes in the X. griffiniae clade remain unknown.
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Affiliation(s)
- Ryan Musumba Awori
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Elakistos Biosciences, PO Box 19301-00100, Nairobi, Kenya
| | - Charles N. Waturu
- Horticulture Research Institute, Kenya Agricultural and Livestock Research Organisation, PO Box 220 Thika
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Nelson O. Amugune
- Department of Biology, University of Nairobi, PO Box 30197-00100, Nairobi, Kenya
| | - Helge B. Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
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200
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Gohil P, Nanavati B, Patel K, Suthar V, Joshi M, Patil DB, Joshi CG. Assessing the efficacy of probiotics in augmenting bovine reproductive health: an integrated in vitro, in silico, and in vivo study. Front Microbiol 2023; 14:1137611. [PMID: 37275132 PMCID: PMC10232901 DOI: 10.3389/fmicb.2023.1137611] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
The aim of this study was to isolate and characterize bovine-vaginal probiotics genotypically and phenotypically using in silico and evaluate their in vivo performance in buffaloes with endometritis. For the in vitro isolation and characterization, vaginal swabs were collected from 34 cows and 17 buffaloes, and 709 primary bacterial isolates with probiotic activity were obtained using MRS agar media. Two isolates Lactiplantibacillus plantarum KUGBRC (LPKUGBRC) and Pediococcus pentosaceus GBRCKU (PPGBRCKU) demonstrated optimum in vitro probiotic activities as compared to Lacticaseibacillus rhamnosus GG including, acid production, secretion of fatty acids and exopolysaccharide, cell surface hydrophobicity, self-aggregating and co-aggregating capacity with pathogens, anti-microbial activity and bacteriocin-like compounds against pathogens Escherichia coli and Staphylococcus aureus in cell-free supernatant and absence of hemolytic activity. Their phenotypic capacity was confirmed by analyzing the whole genome sequencing data and identifying genes and pathways associated with probiotic properties. These probiotic isolates have shown no virulence genes were discovered in their genomic study. In vivo study of 92 buffaloes suffering from clinical endometritis with purulent cervico-vaginal mucus (CVM) were randomly allocated 40 × 108 CFU/ml LPKUGBRC and PPGBRCKU and 40 ml Normal saline. The LPKUGBRC reduced the duration between administration of probiotic to induction of healthy estrus significantly. However, no effect was observed on pregnancy rate. These results suggest that LPKUGBRC and PPGBRCKU probiotic bacteria demonstrate probiotic efficiency and adaptability. Further sourced from the same niche as the targeted infection, they offer a distinct advantage in targeting the specific microbial population associated with endometritis. The findings of this study highlight the potential of LPKUGBRC and PPGBRCKU probiotics in treating endometritis and suggest further exploration of their clinical applications.
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Affiliation(s)
- Purva Gohil
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Bhavya Nanavati
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Kajal Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Vishal Suthar
- Directorate of Research, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Deepak B. Patil
- Directorate of Research, Kamdhenu University, Gandhinagar, Gujarat, India
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