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Article: Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean.

Coutinho, Felipe Hernandes / Rosselli, Riccardo / Rodríguez-Valera, Francisco

mSystems

2019 Volume 4, Issue 6

Abstract: The evolutionary interactions between viruses and their prokaryotic hosts remain a little-known aspect of microbial evolution. Most studies on this topic were carried out in pure cultures that challenge one virus with one bacterial clone at a time, which ...

Abstract	The evolutionary interactions between viruses and their prokaryotic hosts remain a little-known aspect of microbial evolution. Most studies on this topic were carried out in pure cultures that challenge one virus with one bacterial clone at a time, which is very removed from real-life situations. Few studies have addressed trends of microdiversity in marine viral communities throughout depth gradients. We analyzed metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zones at depths of 15, 45, 60, and 2,000 m during the summer stratification of the water column. We evaluated microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations in viral genes. Our results demonstrated clear depth-dependent trends in the frequency of polymorphic sites and nonsynonymous mutations among genes encoding metabolic, structural, and replication proteins. These differences were linked to changes in energy availability, host and viral densities, and the proportions of actively replicating viruses. We propose the hypothesis that in the energy-rich, high-host-density, euphotic depths, selection acts to favor diversity of the host recognition machinery to increase host range, while in energy-depleted aphotic waters, selection acts on viral replication fitness, enhancing diversity in auxiliary metabolic genes.
Language	English
Publishing date	2019-11-05
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00554-19
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ecological landscape explains aquifers microbial structure.

Barbosa, Felipe A S / Brait, Leonardo A S / Coutinho, Felipe Hernandes / Ferreira, Camilo M / Moreira, Eduardo Freitas / de Queiroz Salles, Lucas / Meirelles, Pedro Milet

The Science of the total environment

2022 , Page(s) 160822

Abstract: Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer ... ...

Abstract	Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.
Language	English
Publishing date	2022-12-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.160822
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Article ; Online: RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.

Coutinho, Felipe Hernandes / Zaragoza-Solas, Asier / López-Pérez, Mario / Barylski, Jakub / Zielezinski, Andrzej / Dutilh, Bas E / Edwards, Robert / Rodriguez-Valera, Francisco

Patterns (New York, N.Y.)

2021 Volume 2, Issue 7, Page(s) 100274

Abstract: Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a ... ...

Abstract	Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.
Language	English
Publishing date	2021-06-15
Publishing country	United States
Document type	Journal Article
ISSN	2666-3899
ISSN (online)	2666-3899
DOI	10.1016/j.patter.2021.100274
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Article ; Online: Genomic basis of antibiotic resistance in Vibrio parahaemolyticus strain JPA1.

Coutinho, Felipe Hernandes / Tschoeke, Diogo Antonio / Clementino, Maysa Mandetta / Thompson, Cristiane Carneiro / Thompson, Fabiano Lopes

Memorias do Instituto Oswaldo Cruz

2019 Volume 114, Page(s) e190053

Abstract: A multi-resistant strain of Vibrio parahaemolyticus was isolated from a tropical estuary in Rio de Janeiro, Brazil. Genome sequencing was conducted to establish the molecular basis of antibiotic resistance in this organism. The genetic content of this ... ...

Abstract	A multi-resistant strain of Vibrio parahaemolyticus was isolated from a tropical estuary in Rio de Janeiro, Brazil. Genome sequencing was conducted to establish the molecular basis of antibiotic resistance in this organism. The genetic content of this strain revealed it to be a non-virulent lineage that nevertheless possesses several antibiotic resistance determinants.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genomics ; Microbial Sensitivity Tests ; Vibrio parahaemolyticus/drug effects ; Vibrio parahaemolyticus/genetics ; Vibrio parahaemolyticus/isolation & purification ; Water Microbiology
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2019-04-25
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	953293-6
ISSN	1678-8060 ; 0074-0276
ISSN (online)	1678-8060
ISSN	0074-0276
DOI	10.1590/0074-02760190053
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Article: The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective.

López-Pérez, Mario / Haro-Moreno, Jose M / Coutinho, Felipe Hernandes / Martinez-Garcia, Manuel / Rodriguez-Valera, Francisco

mSystems

2020 Volume 5, Issue 5

Abstract: The SAR11 clade ... ...

Abstract	The SAR11 clade of
Language	English
Publishing date	2020-10-06
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00605-20
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Article ; Online: Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability.

Haro-Moreno, Jose M / Coutinho, Felipe Hernandes / Zaragoza-Solas, Asier / Picazo, Antonio / Almagro-Moreno, Salvador / López-Pérez, Mario

FEMS microbiology ecology

2020 Volume 96, Issue 12

Abstract: The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we ...

Abstract	The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.
MeSH term(s)	Animals ; Aquaculture ; Bacteria/genetics ; Dysbiosis ; Humans ; Metagenome ; Metagenomics ; Microbiota
Language	English
Publishing date	2020-12-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiaa218
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Article ; Online: Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses.

Coutinho, Felipe Hernandes / Gregoracci, Gustavo Bueno / Walter, Juline Marta / Thompson, Cristiane Carneiro / Thompson, Fabiano L

Trends in microbiology

2018 Volume 26, Issue 11, Page(s) 955–965

Abstract: Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, ... ...

Abstract	Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.
MeSH term(s)	Archaea/genetics ; Archaea/physiology ; Bacteria/genetics ; Bacterial Physiological Phenomena/genetics ; Biodiversity ; Biological Evolution ; Classification ; Cyanobacteria/physiology ; Ecology ; Ecosystem ; Genomics ; Host Microbial Interactions/physiology ; Marine Biology ; Metagenomics ; Seawater/microbiology ; Seawater/virology ; Virus Physiological Phenomena/genetics ; Viruses/genetics
Language	English
Publishing date	2018-06-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2018.05.015
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Article ; Online: Multi-species host range of staphylococcal phages isolated from wastewater.

Göller, Pauline C / Elsener, Tabea / Lorgé, Dominic / Radulovic, Natasa / Bernardi, Viona / Naumann, Annika / Amri, Nesrine / Khatchatourova, Ekaterina / Coutinho, Felipe Hernandes / Loessner, Martin J / Gómez-Sanz, Elena

Nature communications

2021 Volume 12, Issue 1, Page(s) 6965

Abstract: The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 ... ...

Abstract	The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Ecosystem ; Gene Transfer, Horizontal ; Genome, Viral ; Host Specificity ; Microbial Consortia/genetics ; Microbial Sensitivity Tests ; Phylogeny ; Staphylococcus/classification ; Staphylococcus/drug effects ; Staphylococcus/genetics ; Staphylococcus/virology ; Staphylococcus Phages/classification ; Staphylococcus Phages/genetics ; Staphylococcus Phages/isolation & purification ; Wastewater/microbiology ; Wastewater/virology ; Water Microbiology
Chemical Substances	Anti-Bacterial Agents ; Waste Water
Language	English
Publishing date	2021-11-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-27037-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses

Coutinho, Felipe Hernandes / Gustavo Bueno Gregoracci / Juline Marta Walter / Cristiane Carneiro Thompson / Fabiano L. Thompson

Trends in microbiology. 2018 Nov., v. 26, no. 11

2018

Abstract	Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus–host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.
Keywords	Archaea ; Cyanobacteria ; bacteria ; marine ecosystems ; metagenomics ; models ; prokaryotic cells ; viruses
Language	English
Dates of publication	2018-11
Size	p. 955-965.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2018.05.015
Database	NAL-Catalogue (AGRICOLA)

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