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Worsley SF, Davies CS, Lee CZ, Mannarelli ME, Burke T, Komdeur J, Dugdale HL, Richardson DS. Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population. Mol Ecol 2024:e17477. [PMID: 39010794 DOI: 10.1111/mec.17477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 07/17/2024]
Abstract
In humans, gut microbiome (GM) differences are often correlated with, and sometimes causally implicated in, ageing. However, it is unclear how these findings translate in wild animal populations. Studies that investigate how GM dynamics change within individuals, and with declines in physiological condition, are needed to fully understand links between chronological age, senescence and the GM, but have rarely been done. Here, we use longitudinal data collected from a closed population of Seychelles warblers (Acrocephalus sechellensis) to investigate how bacterial GM alpha diversity, composition and stability are associated with host senescence. We hypothesised that GM diversity and composition will differ, and become more variable, in older adults, particularly in the terminal year prior to death, as the GM becomes increasingly dysregulated due to senescence. However, GM alpha diversity and composition remained largely invariable with respect to adult age and did not differ in an individual's terminal year. Furthermore, there was no evidence that the GM became more heterogenous in senescent age groups (individuals older than 6 years), or in the terminal year. Instead, environmental variables such as season, territory quality and time of day, were the strongest predictors of GM variation in adult Seychelles warblers. These results contrast with studies on humans, captive animal populations and some (but not all) studies on non-human primates, suggesting that GM deterioration may not be a universal hallmark of senescence in wild animal species. Further work is needed to disentangle the factors driving variation in GM-senescence relationships across different host taxa.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | - Chuen Zhang Lee
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | | | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Nature Seychelles, Mahé, Republic of Seychelles
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2
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Bellomo AR, Rotondi G, Rago P, Bloise S, Di Ruzza L, Zingoni A, Di Valerio S, Valzano E, Di Pierro F, Cazzaniga M, Bertuccioli A, Guasti L, Zerbinati N, Lubrano R. Effect of Bifidobacterium bifidum Supplementation in Newborns Born from Cesarean Section on Atopy, Respiratory Tract Infections, and Dyspeptic Syndromes: A Multicenter, Randomized, and Controlled Clinical Trial. Microorganisms 2024; 12:1093. [PMID: 38930475 PMCID: PMC11205812 DOI: 10.3390/microorganisms12061093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
Cesarean section is considered a possible trigger of atopy and gut dysbiosis in newborns. Bifidobacteria, and specifically B. bifidum, are thought to play a central role in reducing the risk of atopy and in favoring gut eubiosis in children. Nonetheless, no trial has ever prospectively investigated the role played by this single bacterial species in preventing atopic manifestations in children born by cesarean section, and all the results published so far refer to mixtures of probiotics. We have therefore evaluated the impact of 6 months of supplementation with B. bifidum PRL2010 on the incidence, in the first year of life, of atopy, respiratory tract infections, and dyspeptic syndromes in 164 children born by cesarean (versus 249 untreated controls). The results of our multicenter, randomized, and controlled trial have shown that the probiotic supplementation significantly reduced the incidence of atopic dermatitis, upper and lower respiratory tract infections, and signs and symptoms of dyspeptic syndromes. Concerning the gut microbiota, B. bifidum supplementation significantly increased α-biodiversity and the relative values of the phyla Bacteroidota and Actinomycetota, of the genus Bacteroides, Bifidobacterium and of the species B. bifidum and reduced the relative content of Escherichia/Shigella and Haemophilus. A 6-month supplementation with B. bifidum in children born by cesarean section reduces the risk of gut dysbiosis and has a positive clinical impact that remains observable in the following 6 months of follow-up.
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Affiliation(s)
- Anna Rita Bellomo
- Dipartimento Materno Infantile e di Scienze Urologiche, Sapienza Università di Roma, UOC di Pediatria e Neonatologia-Polo Pontino, 04100 Latina, Italy; (A.R.B.); (P.R.)
| | - Giulia Rotondi
- Pediatric Surgery Unit, Gaslini Children Hospital and Research Institute, 16147 Genoa, Italy
| | - Prudenza Rago
- Dipartimento Materno Infantile e di Scienze Urologiche, Sapienza Università di Roma, UOC di Pediatria e Neonatologia-Polo Pontino, 04100 Latina, Italy; (A.R.B.); (P.R.)
| | - Silvia Bloise
- Dipartimento Materno Infantile e di Scienze Urologiche, Sapienza Università di Roma, UOC di Pediatria e Neonatologia-Polo Pontino, 04100 Latina, Italy; (A.R.B.); (P.R.)
| | - Luigi Di Ruzza
- UOC Pediatria e Nido, Ospedale S.S. Trinità, 03039 Sora, Italy
| | - Annamaria Zingoni
- UOC Pediatria e Neonatologia, Ospedale G.B. Grassi, 00122 Ostia, Italy
| | - Susanna Di Valerio
- UOC Neonatologia e Terapia Intensiva Neonatale, Ospedale S. Spirito, 65124 Pescara, Italy
| | - Eliana Valzano
- UOC Neonatologia e Terapia Intensiva Neonatale, Ospedale S. Spirito, 65124 Pescara, Italy
| | - Francesco Di Pierro
- Scientific & Research Department, Velleja Research, 20125 Milan, Italy
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | | | - Alexander Bertuccioli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy;
| | - Luigina Guasti
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Nicola Zerbinati
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Riccardo Lubrano
- Dipartimento Materno Infantile e di Scienze Urologiche, Sapienza Università di Roma, UOC di Pediatria e Neonatologia-Polo Pontino, 04100 Latina, Italy; (A.R.B.); (P.R.)
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3
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Pereira H, Chakarov N, Hoffman JI, Rinaud T, Ottensmann M, Gladow KP, Tobias B, Caspers BA, Maraci Ö, Krüger O. Early-life factors shaping the gut microbiota of Common buzzard nestlings. Anim Microbiome 2024; 6:27. [PMID: 38745254 DOI: 10.1186/s42523-024-00313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors. RESULTS We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition. CONCLUSION Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.
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Affiliation(s)
- Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany.
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Department of Evolutionary Population Genetics, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Kai-Philipp Gladow
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Busche Tobias
- Medical School East Westphalia-Lippe & Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, NRW, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
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Du H, Liu J, Jude KM, Yang X, Li Y, Bell B, Yang H, Kassardjian A, Mobedi A, Parekh U, Sperberg RAP, Julien JP, Mellins ED, Garcia KC, Huang PS. A general platform for targeting MHC-II antigens via a single loop. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577489. [PMID: 38352315 PMCID: PMC10862749 DOI: 10.1101/2024.01.26.577489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Class-II major histocompatibility complexes (MHC-IIs) are central to the communications between CD4+ T cells and antigen presenting cells (APCs), but intrinsic structural features associated with MHC-II make it difficult to develop a general targeting system with high affinity and antigen specificity. Here, we introduce a protein platform, Targeted Recognition of Antigen-MHC Complex Reporter for MHC-II (TRACeR-II), to enable the rapid development of peptide-specific MHC-II binders. TRACeR-II has a small helical bundle scaffold and uses an unconventional mechanism to recognize antigens via a single loop. This unique antigen-recognition mechanism renders this platform highly versatile and amenable to direct structural modeling of the interactions with the antigen. We demonstrate that TRACeR-II binders can be rapidly evolved across multiple alleles, while computational protein design can produce specific binding sequences for a SARS-CoV-2 peptide of unknown complex structure. TRACeR-II sheds light on a simple and straightforward approach to address the MHC peptide targeting challenge, without relying on combinatorial selection on complementarity determining region (CDR) loops. It presents a promising basis for further exploration in immune response modulation as well as a broad range of theragnostic applications.
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Affiliation(s)
- Haotian Du
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jingjia Liu
- Department of Bioengineering, Stanford University, CA, USA
| | - Kevin M. Jude
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xinbo Yang
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ying Li
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Braxton Bell
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Hongli Yang
- Department of Bioengineering, Stanford University, CA, USA
| | - Audrey Kassardjian
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ali Mobedi
- Department of Bioengineering, Stanford University, CA, USA
| | - Udit Parekh
- Department of Bioengineering, Stanford University, CA, USA
| | | | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Elizabeth D. Mellins
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - K. Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, CA, USA
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Otálora-Otálora BA, López-Rivera JJ, Aristizábal-Guzmán C, Isaza-Ruget MA, Álvarez-Moreno CA. Host Transcriptional Regulatory Genes and Microbiome Networks Crosstalk through Immune Receptors Establishing Normal and Tumor Multiomics Metafirm of the Oral-Gut-Lung Axis. Int J Mol Sci 2023; 24:16638. [PMID: 38068961 PMCID: PMC10706695 DOI: 10.3390/ijms242316638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/13/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
The microbiome has shown a correlation with the diet and lifestyle of each population in health and disease, the ability to communicate at the cellular level with the host through innate and adaptative immune receptors, and therefore an important role in modulating inflammatory process related to the establishment and progression of cancer. The oral cavity is one of the most important interaction windows between the human body and the environment, allowing the entry of an important number of microorganisms and their passage across the gastrointestinal tract and lungs. In this review, the contribution of the microbiome network to the establishment of systemic diseases like cancer is analyzed through their synergistic interactions and bidirectional crosstalk in the oral-gut-lung axis as well as its communication with the host cells. Moreover, the impact of the characteristic microbiota of each population in the formation of the multiomics molecular metafirm of the oral-gut-lung axis is also analyzed through state-of-the-art sequencing techniques, which allow a global study of the molecular processes involved of the flow of the microbiota environmental signals through cancer-related cells and its relationship with the establishment of the transcription factor network responsible for the control of regulatory processes involved with tumorigenesis.
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Affiliation(s)
| | - Juan Javier López-Rivera
- Grupo de Investigación INPAC, Specialized Laboratory, Clinica Universitaria Colombia, Clínica Colsanitas S.A., Bogotá 111321, Colombia;
| | - Claudia Aristizábal-Guzmán
- Grupo de Investigación INPAC, Unidad de Investigación, Fundación Universitaria Sanitas, Bogotá 110131, Colombia;
| | - Mario Arturo Isaza-Ruget
- Keralty, Sanitas International Organization, Grupo de Investigación INPAC, Fundación Universitaria Sanitas, Bogotá 110131, Colombia;
| | - Carlos Arturo Álvarez-Moreno
- Infectious Diseases Department, Clinica Universitaria Colombia, Clínica Colsanitas S.A., Bogotá 111321, Colombia;
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Florkowski MR, Hamer SA, Yorzinski JL. Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome. FEMS Microbiol Ecol 2023; 99:fiad096. [PMID: 37586886 DOI: 10.1093/femsec/fiad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/07/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.
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Affiliation(s)
- Melanie R Florkowski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
| | - Sarah A Hamer
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Schubot Center for Avian Health, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 701 Farm to Market Service Road, College Station, TX 77840, United States
| | - Jessica L Yorzinski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Department of Ecology and Conservation Biology, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
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7
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Liukkonen M, Hukkanen M, Cossin-Sevrin N, Stier A, Vesterinen E, Grond K, Ruuskanen S. No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings. Anim Microbiome 2023; 5:19. [PMID: 36949549 PMCID: PMC10031902 DOI: 10.1186/s42523-023-00241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured. RESULTS Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival. CONCLUSIONS We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland.
| | - Mikaela Hukkanen
- Department of Biology, University of Turku, Turku, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622, Lyon, France
- Institut Pluridisciplinaire Hubert Curien, UMR7178, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Department of Biology, University of Turku, Turku, Finland
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8
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Ma Y, He J, Sieber M, von Frieling J, Bruchhaus I, Baines JF, Bickmeyer U, Roeder T. The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity. Commun Biol 2023; 6:289. [PMID: 36934156 PMCID: PMC10024726 DOI: 10.1038/s42003-023-04671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/07/2023] [Indexed: 03/20/2023] Open
Abstract
The close association between animals and their associated microbiota is usually beneficial for both partners. Here, we used a simple marine model invertebrate, the flatworm Macrostomum lignano, to characterize the host-microbiota interaction in detail. This analysis revealed that the different developmental stages each harbor a specific microbiota. Studies with gnotobiotic animals clarified the physiological significance of the microbiota. While no fitness benefits were mediated by the microbiota when food was freely available, animals with microbiota showed significantly increased fitness with a reduced food supply. The microbiota of M. lignano shows circadian rhythmicity, affecting both the total bacterial load and the behavior of specific taxa. Moreover, the presence of the worm influences the composition of the bacterial consortia in the environment. In summary, the Macrostomum-microbiota system described here can serve as a general model for host-microbe interactions in marine invertebrates.
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Affiliation(s)
- Yuanyuan Ma
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Jinru He
- Kiel University, Zoological Institute, Cell and Developmental Biology, Kiel, Germany
| | - Michael Sieber
- Max-Planck Institute for Evolutionary Biology, Dept. Evolutionary Theory, Plön, Germany
| | - Jakob von Frieling
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Iris Bruchhaus
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John F Baines
- Kiel University, Medical Faculty, Institute for Experimental Medicine, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, Group Evolutionary Medicine, Plön, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institute, Biosciences, Ecological Chemistry, Bremerhaven, Germany
| | - Thomas Roeder
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany.
- German Center for Lung Research (DZL), Airway Research Center North, Kiel, Germany.
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9
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Worsley SF, Davies CS, Mannarelli ME, Komdeur J, Dugdale HL, Richardson DS. Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler. MICROBIOME 2022; 10:242. [PMID: 36575553 PMCID: PMC9795730 DOI: 10.1186/s40168-022-01432-7] [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: 07/25/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Considerable research has focussed on the importance of bacterial communities within the vertebrate gut microbiome (GM). However, studies investigating the significance of other microbial kingdoms, such as fungi, are notably lacking, despite their potential to influence host processes. Here, we characterise the fungal GM of individuals living in a natural population of Seychelles warblers (Acrocephalus sechellensis). We evaluate the extent to which fungal GM structure is shaped by environment and host factors, including genome-wide heterozygosity and variation at key immune genes (major histocompatibility complex (MHC) and Toll-like receptor (TLR)). Importantly, we also explore the relationship between fungal GM differences and subsequent host survival. To our knowledge, this is the first time that the genetic drivers and fitness consequences of fungal GM variation have been characterised for a wild vertebrate population. RESULTS Environmental factors, including season and territory quality, explain the largest proportion of variance in the fungal GM. In contrast, neither host age, sex, genome-wide heterozygosity, nor TLR3 genotype was associated with fungal GM differences in Seychelles warblers. However, the presence of four MHC-I alleles and one MHC-II allele was associated with changes in fungal GM alpha diversity. Changes in fungal richness ranged from between 1 and 10 sequencing variants lost or gained; in some cases, this accounted for 20% of the fungal variants carried by an individual. In addition to this, overall MHC-I allelic diversity was associated with small, but potentially important, changes in fungal GM composition. This is evidenced by the fact that fungal GM composition differed between individuals that survived or died within 7 months of being sampled. CONCLUSIONS Our results suggest that environmental factors play a primary role in shaping the fungal GM, but that components of the host immune system-specifically the MHC-may also contribute to the variation in fungal communities across individuals within wild populations. Furthermore, variation in the fungal GM can be associated with differential survival in the wild. Further work is needed to establish the causality of such relationships and, thus, the extent to which components of the GM may impact host evolution. Video Abstract.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Maria-Elena Mannarelli
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles.
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