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11 pages, 5 figures, 1 table, supplementary information https://doi.org/10.1038/s41396-021-00900-6 ; Bacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach ('PhageFISH-CLEM') localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts ; We acknowledge funding by the DFG CRC1182 to UH (TPC4.3), TL (TPC4.2). MTJ was supported by a grant of the German Excellence Initiative to the Graduate School of Life Sciences, University of Wuerzburg, and a Young Investigator Award of the CRC1182. SMM was supported by the Studienstiftung des Deutschen Volkes (German Academic Scholarship Foundation). CS was supported by the grants DFG STI700/1-1 and GRK2581 (P6). MR was supported by the Spanish Government grant (RTI2018-094187-B100) and 'Generalitat de Catalunya' research group grant (2017SGR1011). BED was supported by the Netherlands Organisation for Scientific Research (NWO) Vidi grant 864.14.004 and by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI. /./ Open Access funding enabled and organized by Projekt DEA ; With the funding support of the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI) ; Peer reviewed

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host-gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host–gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.

Funding Information: E.M.A. gratefully acknowledges funding by the U.K. Biotechnology and Biological Sciences Research Council (BBSRC); this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. A.J.D. is supported by the U.K. Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN128309). N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF); the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. H.M.O was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC. D.L.R. is supported by the U.K. Medical Research Council (MC_UU_1201412). R.J.O. and D.B.S. are supported by the Wellcome Trust (WT108418AIA). S.S. acknowledges partial support from the Special Research Initiative (MAFES), Mississippi State University, and from the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services, or of the institutions and companies affiliated with the authors. Publisher Copyright: © 2021, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply. ; This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of 'virus' and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes. ; publishersversion ; inpress