201
|
Microbiome composition modulates secondary metabolism in a multispecies bacterial community. Proc Natl Acad Sci U S A 2022; 119:e2212930119. [PMID: 36215464 PMCID: PMC9586298 DOI: 10.1073/pnas.2212930119] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions and responses to environmental change. Despite the importance of secondary metabolites in human health and microbial ecology, little is known about their roles and regulation in the context of multispecies communities. In a simplified model of the rhizosphere composed of Bacillus cereus, Flavobacterium johnsoniae, and Pseudomonas koreensis, we show that the dynamics of secondary metabolism depend on community species composition and interspecies interactions. Comparative metatranscriptomics and metametabolomics reveal that the abundance of transcripts of biosynthetic gene clusters (BGCs) and metabolomic molecular features differ between monocultures or dual cultures and a tripartite community. In both two- and three-member cocultures, P. koreensis modified expression of BGCs for zwittermicin, petrobactin, and other secondary metabolites in B. cereus and F. johnsoniae, whereas the BGC transcriptional response to the community in P. koreensis itself was minimal. Pairwise and tripartite cocultures with P. koreensis displayed unique molecular features that appear to be derivatives of lokisin, suggesting metabolic handoffs between species. Deleting the BGC for koreenceine, another P. koreensis metabolite, altered transcript and metabolite profiles across the community, including substantial up-regulation of the petrobactin and bacillibactin BGCs in B. cereus, suggesting that koreenceine represses siderophore production. Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.
Collapse
|
202
|
Wang D, Wang Y, Liu L, Chen Y, Wang C, Xu X, Yang Y, Wang Y, Zhang T. Niche differentiation and symbiotic association among ammonia/nitrite oxidizers in a full-scale rotating biological contactor. WATER RESEARCH 2022; 225:119137. [PMID: 36198208 DOI: 10.1016/j.watres.2022.119137] [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: 06/29/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Although the distribution of ammonia/nitrite oxidizers had been profiled in different habitats, current understanding is still limited regarding their niche differentiation in the integrated biofilm reactors, the symbiotic associations of ammonia/nitrite oxidizers, as well as the parasitic interaction between viruses and those functional organisms involved in the nitrogen cycle. Here, the integrated metagenomics and metatranscriptomics are applied to profile the ammonia/nitrite oxidizers communities and transcriptional activities changes along the flowpath of a concatenated full-scale rotating biological contactor (RBC) (frontend Stage-A and backend Stage-B). 19 metagenome-assembled genomes (MAGs) of ammonia/nitrite oxidizers were recovered by using a hybrid assembly approach, including four ammonia-oxidizing bacteria (AOB), two ammonia-oxidizing archaea (AOA), two complete ammonia oxidation bacteria (comammox), eight nitrite-oxidizing bacteria (NOB), and three anaerobic ammonium oxidation bacteria (anammox). Diverse AOB and anammox dominated Stage-A and collectively contributed to nitrogen conversion. With the decline of ammonia concentration along the flowpath, comammox and AOA appeared and increased in relative abundance in Stage-B, accounting for 8.8% of the entire community at the end of this reactor, and their dominating role in nitrogen turnover was indicated by the high transcription activity of their corresponding function genes. Moreover, the variation in the abundance of viruses infecting ammonia and nitrite oxidizers suggests that viruses likely act as a biotic factor mediating ammonia/nitrite oxidizer populations. This study demonstrates that complex factors shaped niche differentiation and symbiotic associations of ammonia/nitrite oxidizers in the RBC and highlights the importance of RBCs as model systems for the investigation of biotic and abiotic factors affecting the composition of microbiomes.
Collapse
Affiliation(s)
- Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yiqiang Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China; School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China; Shenzhen Bay Laboratory, Shenzhen, China.
| |
Collapse
|
203
|
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians. Nat Commun 2022; 13:6044. [PMID: 36229545 PMCID: PMC9561172 DOI: 10.1038/s41467-022-33782-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022] Open
Abstract
Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
Collapse
|
204
|
Hickl O, Queirós P, Wilmes P, May P, Heintz-Buschart A. binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets. Brief Bioinform 2022; 23:6760137. [PMID: 36239393 PMCID: PMC9677464 DOI: 10.1093/bib/bbac431] [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: 06/09/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022] Open
Abstract
The reconstruction of genomes is a critical step in genome-resolved metagenomics and for multi-omic data integration from microbial communities. Here, we present binny, a binning tool that produces high-quality metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes. Based on established metrics, binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods and finds unique genomes that could not be detected by other methods. binny uses k-mer-composition and coverage by metagenomic reads for iterative, nonlinear dimension reduction of genomic signatures as well as subsequent automated contig clustering with cluster assessment using lineage-specific marker gene sets. When compared with seven widely used binning algorithms, binny provides substantial amounts of uniquely identified MAGs and almost always recovers the most near-complete ($\gt 95\%$ pure, $\gt 90\%$ complete) and high-quality ($\gt 90\%$ pure, $\gt 70\%$ complete) genomes from simulated datasets from the Critical Assessment of Metagenome Interpretation initiative, as well as substantially more high-quality draft genomes, as defined by the Minimum Information about a Metagenome-Assembled Genome standard, from a real-world benchmark comprised of metagenomes from various environments than any other tested method.
Collapse
Affiliation(s)
| | | | | | - Patrick May
- Corresponding authors: Patrick May, Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 1 Boulevard du Jazz, L-4370, Esch-sur-Alzette, Luxembourg. Tel: +352 46 6644 6263; E-mail: ; Anna Heintz-Buschart, Biosystems Data Analysis, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands. Tel: +31 020 525 6547; E-mail:
| | - Anna Heintz-Buschart
- Corresponding authors: Patrick May, Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 1 Boulevard du Jazz, L-4370, Esch-sur-Alzette, Luxembourg. Tel: +352 46 6644 6263; E-mail: ; Anna Heintz-Buschart, Biosystems Data Analysis, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands. Tel: +31 020 525 6547; E-mail:
| |
Collapse
|
205
|
Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 2022; 38:5315-5316. [PMID: 36218463 PMCID: PMC9710552 DOI: 10.1093/bioinformatics/btac672] [Citation(s) in RCA: 275] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification. AVAILABILITY AND IMPLEMENTATION GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | - Aaron J Mussig
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | | |
Collapse
|
206
|
Garritano AN, Song W, Thomas T. Carbon fixation pathways across the bacterial and archaeal tree of life. PNAS NEXUS 2022; 1:pgac226. [PMID: 36712370 PMCID: PMC9802188 DOI: 10.1093/pnasnexus/pgac226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 10/01/2022] [Indexed: 11/17/2022]
Abstract
Carbon fixation is a critical process for our planet; however, its distribution across the bacterial and archaeal domains of life has not been comprehensively studied. Here, we performed an analysis of 52,515 metagenome-assembled genomes and discover carbon fixation pathways in 1,007 bacteria and archaea. We reveal the genomic potential for carbon fixation through the reverse tricarboxylic acid cycle in previously unrecognized archaeal and bacterial phyla (i.e. Thermoplasmatota and Elusimicrobiota) and show that the 3-hydroxypropionate bi-cycle is not, as previously thought, restricted to the phylum Chloroflexota. The data also substantially expand the phylogenetic breadth for autotrophy through the dicarboxylate/4-hydroxybutyrate cycle and the Calvin-Benson-Bassham cycle. Finally, the genomic potential for carbon fixation through the 3-hydroxypropionate/4-hydroxybutyrate cycle, previously exclusively found in Archaea, was also detected in the Bacteria. Carbon fixation thus appears to be much more widespread than previously known, and this study lays the foundation to better understand the role of archaea and bacteria in global primary production and how they contribute to microbial carbon sinks.
Collapse
Affiliation(s)
- Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW 2052, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW 2052, Australia
| | | |
Collapse
|
207
|
Zhang X, Huang Y, Liu Y, Xu W, Pan J, Zheng X, Du H, Zhang C, Lu Z, Zou D, Liu Z, Cai M, Xiong J, Zhu Y, Dong Z, Jiang H, Dong H, Jiang J, Luo Z, Huang L, Li M. An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales. Mol Biol Evol 2022; 39:6742362. [PMID: 36181435 PMCID: PMC9585477 DOI: 10.1093/molbev/msac213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.
Collapse
Affiliation(s)
- Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yuhan Huang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huan Du
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Juquan Jiang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng Li
- Corresponding author: E-mail:
| |
Collapse
|
208
|
Díaz Rodríguez CA, Díaz-García L, Bunk B, Spröer C, Herrera K, Tarazona NA, Rodriguez-R LM, Overmann J, Jiménez DJ. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation. ISME COMMUNICATIONS 2022; 2:89. [PMID: 37938754 PMCID: PMC9723784 DOI: 10.1038/s43705-022-00176-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2023]
Abstract
The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.
Collapse
Affiliation(s)
- Carlos Andrés Díaz Rodríguez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, Sheffield, UK
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katherine Herrera
- Department of Civil and Environmental Engineering, Universidad de los Andes, Bogotá, Colombia
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
| |
Collapse
|
209
|
Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe IC, Venter SN, Whitman WB. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat Microbiol 2022; 7:1702-1708. [PMID: 36123442 PMCID: PMC9519449 DOI: 10.1038/s41564-022-01214-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/25/2022] [Indexed: 01/03/2023]
Abstract
Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry ( https://seqco.de/ ), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.
Collapse
Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Spain
| | - Iain C Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | |
Collapse
|
210
|
Imachi H, Nobu MK, Miyazaki M, Tasumi E, Saito Y, Sakai S, Ogawara M, Ohashi A, Takai K. Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study. Nat Protoc 2022; 17:2784-2814. [DOI: 10.1038/s41596-022-00735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
|
211
|
Szydlowski L, Ehlich J, Szczerbiak P, Shibata N, Goryanin I. Novel species identification and deep functional annotation of electrogenic biofilms, selectively enriched in a microbial fuel cell array. Front Microbiol 2022; 13:951044. [PMID: 36188001 PMCID: PMC9517587 DOI: 10.3389/fmicb.2022.951044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, electrogenic microbial communities originating from a single source were multiplied using our custom-made, 96-well-plate-based microbial fuel cell (MFC) array. Developed communities operated under different pH conditions and produced currents up to 19.4 A/m3 (0.6 A/m2) within 2 days of inoculation. Microscopic observations [combined scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS)] revealed that some species present in the anodic biofilm adsorbed copper on their surface because of the bioleaching of the printed circuit board (PCB), yielding Cu2 + ions up to 600 mg/L. Beta- diversity indicates taxonomic divergence among all communities, but functional clustering is based on reactor pH. Annotated metagenomes showed the high presence of multicopper oxidases and Cu-resistance genes, as well as genes encoding aliphatic and aromatic hydrocarbon-degrading enzymes, corresponding to PCB bioleaching. Metagenome analysis revealed a high abundance of Dietzia spp., previously characterized in MFCs, which did not grow at pH 4. Binning metagenomes allowed us to identify novel species, one belonging to Actinotalea, not yet associated with electrogenicity and enriched only in the pH 7 anode. Furthermore, we identified 854 unique protein-coding genes in Actinotalea that lacked sequence homology with other metagenomes. The function of some genes was predicted with high accuracy through deep functional residue identification (DeepFRI), with several of these genes potentially related to electrogenic capacity. Our results demonstrate the feasibility of using MFC arrays for the enrichment of functional electrogenic microbial consortia and data mining for the comparative analysis of either consortia or their members.
Collapse
Affiliation(s)
- Lukasz Szydlowski
- Biological Systems Unit, Okinawa Institute of Science and Technology, Onna, Japan
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- *Correspondence: Lukasz Szydlowski,
| | - Jiri Ehlich
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Pawel Szczerbiak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Noriko Shibata
- Biological Systems Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Igor Goryanin
- Biological Systems Unit, Okinawa Institute of Science and Technology, Onna, Japan
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
- Tianjin Institute of Industrial Biotechnology, Tianjin, China
| |
Collapse
|
212
|
Khan J, Kokot M, Deorowicz S, Patro R. Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2. Genome Biol 2022; 23:190. [PMID: 36076275 PMCID: PMC9454175 DOI: 10.1186/s13059-022-02743-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck. We present Cuttlefish 2, significantly advancing the state-of-the-art for this problem. On a commodity server, it reduces the graph construction time for 661K bacterial genomes, of size 2.58Tbp, from 4.5 days to 17-23 h; and it constructs the graph for 1.52Tbp white spruce reads in approximately 10 h, while the closest competitor requires 54-58 h, using considerably more memory.
Collapse
Affiliation(s)
- Jamshed Khan
- Department of Computer Science, University of Maryland, College Park, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA
| | - Marek Kokot
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Sebastian Deorowicz
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA
| |
Collapse
|
213
|
Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst Appl Microbiol 2022; 45:126305. [PMID: 36049255 PMCID: PMC9489671 DOI: 10.1016/j.syapm.2022.126305] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022]
Abstract
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.
Collapse
Affiliation(s)
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innrain 15 / 01-05, Innsbruck 6020, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| |
Collapse
|
214
|
Zeng S, Patangia D, Almeida A, Zhou Z, Mu D, Paul Ross R, Stanton C, Wang S. A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. Nat Commun 2022; 13:5139. [PMID: 36050292 PMCID: PMC9437082 DOI: 10.1038/s41467-022-32805-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present the Early-Life Gut Genomes (ELGG) catalog with 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography. The ELGG substantially expanded the phylogenetic diversity by 38% over the isolate microbial genomes, and the genomic landscape of the early-life microbiome by increasing recruitment of metagenomic reads to 82.8%. More than 60% of the ELGG species lack an isolate representative. The conspecific genomes of the most abundant species from children differed in gene diversity and functions compared to adults. The ELGG genomes encode over 80 million protein sequences, forming the Early-Life Gut Proteins (ELGP) catalog with over four million protein clusters, 29.5% of which lacked functional annotations. The ELGG and ELGP references provided new insights into the early-life human gut microbiome and will facilitate studies to understand the development and mechanisms of disturbances of the human gut microbiome in early life. Here the authors present a large-scale resource of the early-life human gut microbiome from children under three years old, which comprises 32,277 metagenome-assembled gut genomes, representing 2172 species, and more than 80 million gut proteins representing >4 million protein clusters, spanning multiple clinical factors including age, delivery mode, gestational age, and feeding patterns.
Collapse
Affiliation(s)
- Shuqin Zeng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Dhrati Patangia
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Zhemin Zhou
- Pasteurien College, Medical College of Soochow University, Soochow University, Suzhou, China
| | - Dezhi Mu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
| |
Collapse
|
215
|
Abstract
Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic data sets. We propose a novel approach to automate coassembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous coassembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing coassembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.
Collapse
|
216
|
Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biol 2022; 23:182. [PMID: 36038949 PMCID: PMC9421119 DOI: 10.1186/s13059-022-02735-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/21/2022] [Indexed: 01/22/2023] Open
Abstract
With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. By identifying nucleotides across genomes which share a common ancestor, multiple genome alignments commonly serve as the bedrock for comparative genomics studies. In this review, we provide an overview of the algorithmic template that most multiple genome alignment methods follow. We also discuss prospective areas of improvement of multiple genome alignment for keeping up with continuously arriving high-quality T2T assembled genomes and for unlocking clinically-relevant insights.
Collapse
Affiliation(s)
- Bryce Kille
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Advait Balaji
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael Nute
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA.
| |
Collapse
|
217
|
Zhai Y, Wei C. Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes. Front Microbiol 2022; 13:948138. [PMID: 36081802 PMCID: PMC9445621 DOI: 10.3389/fmicb.2022.948138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.
Collapse
|
218
|
Avalon NE, Murray AE, Baker BJ. Integrated Metabolomic-Genomic Workflows Accelerate Microbial Natural Product Discovery. Anal Chem 2022; 94:11959-11966. [PMID: 35994737 PMCID: PMC9453739 DOI: 10.1021/acs.analchem.2c02245] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pairing of analytical chemistry with genomic techniques represents a new wave in natural product chemistry. With an increase in the availability of sequencing and assembly of microbial genomes, interrogation into the biosynthetic capability of producers with valuable secondary metabolites is possible. However, without the development of robust, accessible, and medium to high throughput tools, the bottleneck in pairing metabolic potential and compound isolation will continue. Several innovative approaches have proven useful in the nascent stages of microbial genome-informed drug discovery. Here, we consider a number of these approaches which have led to prioritization of strain targets and have mitigated rediscovery rates. Likewise, we discuss integration of principles of comparative evolutionary studies and retrobiosynthetic predictions to better understand biosynthetic mechanistic details and link genome sequence to structure. Lastly, we discuss advances in engineering, chemistry, and molecular networking and other computational approaches that are accelerating progress in the field of omic-informed natural product drug discovery. Together, these strategies enhance the synergy between cutting edge omics, chemical characterization, and computational technologies that pitch the discovery of natural products with pharmaceutical and other potential applications to the crest of the wave where progress is ripe for rapid advances.
Collapse
Affiliation(s)
- Nicole E Avalon
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada 89512, United States
| | - Bill J Baker
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| |
Collapse
|
219
|
Lima LFO, Alker AT, Papudeshi B, Morris MM, Edwards RA, de Putron SJ, Dinsdale EA. Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02094-6. [PMID: 35965269 DOI: 10.1007/s00248-022-02094-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.
Collapse
Affiliation(s)
- Laís F O Lima
- Department of Biology, San Diego State University, San Diego, CA, USA
- College of Biological Sciences, University of California Davis, Davis, CA, USA
| | - Amanda T Alker
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Bhavya Papudeshi
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Megan M Morris
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | | | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, San Diego, CA, USA.
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.
| |
Collapse
|
220
|
de Lorenzo V. Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210395. [PMID: 35757882 PMCID: PMC9234819 DOI: 10.1098/rstb.2021.0395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
Collapse
Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
| |
Collapse
|
221
|
Crits-Christoph A, Diamond S, Al-Shayeb B, Valentin-Alvarado L, Banfield JF. A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters. ISME COMMUNICATIONS 2022; 2:70. [PMID: 37938723 PMCID: PMC9723581 DOI: 10.1038/s43705-022-00140-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/11/2022] [Accepted: 06/09/2022] [Indexed: 07/01/2023]
Abstract
Bacteria of the phylum Acidobacteria are one of the most abundant groups across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, genomes of Acidobacteria species with unusually large repertoires of biosynthetic gene clusters (BGCs) were reconstructed from grassland soil metagenomes, but the degree to which species with this trait are widespread is still unknown. To investigate this, we assembled 46 metagenome-assembled genomes recovered from permanently saturated organic-rich soils of a vernal (spring) pool ecosystem in Northern California. We obtained high and medium-quality draft genomes for three novel species from Candidatus Angelobacter (a proposed subdivision 1 Acidobacterial genus), a genus that is genomically enriched in genes for specialized metabolite biosynthesis. Acidobacteria were particularly abundant in the vernal pool sediments, and a Ca. Angelobacter species was the most abundant bacterial species detected in some samples. We identified numerous diverse biosynthetic gene clusters in these genomes, and also in five additional genomes from other publicly available soil metagenomes for other related Ca. Angelobacter species. Metabolic analysis indicates that Ca. Angelobacter likely are aerobes that ferment organic carbon, with potential to contribute to carbon compound turnover in soils. Using metatranscriptomics, we identified in situ metabolic activity and expression of specialized metabolic traits for two species from this genus. In conclusion, we expand genomic sampling of the uncultivated Ca. Angelobacter, and show that they represent common and sometimes highly abundant members of dry and saturated soil communities, with a high degree of capacity for synthesis of diverse specialized metabolites.
Collapse
Affiliation(s)
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
222
|
Silva JM, Pratas D, Caetano T, Matos S. The complexity landscape of viral genomes. Gigascience 2022; 11:6661051. [PMID: 35950839 PMCID: PMC9366995 DOI: 10.1093/gigascience/giac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/25/2022] [Accepted: 07/26/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Viruses are among the shortest yet highly abundant species that harbor minimal instructions to infect cells, adapt, multiply, and exist. However, with the current substantial availability of viral genome sequences, the scientific repertory lacks a complexity landscape that automatically enlights viral genomes' organization, relation, and fundamental characteristics. RESULTS This work provides a comprehensive landscape of the viral genome's complexity (or quantity of information), identifying the most redundant and complex groups regarding their genome sequence while providing their distribution and characteristics at a large and local scale. Moreover, we identify and quantify inverted repeats abundance in viral genomes. For this purpose, we measure the sequence complexity of each available viral genome using data compression, demonstrating that adequate data compressors can efficiently quantify the complexity of viral genome sequences, including subsequences better represented by algorithmic sources (e.g., inverted repeats). Using a state-of-the-art genomic compressor on an extensive viral genomes database, we show that double-stranded DNA viruses are, on average, the most redundant viruses while single-stranded DNA viruses are the least. Contrarily, double-stranded RNA viruses show a lower redundancy relative to single-stranded RNA. Furthermore, we extend the ability of data compressors to quantify local complexity (or information content) in viral genomes using complexity profiles, unprecedently providing a direct complexity analysis of human herpesviruses. We also conceive a features-based classification methodology that can accurately distinguish viral genomes at different taxonomic levels without direct comparisons between sequences. This methodology combines data compression with simple measures such as GC-content percentage and sequence length, followed by machine learning classifiers. CONCLUSIONS This article presents methodologies and findings that are highly relevant for understanding the patterns of similarity and singularity between viral groups, opening new frontiers for studying viral genomes' organization while depicting the complexity trends and classification components of these genomes at different taxonomic levels. The whole study is supported by an extensive website (https://asilab.github.io/canvas/) for comprehending the viral genome characterization using dynamic and interactive approaches.
Collapse
Affiliation(s)
- Jorge Miguel Silva
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Diogo Pratas
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal.,Department of Virology, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
| | - Tânia Caetano
- Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
| | - Sérgio Matos
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
| |
Collapse
|
223
|
Abstract
Anthropogenic organophosphorus compounds (AOPCs), such as phosphotriesters, are used extensively as plasticizers, flame retardants, nerve agents, and pesticides. To date, only a handful of soil bacteria bearing a phosphotriesterase (PTE), the key enzyme in the AOPC degradation pathway, have been identified. Therefore, the extent to which bacteria are capable of utilizing AOPCs as a phosphorus source, and how widespread this adaptation may be, remains unclear. Marine environments with phosphorus limitation and increasing levels of pollution by AOPCs may drive the emergence of PTE activity. Here, we report the utilization of diverse AOPCs by four model marine bacteria and 17 bacterial isolates from the Mediterranean Sea and the Red Sea. To unravel the details of AOPC utilization, two PTEs from marine bacteria were isolated and characterized, with one of the enzymes belonging to a protein family that, to our knowledge, has never before been associated with PTE activity. When expressed in Escherichia coli with a phosphodiesterase, a PTE isolated from a marine bacterium enabled growth on a pesticide analog as the sole phosphorus source. Utilization of AOPCs may provide bacteria a source of phosphorus in depleted environments and offers a prospect for the bioremediation of a pervasive class of anthropogenic pollutants.
Collapse
|
224
|
Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
Collapse
Affiliation(s)
- Pedro Escudeiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Christopher S. Henry
- Argonne National Laboratory, Lemont, Illinois, USA,University of Chicago, Chicago, Illinois, USA
| | - Ricardo P.M. Dias
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,Corresponding author.
| |
Collapse
|
225
|
Begmatov S, Beletsky AV, Dedysh SN, Mardanov AV, Ravin NV. Genome analysis of the candidate phylum MBNT15 bacterium from a boreal peatland predicted its respiratory versatility and dissimilatory iron metabolism. Front Microbiol 2022; 13:951761. [PMID: 35992725 PMCID: PMC9386147 DOI: 10.3389/fmicb.2022.951761] [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: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Uncultured bacteria of the candidate phylum MBNT15, distantly related to Desulfobacterota, have been identified in a broad range of mostly organic-rich aquatic environments. We assembled a near-complete genome of a member of MBNT15 from a boreal peatland metagenome and used genomic data to analyze the metabolic pathways of this bacterium and its ecological role. This bacterium, designated SHF-111, was predicted to be rod shaped, it lacks flagellar machinery but twitching motility is encoded. Genome-based phylogenetic analysis supported the phylum-level classification of the MBNT15 lineage. Genome annotation and metabolic reconstruction revealed the presence of the Embden-Meyerhof, Entner-Doudoroff and pentose phosphate pathways, as well as the complete tricarboxylic acid (TCA) cycle, and suggested a facultatively anaerobic chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, fatty acids and simple sugars, and completely oxidize these substrates through aerobic and anaerobic respiration. The SHF-111 genome encodes multiple multiheme c-type cytochromes that probably enable dissimilatory iron reduction. Consistently, the relative abundance of MBNT15 in peatlands positively correlated with iron concentration. Apparently, in the wetland ecosystem, MBNT15 representatives play the role of scavengers, carrying out the complete mineralization of low molecular weight organic substances formed as a result of microbial degradation of complex polymeric substrates. Comparative genome analysis of the MBNT15 phylum revealed that vast majority of its members are capable of aerobic respiration and dissimilatory iron reduction and some species also can reduce sulfur and nitrogen compounds, but not sulfate. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Deferrimicrobium borealis, within a candidate phylum Deferrimicrobiota.
Collapse
Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
226
|
de la Haba RR, Antunes A, Hedlund BP. Editorial: Extremophiles: Microbial genomics and taxogenomics. Front Microbiol 2022; 13:984632. [PMID: 35983330 PMCID: PMC9379316 DOI: 10.3389/fmicb.2022.984632] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
- *Correspondence: Rafael R. de la Haba
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Macau, Macau SAR, China
- André Antunes
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
- Brian P. Hedlund
| |
Collapse
|
227
|
Diaphorin, a Polyketide Produced by a Bacterial Symbiont of the Asian Citrus Psyllid, Inhibits the Growth and Cell Division of Bacillus subtilis but Promotes the Growth and Metabolic Activity of Escherichia coli. Microbiol Spectr 2022; 10:e0175722. [PMID: 35894614 PMCID: PMC9430481 DOI: 10.1128/spectrum.01757-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diaphorin is a polyketide produced by “Candidatus Profftella armatura” (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin, which is present in D. citri at concentrations of 2 to 20 mM, has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). Their growth and morphological features were analyzed using spectrophotometry, optical microscopy followed by image analysis, and transmission electron microscopy. The metabolic activity of E. coli was further assessed using the β-galactosidase assay. The results revealed that physiological concentrations of diaphorin inhibit the growth and cell division of B. subtilis but promote the growth and metabolic activity of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host plus symbionts) against some bacterial lineages but is metabolically beneficial for others, which potentially include obligate symbionts of D. citri. IMPORTANCE Certain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of microbiomes in animal hosts but also may potentially be exploited to promote the effectiveness of industrial material production by microorganisms.
Collapse
|
228
|
Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification. mSystems 2022; 7:e0035722. [PMID: 35862823 PMCID: PMC9426513 DOI: 10.1128/msystems.00357-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.
Collapse
|
229
|
Dong Y, Tebo BM. Editorial: Insights in Microbiological Chemistry and Geomicrobiology: 2021. Front Microbiol 2022; 13:970474. [PMID: 35903475 PMCID: PMC9325411 DOI: 10.3389/fmicb.2022.970474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China
- *Correspondence: Yiran Dong
| | - Bradley M. Tebo
- Department of Chemistry, University of Washington, Seattle, WA, United States
- Bradley M. Tebo
| |
Collapse
|
230
|
Buck M, Mehrshad M, Bertilsson S. mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation. NAR Genom Bioinform 2022; 4:lqac060. [PMID: 35979445 PMCID: PMC9376867 DOI: 10.1093/nargab/lqac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/25/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled genomes or through single-cell genomes. While this expanded diversity can provide novel insights into microbial population structure, most tools available for core-genome estimation are sensitive to genome completeness. Consequently, a major portion of the huge phylogenetic diversity uncovered by environmental genomic approaches remains excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core genome for sets of genomes of highly diverse completeness range. The likelihood for each gene cluster to belong to core or accessory genome is estimated by computing the probability of its presence/absence pattern in the target genome set. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates to state-of-the-art tools Roary and PPanGGOLiN for high-quality genomes and is capable of using genomes at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.
Collapse
Affiliation(s)
- Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
| |
Collapse
|
231
|
Sereika M, Kirkegaard RH, Karst SM, Michaelsen TY, Sørensen EA, Wollenberg RD, Albertsen M. Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nat Methods 2022; 19:823-826. [PMID: 35789207 PMCID: PMC9262707 DOI: 10.1038/s41592-022-01539-7] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/24/2022] [Indexed: 12/26/2022]
Abstract
Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.
Collapse
Affiliation(s)
- Mantas Sereika
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Rasmus Hansen Kirkegaard
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark.,Joint Microbiome Facility, University of Vienna, Vienna, Austria
| | | | | | | | | | - Mads Albertsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
| |
Collapse
|
232
|
Venturini AM, Gontijo JB, Mandro JA, Paula FS, Yoshiura CA, da França AG, Tsai SM. Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils. Microb Genom 2022; 8. [PMID: 35894927 PMCID: PMC9455692 DOI: 10.1099/mgen.0.000853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.
Collapse
Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, USA
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jéssica A Mandro
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| |
Collapse
|
233
|
Co-Occurrence Relationship and Stochastic Processes Affect Sedimentary Archaeal and Bacterial Community Assembly in Estuarine-Coastal Margins. Microorganisms 2022; 10:microorganisms10071339. [PMID: 35889058 PMCID: PMC9318014 DOI: 10.3390/microorganisms10071339] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/24/2022] Open
Abstract
Sedimentary microorganisms play crucial roles in maintaining the functional stability of aquatic ecosystems. However, their taxonomic composition and assembly processes are not well known in estuarine−coastal margins because of their complex environment. We investigated microbial communities, co-occurrence relationships, and underlying mechanisms in 33 surface sediment samples collected in the Jiulong River Estuary and the Taiwan Strait to reveal their composition dynamics. The abundance, diversity, and composition of microorganisms demonstrated obvious spatial variables. Methanobacterium and Methanosarcina, as well as Candidatus_Nitrosopumilus and Nitrososphaeraceae were the main methanogenic and ammonia-oxidizing archaea, with an average abundance of more than 5.91% and 4.27%, respectively. Along with a salinity gradient increase, the relative abundance of methanogenic archaea (from 42.9% to 16.6%) contrasted with the trend of ammonia-oxidizing archaea (from 6.04% to 18.7%). The number of methanogenic archaea gradually decreased with increasing geographic distance (p < 0.05), whereas ammonia-oxidizing archaea showed no significant change (p > 0.05). In co-occurrence patterns, closer inter-taxa connections were observed among archaea−archaea and bacteria−bacteria than in archaea−bacteria, which indicated that coexistence within the same kingdom was greater than interaction between different kingdoms in shaping the community structure along the salinity gradient. Furthermore, null model analyses of the microbial community showed that undominated was the most prominent process, explaining over 44.9% of community variation, followed by heterogeneous selection and dispersal limitation, which contributed to 27.7% and 16.3%, respectively. We demonstrated that stochasticity, rather than determinism, regulates community assembly. These results further highlight that intra-kingdom co-occurrence and stochastic processes shape the structure and assembly of microbial communities in estuarine−coastal margins.
Collapse
|
234
|
Liu Y, Ji M, Yu T, Zaugg J, Anesio AM, Zhang Z, Hu S, Hugenholtz P, Liu K, Liu P, Chen Y, Luo Y, Yao T. A genome and gene catalog of glacier microbiomes. Nat Biotechnol 2022; 40:1341-1348. [PMID: 35760913 DOI: 10.1038/s41587-022-01367-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/19/2022] [Indexed: 12/31/2022]
Abstract
Glaciers represent a unique inventory of microbial genetic diversity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional diversity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.
Collapse
Affiliation(s)
- Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China. .,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Tao Yu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Julian Zaugg
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St. Lucia, QLD, Australia
| | - Alexandre M Anesio
- Department of Environmental Science, iClimate, Aarhus University, Roskilde, Denmark
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St. Lucia, QLD, Australia
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Pengfei Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Luo
- University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Tandong Yao
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
235
|
Legeay J, Hijri M. A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02060-2. [PMID: 35739325 DOI: 10.1007/s00248-022-02060-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
In the last decade, various large-scale projects describing soil microbial diversity across large geographical gradients have been undertaken. However, many questions remain unanswered about the best ways to conduct these studies. In this review, we present an overview of the experience gathered during these projects, and of the challenges that future projects will face, such as standardization of protocols and results, considering the temporal variation of microbiomes, and the legal constraints limiting such studies. We also present the arguments for and against the exhaustive description of soil microbiomes. Finally, we look at future developments of soil microbiome studies, notably emphasizing the important role of cultivation techniques.
Collapse
Affiliation(s)
- Jean Legeay
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
| | - Mohamed Hijri
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Institut de La Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montreal, QE, H1X 2B2, Canada
| |
Collapse
|
236
|
The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments. Sci Data 2022; 9:305. [PMID: 35715423 PMCID: PMC9205870 DOI: 10.1038/s41597-022-01392-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/12/2022] [Indexed: 12/22/2022] Open
Abstract
Marine microorganisms are immensely diverse and play fundamental roles in global geochemical cycling. Recent metagenome-assembled genome studies, with particular attention to large-scale projects such as Tara Oceans, have expanded the genomic repertoire of marine microorganisms. However, published marine metagenome data is still underexplored. We collected 2,057 marine metagenomes covering various marine environments and developed a new genome reconstruction pipeline. We reconstructed 52,325 qualified genomes composed of 8,466 prokaryotic species-level clusters spanning 59 phyla, including genomes from the deep-sea characterized as deeper than 1,000 m (n = 3,337), low-oxygen zones of <90 μmol O2 per kg water (n = 7,884), and polar regions (n = 7,752). Novelty evaluation using a genome taxonomy database shows that 6,256 species (73.9%) are novel and include genomes of high taxonomic novelty, such as new class candidates. These genomes collectively expanded the known phylogenetic diversity of marine prokaryotes by 34.2%, and the species representatives cover 26.5–42.0% of prokaryote-enriched metagenomes. Thoroughly leveraging accumulated metagenomic data, this genome resource, named the OceanDNA MAG catalog, illuminates uncharacterized marine microbial ‘dark matter’ lineages. Measurement(s) | microbial community | Technology Type(s) | marine metagenome | Sample Characteristic - Organism | Bacteria • Archaea | Sample Characteristic - Environment | marine biome |
Collapse
|
237
|
Improvement of eukaryotic protein predictions from soil metagenomes. Sci Data 2022; 9:311. [PMID: 35710557 PMCID: PMC9203802 DOI: 10.1038/s41597-022-01420-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI’s IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes. Measurement(s) | gene prediction objective | Technology Type(s) | Bioinformatics | Sample Characteristic - Organism | Eukaryota | Sample Characteristic - Environment | bulk soil • rhizosphere • rhizosphere environment | Sample Characteristic - Location | world |
Collapse
|
238
|
Liu Z, Yan Q, Jiang C, Li J, Jian H, Fan L, Zhang R, Xiao X, Meng D, Liu X, Wang J, Yin H. Growth rate determines prokaryote-provirus network modulated by temperature and host genetic traits. MICROBIOME 2022; 10:92. [PMID: 35701838 PMCID: PMC9195381 DOI: 10.1186/s40168-022-01288-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Prokaryote-virus interactions play key roles in driving biogeochemical cycles. However, little is known about the drivers shaping their interaction network structures, especially from the host features. Here, we compiled 7656 species-level genomes in 39 prokaryotic phyla across environments globally and explored how their interaction specialization is constrained by host life history traits, such as growth rate. RESULTS We first reported that host growth rate indicated by the reverse of minimal doubling time was negatively related to interaction specialization for host in host-provirus network across various ecosystems and taxonomy groups. Such a negative linear growth rate-specialization relationship (GrSR) was dependent on host optimal growth temperature (OGT), and stronger toward the two gradient ends of OGT. For instance, prokaryotic species with an OGT ≥ 40 °C showed a stronger GrSR (Pearson's r = -0.525, P < 0.001). Significant GrSRs were observed with the presences of host genes in promoting the infection cycle at stages of adsorption, establishment, and viral release, but nonsignificant with the presence of immune systems, such as restriction-modification systems and CRISPR-Cas systems. Moreover, GrSR strength was increased with the presence of temperature-dependent lytic switches, which was also confirmed by mathematical modeling. CONCLUSIONS Together, our results advance our understanding of the interactions between prokaryotes and proviruses and highlight the importance of host growth rate in interaction specialization during lysogenization. Video Abstract.
Collapse
Affiliation(s)
- Zhenghua Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410125, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, The Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Delong Meng
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Huaqun Yin
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.
| |
Collapse
|
239
|
Olm MR, Dahan D, Carter MM, Merrill BD, Yu FB, Jain S, Meng XD, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science 2022; 376:1220-1223. [PMID: 35679413 PMCID: PMC9894631 DOI: 10.1126/science.abj2972] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species. Industrialized infants-even those who are breastfed-have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.
Collapse
Affiliation(s)
- Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew M. Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hannah Wastyk
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan Holmes
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Corresponding author:
| |
Collapse
|
240
|
Bourquin M, Busi SB, Fodelianakis S, Peter H, Washburne A, Kohler TJ, Ezzat L, Michoud G, Wilmes P, Battin TJ. The microbiome of cryospheric ecosystems. Nat Commun 2022; 13:3087. [PMID: 35655063 PMCID: PMC9163120 DOI: 10.1038/s41467-022-30816-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/20/2022] [Indexed: 01/03/2023] Open
Abstract
The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology. The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires.
Collapse
Affiliation(s)
- Massimo Bourquin
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
| | - Susheel Bhanu Busi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | | | - Tyler J Kohler
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Leïla Ezzat
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg.,Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Tom J Battin
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
| |
Collapse
|
241
|
It’s time for a new type of type to facilitate naming the microbial world. New Microbes New Infect 2022; 47:100991. [PMID: 35800027 PMCID: PMC9253472 DOI: 10.1016/j.nmni.2022.100991] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/09/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Since January 1, 2001, the only acceptable nomenclatural type for species under the International Code of Nomenclature of Prokaryotes (ICNP) has been pure cultures. Here, we argue that this requirement is discordant with the more inclusive nature of nomenclatural types accepted under other codes of nomenclature and posit that the unique rigidity of the ICNP has failed to serve the broad research community and has stifled progress. This case is based on the axiom that many archaea and bacteria are interdependent in nature and therefore difficult, if not impossible, to grow, preserve, and distribute as pure cultures. As such, a large proportion of Earth's biodiversity cannot be named under the current system, which limits our ability to communicate about microbial diversity within and beyond the microbiology research community. Genome sequence data are now encouraged for valid publication of new taxa in microbial systematics journals, and metagenome-assembled genomes and single cell-amplified genomes are being generated rapidly from every biome on Earth. Thus, genome sequences are available for both cultivated and uncultivated microorganisms and can readily serve as a new category of nomenclatural type, allowing for a unified nomenclature for all archaea and bacteria, whether or not they are available as pure cultures. Ideally this would be under a single code of nomenclature but, as we review here, the newly established SeqCode will operate in parallel with the ICNP as a first step toward this goal.
Collapse
|
242
|
Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R. A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. Biotechniques 2022; 73:34-46. [PMID: 35713407 PMCID: PMC9361692 DOI: 10.2144/btn-2022-0032] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.
Collapse
Affiliation(s)
- Justin P Shaffer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carolina S Carpenter
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cameron Martino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
- Bioinformatics & Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Rodolfo A Salido
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, University of California, San Diego, La Jolla, CA 92093, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
- InterOme, Inc. Carlsbad, CA 92008, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
- Micronoma Inc. San Diego, CA 92121, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
243
|
Halter T, Köstlbacher S, Collingro A, Sixt BS, Tönshoff ER, Hendrickx F, Kostanjšek R, Horn M. Ecology and evolution of chlamydial symbionts of arthropods. ISME COMMUNICATIONS 2022; 2:45. [PMID: 37938728 PMCID: PMC9723776 DOI: 10.1038/s43705-022-00124-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 05/08/2023]
Abstract
The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16 S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.
Collapse
Affiliation(s)
- Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Barbara S Sixt
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Elena R Tönshoff
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich (ETH), Zurich, Switzerland
| | | | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| |
Collapse
|
244
|
Barcoto MO, Rodrigues A. Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. Front Microbiol 2022; 13:812143. [PMID: 35685924 PMCID: PMC9171207 DOI: 10.3389/fmicb.2022.812143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.
Collapse
Affiliation(s)
- Mariana O. Barcoto
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| |
Collapse
|
245
|
Lima ST, Fallon TR, Cordoza JL, Chekan JR, Delbaje E, Hopiavuori AR, Alvarenga DO, Wood SM, Luhavaya H, Baumgartner JT, Dörr FA, Etchegaray A, Pinto E, McKinnie SMK, Fiore MF, Moore BS. Biosynthesis of Guanitoxin Enables Global Environmental Detection in Freshwater Cyanobacteria. J Am Chem Soc 2022; 144:9372-9379. [PMID: 35583956 DOI: 10.1021/jacs.2c01424] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Harmful cyanobacterial blooms (cyanoHABs) cause recurrent toxic events in global watersheds. Although public health agencies monitor the causal toxins of most cyanoHABs and scientists in the field continue developing precise detection and prediction tools, the potent anticholinesterase neurotoxin, guanitoxin, is not presently environmentally monitored. This is largely due to its incompatibility with widely employed analytical methods and instability in the environment, despite guanitoxin being among the most lethal cyanotoxins. Here, we describe the guanitoxin biosynthesis gene cluster and its rigorously characterized nine-step metabolic pathway from l-arginine in the cyanobacterium Sphaerospermopsis torques-reginae ITEP-024. Through environmental sequencing data sets, guanitoxin (gnt) biosynthetic genes are repeatedly detected and expressed in municipal freshwater bodies that have undergone past toxic events. Knowledge of the genetic basis of guanitoxin biosynthesis now allows for environmental, biosynthetic gene monitoring to establish the global scope of this neurotoxic organophosphate.
Collapse
Affiliation(s)
- Stella T Lima
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13416-000, Brazil.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Timothy R Fallon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jennifer L Cordoza
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States.,Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Austin R Hopiavuori
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Danillo O Alvarenga
- Department of Biology, University of Copenhagen, Copenhagen, DK 2100, Denmark
| | - Steffaney M Wood
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jackson T Baumgartner
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Felipe A Dörr
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Ribeirao Preto, Sao Paulo 05508-000, Brazil
| | - Augusto Etchegaray
- Center for Life Sciences, Graduate Program in Health Sciences, Pontifical Catholic University of Campinas (PUC-Campinas), Campinas, Sao Paulo 13087-571, Brazil
| | - Ernani Pinto
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Shaun M K McKinnie
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093, United States
| |
Collapse
|
246
|
Smith BJ, Li X, Shi ZJ, Abate A, Pollard KS. Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts. FRONTIERS IN BIOINFORMATICS 2022; 2:867386. [PMID: 36304283 PMCID: PMC9580935 DOI: 10.3389/fbinf.2022.867386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022] Open
Abstract
While genome databases are nearing a complete catalog of species commonly inhabiting the human gut, their representation of intraspecific diversity is lacking for all but the most abundant and frequently studied taxa. Statistical deconvolution of allele frequencies from shotgun metagenomic data into strain genotypes and relative abundances is a promising approach, but existing methods are limited by computational scalability. Here we introduce StrainFacts, a method for strain deconvolution that enables inference across tens of thousands of metagenomes. We harness a “fuzzy” genotype approximation that makes the underlying graphical model fully differentiable, unlike existing methods. This allows parameter estimates to be optimized with gradient-based methods, speeding up model fitting by two orders of magnitude. A GPU implementation provides additional scalability. Extensive simulations show that StrainFacts can perform strain inference on thousands of metagenomes and has comparable accuracy to more computationally intensive tools. We further validate our strain inferences using single-cell genomic sequencing from a human stool sample. Applying StrainFacts to a collection of more than 10,000 publicly available human stool metagenomes, we quantify patterns of strain diversity, biogeography, and linkage-disequilibrium that agree with and expand on what is known based on existing reference genomes. StrainFacts paves the way for large-scale biogeography and population genetic studies of microbiomes using metagenomic data.
Collapse
Affiliation(s)
- Byron J. Smith
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Zhou Jason Shi
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, United States
- Chan-Zuckerberg Biohub, San Francisco, CA, United States
| | - Adam Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
- Chan-Zuckerberg Biohub, San Francisco, CA, United States
| | - Katherine S. Pollard
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
- Chan-Zuckerberg Biohub, San Francisco, CA, United States
- *Correspondence: Katherine S. Pollard,
| |
Collapse
|
247
|
Abstract
Environmental community sequencing is suitable for producing metagenome assembled genomes (MAGs) of prokaryotes, but there is the perception that it cannot work for eukaryotes. In this issue of Cell Genomics, Delmont et al1 process a massive sequencing dataset from marine plankton to produce 683 eukaryotic MAGs; the study also includes useful functional information.
Collapse
Affiliation(s)
- Ramon Massana
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain,Corresponding author
| | - David López-Escardó
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| |
Collapse
|
248
|
Vollmers J, Wiegand S, Lenk F, Kaster AK. How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner. Nucleic Acids Res 2022; 50:e76. [PMID: 35536293 PMCID: PMC9303271 DOI: 10.1093/nar/gkac294] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022] Open
Abstract
As of today, the majority of environmental microorganisms remain uncultured and is therefore referred to as ‘microbial dark matter’ (MDM). Hence, genomic insights into these organisms are limited to cultivation-independent approaches such as single-cell- and metagenomics. However, without access to cultured representatives for verifying correct taxon-assignments, MDM genomes may cause potentially misleading conclusions based on misclassified or contaminant contigs, thereby obfuscating our view on the uncultured microbial majority. Moreover, gradual database contaminations by past genome submissions can cause error propagations which affect present as well as future comparative genome analyses. Consequently, strict contamination detection and filtering need to be applied, especially in the case of uncultured MDM genomes. Current genome reporting standards, however, emphasize completeness over purity and the de facto gold standard genome assessment tool, checkM, discriminates against uncultured taxa and fragmented genomes. To tackle these issues, we present a novel contig classification, screening, and filtering workflow and corresponding open-source python implementation called MDMcleaner, which was tested and compared to other tools on mock and real datasets. MDMcleaner revealed substantial contaminations overlooked by current screening approaches and sensitively detects misattributed contigs in both novel genomes and the underlying reference databases, thereby greatly improving our view on ‘microbial dark matter’.
Collapse
Affiliation(s)
- John Vollmers
- Institute for Biological Interfaces 5 (Institut für Biologische Grenzflächen IBG 5), Karlsruhe Institute of Technology (KIT) 76344, Eggenstein-Leopoldshafen, Germany
| | - Sandra Wiegand
- Institute for Biological Interfaces 5 (Institut für Biologische Grenzflächen IBG 5), Karlsruhe Institute of Technology (KIT) 76344, Eggenstein-Leopoldshafen, Germany
| | - Florian Lenk
- Institute for Biological Interfaces 5 (Institut für Biologische Grenzflächen IBG 5), Karlsruhe Institute of Technology (KIT) 76344, Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (Institut für Biologische Grenzflächen IBG 5), Karlsruhe Institute of Technology (KIT) 76344, Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
249
|
Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
Collapse
Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| |
Collapse
|
250
|
Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E, Frolova A, Mason-Buck G, Iraola G, Jang S, Łabaj P, Lee PKH, Nieto-Caballero M, Osuolale OO, Ouzounis CA, Perlin MH, Prithiviraj B, Rascovan N, Różańska A, Schriml LM, Semmler T, Suzuki H, Ugalde JA, Young B, Werner J, Zambrano MM, Zhao Y, Mason C, Shi T. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. ENVIRONMENTAL RESEARCH 2022; 207:112183. [PMID: 34637759 DOI: 10.1016/j.envres.2021.112183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.
Collapse
Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - David Danko
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Argentina
| | | | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Youping Deng
- University of Hawaii, John A. Burns School of Mecidine, USA
| | - Emmanuel Dias-Neto
- Medical Genomics Group, A.C. Camargo Cancer Center and LIM-27 Faculdade de Medicina, USP, São Paulo, Brazil
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Science of Ukraine, Ukraine
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile; Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Paweł Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Poland
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marina Nieto-Caballero
- University of Colorado at Boulder, Civil, Environmental and Architectural Department, Boulder, 80303, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Nigeria
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas, Thessalonica, GR, 57001, Greece
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA
| | - Bharath Prithiviraj
- Reckitt Health, Montvale, NJ, USA; Dept. of Biology, City University of New York, Brooklyn, 11210, NY, USA
| | - Nicolás Rascovan
- Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, France
| | - Anna Różańska
- Jagiellonian University, Faculty of Medicine, Department of Microbiology, Poland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, USA
| | | | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Germany
| | - Ben Young
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China
| | - Christopher Mason
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
| |
Collapse
|