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Degregori S, Wang X, Kommala A, Schulhof N, Moradi S, MacDonald A, Eblen K, Jukovich S, Smith E, Kelleher E, Suzuki K, Hall Z, Knight R, Amato KR. Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices. Biol Rev Camb Philos Soc 2025; 100:748-763. [PMID: 39530277 PMCID: PMC11885713 DOI: 10.1111/brv.13161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 10/20/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024]
Abstract
Comparative approaches in animal gut microbiome research have revealed patterns of phylosymbiosis, dietary and physiological convergences, and environment-host interactions. However, most large-scale comparative studies, especially those that are highly cited, have focused on mammals, and efforts to integrate comparative approaches with existing ecological frameworks are lacking. While mammals serve as useful model organisms, developing generalised principles of how animal gut microbiomes are shaped and how these microbiomes interact bidirectionally with host ecology and evolution requires a more complete sampling of the animal kingdom. Here, we provide an overview of what past comparative studies have taught us about the gut microbiome, and how community ecology theory may help resolve certain contradictions in comparative gut microbiome research. We explore whether certain hypotheses are supported across clades, and how the disproportionate focus on mammals has introduced potential bias into gut microbiome theory. We then introduce a methodological solution by which public gut microbiome data of understudied hosts can be compiled and analysed in a comparative context. Our aggregation and analysis of 179 studies shows that generating data sets with rich host diversity is possible with public data and that key gut microbes associated with mammals are widespread across the animal kingdom. We also show the effects that sample size and taxonomic rank have on comparative gut microbiome studies and that results of multivariate analyses can vary significantly with these two parameters. While challenges remain in developing a universal model of the animal gut microbiome, we show that existing ecological frameworks can help bring us one step closer to integrating the gut microbiome into animal ecology and evolution.
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Affiliation(s)
- Samuel Degregori
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Xiaolin Wang
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Akhil Kommala
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Noah Schulhof
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Sadaf Moradi
- Department of Ecology and Evolutionary BiologyUniversity of California621 Young Drive SouthLos AngelesCA90095USA
| | - Allison MacDonald
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Kaitlin Eblen
- Department of Ecology and Evolutionary BiologyUniversity of California621 Young Drive SouthLos AngelesCA90095USA
| | - Sophia Jukovich
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Emma Smith
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Emily Kelleher
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Kota Suzuki
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Zoey Hall
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
| | - Rob Knight
- Department of PediatricsUniversity of CaliforniaSan DiegoLa JollaCA92093USA
| | - Katherine Ryan Amato
- Department of AnthropologyNorthwestern University1810 Hinman AvenueEvanstonIL60208USA
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Oliveira TMP, Rojas MVR, Amorim JA, Alonso DP, de Carvalho DP, Ribeiro KAN, Sallum MAM. Bacterial diversity on larval and female Mansonia spp. from different localities of Porto Velho, Rondonia, Brazil. PLoS One 2023; 18:e0293946. [PMID: 38011160 PMCID: PMC10681206 DOI: 10.1371/journal.pone.0293946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/21/2023] [Indexed: 11/29/2023] Open
Abstract
Studies based on the bacterial diversity present in Mansonia spp. are limited; therefore, the aim of this study was to investigate the bacterial diversity in females and larvae of Mansonia spp., describe the differences between the groups identified, and compare the microbiota of larvae from different collection sites. Sequences of the 16S rRNA region from the larvae and females of Mansonia spp. were analyzed. Diversity analyzes were performed to verify the possible bacterial differences between the groups and the collection sites. The results showed Pseudomonas was the most abundant genus in both females and larvae, followed by Wolbachia in females and Rikenellaceae and Desulfovibrio in larvae. Desulfovibrio and Sulfurospirillum, sulfate- and sulfur-reducing bacteria, respectively, were abundant on the larvae. Aminomonas, an amino acid-degrading bacterium, was found only in larvae, whereas Rickettsia was identified in females. Bacterial diversity was observed between females and larvae of Mansonia and between larvae from different collection sites. In addition, the results suggest that the environment influenced bacterial diversity.
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Affiliation(s)
- Tatiane M. P. Oliveira
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Martha V. R. Rojas
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jandui A. Amorim
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Diego P. Alonso
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
- Instituto de Biotecnologia da UNESP (IBTEC-Campus Botucatu), Botucatu, SP, Brazil
| | | | | | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
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Mateos-Hernández L, Maitre A, Abuin-Denis L, Obregon D, Martin E, Luis P, Maye J, Wu-Chuang A, Valiente Moro C, Cabezas-Cruz A. Hierarchical shift of the Aedes albopictus microbiota caused by antimicrobiota vaccine increases fecundity and egg-hatching rate in female mosquitoes. FEMS Microbiol Ecol 2023; 99:fiad140. [PMID: 37898556 DOI: 10.1093/femsec/fiad140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/16/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023] Open
Abstract
Recent studies show that mosquito-microbiota interactions affects vector competence and fitness. We investigated if host antibodies modifying microbiota impact mosquito physiology. We focused on three prevalent bacteria (Acinetobacter, Pantoea, and Chryseobacterium), originally isolated from the Asian tiger mosquito Aedes albopictus. Our goal was to assess the impact of host antibodies on mosquito microbiota and life traits. Female mosquitoes were fed with blood from rabbits immunized with each bacterium or a mock vaccine. We compared various factors, including feeding behavior, survival rates, and reproductive success of the mosquitoes. Interestingly, mosquitoes fed with blood from a Chryseobacterium-immunized rabbit showed a significant increase in fecundity and egg-hatching rate. This outcome correlated with a decrease in the abundance of Chryseobacterium within the mosquito microbiota. While no significant changes were observed in the alpha and beta diversity indexes between the groups, our network analyses revealed an important finding. The antimicrobiota vaccines had a considerable impact on the bacterial community assembly. They reduced network robustness, and altered the hierarchical organization of nodes in the networks. Our findings provide the basis for the rational design of antimicrobiota vaccines to reduce mosquito fitness and potentially induce infection-refractory states in the microbiota to block pathogen transmission.
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Affiliation(s)
- Lourdes Mateos-Hernández
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
| | - Apolline Maitre
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMETLRDE), Corte 20250, France
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte 20250, France
| | - Lianet Abuin-Denis
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 between 158 and 190, P.O. Box 6162, Havana 10600, Cuba
| | - Dasiel Obregon
- School of Environmental Sciences University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Edwige Martin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne 69622, France
| | - Patricia Luis
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne 69622, France
| | - Jennifer Maye
- SEPPIC Paris La Défense, La Garenne Colombes 92250, France
| | - Alejandra Wu-Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
| | - Claire Valiente Moro
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne 69622, France
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort 94701, France
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Bacterial Community Diversity and Bacterial Interaction Network in Eight Mosquito Species. Genes (Basel) 2022; 13:genes13112052. [DOI: 10.3390/genes13112052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
Abstract
Mosquitoes (Diptera: Culicidae) are found widely throughout the world. Several species can transmit pathogens to humans and other vertebrates. Mosquitoes harbor great amounts of bacteria, fungi, and viruses. The bacterial composition of the microbiota of these invertebrates is associated with several factors, such as larval habitat, environment, and species. Yet little is known about bacterial interaction networks in mosquitoes. This study investigates the bacterial communities of eight species of Culicidae collected in Vale do Ribeira (Southeastern São Paulo State) and verifies the bacterial interaction network in these species. Sequences of the 16S rRNA region from 111 mosquito samples were analyzed. Bacterial interaction networks were generated from Spearman correlation values. Proteobacteria was the predominant phylum in all species. Wolbachia was the predominant genus in Haemagogus leucocelaenus. Aedes scapularis, Aedes serratus, Psorophora ferox, and Haemagogus capricornii were the species that showed a greater number of bacterial interactions. Bacterial positive interactions were found in all mosquito species, whereas negative correlations were observed in Hg. leucocelaenus, Ae. scapularis, Ae. serratus, Ps. ferox, and Hg. capricornii. All bacterial interactions with Asaia and Wolbachia were negative in Aedes mosquitoes.
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