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Kim D, El Khoury S, Pérez-Carrascal OM, DeSousa C, Jung DK, Bohley S, Wijaya L, Trang K, Shapira M. Gut microbiome remodeling provides protection from an environmental toxin. iScience 2025; 28:112209. [PMID: 40230520 PMCID: PMC11995125 DOI: 10.1016/j.isci.2025.112209] [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: 08/22/2024] [Revised: 01/09/2025] [Accepted: 03/10/2025] [Indexed: 04/16/2025] Open
Abstract
Gut microbiomes contribute to animal health and fitness. The immense biochemical diversity of bacteria holds particular potential for neutralizing environmental toxins and thus helping hosts deal with new toxic challenges. To explore this potential, we used Caenorhabditis elegans harboring a defined microbiome, and the antibiotic neomycin as a model toxin, differentially affecting microbiome strains, and also toxic to worms. Worms exposed to neomycin showed delayed development and reduced survival but were protected when colonized with neomycin-resistant Stenotrophomonas. 16S rRNA sequencing, bacterial load quantification, genetic manipulation, and behavioral assays showed that protection was linked to enrichment of Stenotrophomonas carrying a neomycin-modifying enzyme. Enrichment was facilitated by altered bacterial competition in the gut, as well as by KGB-1/JNK-dependent behavioral changes. While microbiome remodeling conferred toxin resistance, it was associated with reduced infection resistance and metabolic changes. These findings suggest that microbiome adaptation can help animals cope with stressors but may have long-term consequences that add to effects of direct intoxication.
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Affiliation(s)
- Dan Kim
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sarah El Khoury
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Catherin DeSousa
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Da Kyung Jung
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Seneca Bohley
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lila Wijaya
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kenneth Trang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Trejo‐Meléndez VJ, Ibarra‐Rendón J, Contreras‐Garduño J. The evolution of entomopathogeny in nematodes. Ecol Evol 2024; 14:e10966. [PMID: 38352205 PMCID: PMC10862191 DOI: 10.1002/ece3.10966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/06/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding how parasites evolved is crucial to understand the host and parasite interaction. The evolution of entomopathogenesis in rhabditid nematodes has traditionally been thought to have occurred twice within the phylum Nematoda: in Steinernematidae and Heterorhabditidae families, which are associated with the entomopathogenic bacteria Xenorhabdus and Photorhabdus, respectively. However, nematodes from other families that are associated with entomopathogenic bacteria have not been considered to meet the criteria for "entomopathogenic nematodes." The evolution of parasitism in nematodes suggests that ecological and evolutionary properties shared by families in the order Rhabditida favor the convergent evolution of the entomopathogenic trait in lineages with diverse lifestyles, such as saprotrophs, phoretic, and necromenic nematodes. For this reason, this paper proposes expanding the term "entomopathogenic nematode" considering the diverse modes of this attribute within Rhabditida. Despite studies are required to test the authenticity of the entomopathogenic trait in the reported species, they are valuable links that represent the early stages of specialized lineages to entomopathogenic lifestyle. An ecological and evolutionary exploration of these nematodes has the potential to deepen our comprehension of the evolution of entomopathogenesis as a convergent trait spanning across the Nematoda.
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Affiliation(s)
- V. J. Trejo‐Meléndez
- Edificio de Investigación I, ENES, Unidad Morelia, UNAMMoreliaMichoacánMexico
- Posgrado en Ciencias Biológicas, ENES, Unidad Morelia, UNAMMoreliaMichoacánMexico
| | - J. Ibarra‐Rendón
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV) – IrapuatoIrapuatoGuanajuatoMexico
| | - J. Contreras‐Garduño
- Edificio de Investigación I, ENES, Unidad Morelia, UNAMMoreliaMichoacánMexico
- Institute for Evolution and BiodiversityUniversity of MünsterMünsterGermany
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