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Fields C. The free energy principle induces intracellular compartmentalization. Biochem Biophys Res Commun 2024; 723:150070. [PMID: 38896995 DOI: 10.1016/j.bbrc.2024.150070] [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: 10/21/2023] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 06/21/2024]
Abstract
Living systems at all scales are compartmentalized into interacting subsystems. This paper reviews a mechanism that drives compartmentalization in generic systems at any scale. It first discusses three symmetries of generic physical interactions in a quantum-theoretic description. It then shows that if one of these, a permutation symmetry on the inter-system boundary, is spontaneously broken, the symmetry breaking is amplified by the Free Energy Principle (FEP). It thus shows how compartmentalization generically results from permutation symmetry breaking under the FEP. It finally notes that the FEP asymptotically restores the broken symmetry, showing that the FEP can be regarded as a theory of fluctuations away from a permutation-symmetric boundary, and hence from an entangled joint state of the interacting systems.
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Affiliation(s)
- Chris Fields
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
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2
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Chatterjee S, Leach ST, Lui K, Mishra A. Symbiotic symphony: Understanding host-microbiota dialogues in a spatial context. Semin Cell Dev Biol 2024; 161-162:22-30. [PMID: 38564842 DOI: 10.1016/j.semcdb.2024.03.001] [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: 10/31/2023] [Revised: 02/23/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Modern precision sequencing techniques have established humans as a holobiont that live in symbiosis with the microbiome. Microbes play an active role throughout the life of a human ranging from metabolism and immunity to disease tolerance. Hence, it is of utmost significance to study the eukaryotic host in conjunction with the microbial antigens to obtain a complete picture of the host-microbiome crosstalk. Previous attempts at profiling host-microbiome interactions have been either superficial or been attempted to catalogue eukaryotic transcriptomic profile and microbial communities in isolation. Additionally, the nature of such immune-microbial interactions is not random but spatially organised. Hence, for a holistic clinical understanding of the interplay between hosts and microbiota, it's imperative to concurrently analyze both microbial and host genetic information, ensuring the preservation of their spatial integrity. Capturing these interactions as a snapshot in time at their site of action has the potential to transform our understanding of how microbes impact human health. In examining early-life microbial impacts, the limited presence of communities compels analysis within reduced biomass frameworks. However, with the advent of spatial transcriptomics we can address this challenge and expand our horizons of understanding these interactions in detail. In the long run, simultaneous spatial profiling of host-microbiome dialogues can have enormous clinical implications especially in gaining mechanistic insights into the disease prognosis of localised infections and inflammation. This review addresses the lacunae in host-microbiome research and highlights the importance of profiling them together to map their interactions while preserving their spatial context.
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Affiliation(s)
- Soumi Chatterjee
- Telethon Kids Institute, Perth Children Hospital, Perth, Western Australia 6009, Australia; Curtin Medical School, Curtin University, Perth, Western Australia 6102, Australia
| | - Steven T Leach
- Discipline Paediatrics, School of Clinical Medicine, University of New South Wales, Sydney 2052, Australia
| | - Kei Lui
- Department of Newborn Care, Royal Hospital for Women and Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine, University of New South Wales, Sydney 2052, Australia
| | - Archita Mishra
- Telethon Kids Institute, Perth Children Hospital, Perth, Western Australia 6009, Australia; Curtin Medical School, Curtin University, Perth, Western Australia 6102, Australia.
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3
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Buchanan CE, Galla SJ, Muscarella ME, Forbey JS, Reinking AK, Beck JL. Relating gut microbiome composition and life history metrics for pronghorn (Antilocapra americana) in the Red Desert, Wyoming. PLoS One 2024; 19:e0306722. [PMID: 38985706 PMCID: PMC11236126 DOI: 10.1371/journal.pone.0306722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Host microbial communities (hereafter, the 'microbiome') are recognized as an important aspect of host health and are gaining attention as a useful biomarker to understand the ecology and demographics of wildlife populations. Several studies indicate that the microbiome may contribute to the adaptive capacity of animals to changing environments associated with increasing habitat fragmentation and rapid climate change. To this end, we investigated the gut microbiome of pronghorn (Antilocapra americana), an iconic species in an environment that is undergoing both climatic and anthropogenic change. The bacterial composition of the pronghorn gut microbiome has yet to be described in the literature, and thus our study provides important baseline information about this species. We used 16S rRNA amplicon sequencing of fecal samples to characterize the gut microbiome of pronghorn-a facultative sagebrush (Artemisia spp.) specialist in many regions where they occur in western North America. We collected fecal pellets from 159 captured female pronghorn from four herds in the Red Desert of Wyoming during winters of 2013 and 2014. We found small, but significant differences in diversity of the gut microbiome relative to study area, capture period, and body fat measurements. In addition, we found a difference in gut microbiome composition in pronghorn across two regions separated by Interstate 80. Results indicated that the fecal microbiome may be a potential biomarker for the spatial ecology of free-ranging ungulates. The core gut microbiome of these animals-including bacteria in the phyla Firmicutes (now Bacillota) and Bacteroidota-remained relatively stable across populations and biological metrics. These findings provide a baseline for the gut microbiome of pronghorn that could potentially be used as a target in monitoring health and population structure of pronghorn relative to habitat fragmentation, climate change, and management practices.
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Affiliation(s)
- Courtney E Buchanan
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, United States of America
| | - Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, Idaho, United States of America
| | - Mario E Muscarella
- Institute of Arctic Biology and Department of Biology & Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Jennifer S Forbey
- Department of Biological Sciences, Boise State University, Boise, Idaho, United States of America
| | - Adele K Reinking
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, United States of America
- Cooperative Institute for Research in the Atmosphere, Colorado State University, Fort Collins, Colorado, United States of America
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey L Beck
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, United States of America
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4
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Capp JP, Catania F, Thomas F. From genetic mosaicism to tumorigenesis through indirect genetic effects. Bioessays 2024; 46:e2300238. [PMID: 38736323 DOI: 10.1002/bies.202300238] [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: 12/13/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024]
Abstract
Genetic mosaicism has long been linked to aging, and several hypotheses have been proposed to explain the potential connections between mosaicism and susceptibility to cancer. It has been proposed that mosaicism may disrupt tissue homeostasis by affecting intercellular communications and releasing microenvironmental constraints within tissues. The underlying mechanisms driving these tissue-level influences remain unidentified, however. Here, we present an evolutionary perspective on the interplay between mosaicism and cancer, suggesting that the tissue-level impacts of genetic mosaicism can be attributed to Indirect Genetic Effects (IGEs). IGEs can increase the level of cellular stochasticity and phenotypic instability among adjacent cells, thereby elevating the risk of cancer development within the tissue. Moreover, as cells experience phenotypic changes in response to challenging microenvironmental conditions, these changes can initiate a cascade of nongenetic alterations, referred to as Indirect non-Genetic Effects (InGEs), which in turn catalyze IGEs among surrounding cells. We argue that incorporating both InGEs and IGEs into our understanding of the process of oncogenic transformation could trigger a major paradigm shift in cancer research with far-reaching implications for practical applications.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Francesco Catania
- Institute of Environmental Radioactivity, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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Leonard A, Alberdi A. A global initiative for ecological and evolutionary hologenomics. Trends Ecol Evol 2024; 39:616-620. [PMID: 38777633 DOI: 10.1016/j.tree.2024.03.005] [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: 12/22/2023] [Revised: 03/11/2024] [Accepted: 03/20/2024] [Indexed: 05/25/2024]
Abstract
The Earth Hologenome Initiative (EHI) is a global collaboration to generate and analyse hologenomic data from wild animals and associated microorganisms using standardised methodologies underpinned by open and inclusive research principles. Initially focused on vertebrates, it aims to re-examine ecological and evolutionary questions by studying host-microbiota interactions from a systemic perspective.
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Affiliation(s)
- Aoife Leonard
- Center for Evolutionary Hologenomics (CEH), Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics (CEH), Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen, Denmark.
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Larzul C, Estellé J, Borey M, Blanc F, Lemonnier G, Billon Y, Thiam MG, Quinquis B, Galleron N, Jardet D, Lecardonnel J, Plaza Oñate F, Rogel-Gaillard C. Driving gut microbiota enterotypes through host genetics. MICROBIOME 2024; 12:116. [PMID: 38943206 PMCID: PMC11214205 DOI: 10.1186/s40168-024-01827-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 05/01/2024] [Indexed: 07/01/2024]
Abstract
BACKGROUND Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits. RESULTS We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively. CONCLUSION We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. Video Abstract.
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Grants
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- Enterotypig Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- ANR-11-DPBS-0001 Agence Nationale de la Recherche
- ANR-11-DPBS-0001 Agence Nationale de la Recherche
- ANR-11-DPBS-0001 Agence Nationale de la Recherche
- ANR-11-DPBS-0001 Agence Nationale de la Recherche
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Affiliation(s)
- Catherine Larzul
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, 31326, France.
| | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France.
| | - Marion Borey
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - Gaëtan Lemonnier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | | | | | - Benoît Quinquis
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, 78350, France
| | | | - Deborah Jardet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - Jérôme Lecardonnel
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
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Buschi E, Dell’Anno A, Tangherlini M, Candela M, Rampelli S, Turroni S, Palladino G, Esposito E, Martire ML, Musco L, Stefanni S, Munari C, Fiori J, Danovaro R, Corinaldesi C. Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome. SCIENCE ADVANCES 2024; 10:eadk9117. [PMID: 38905343 PMCID: PMC11192080 DOI: 10.1126/sciadv.adk9117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.
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Affiliation(s)
- Emanuela Buschi
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luigi Musco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica “Anton Dohrn,” Villa Comunale, Napoli, Italy
| | - Cristina Munari
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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8
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Herlemann DPR, Tammert H, Kivistik C, Käiro K, Kisand V. Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water. Microbiologyopen 2024; 13:e13. [PMID: 38825966 PMCID: PMC11144953 DOI: 10.1002/mbo3.1413] [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: 01/30/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 06/04/2024] Open
Abstract
The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.
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Affiliation(s)
- Daniel P. R. Herlemann
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Department of Biological OceanographyLeibniz Institute for Baltic Sea Research Warnemünde (IOW)RostockGermany
| | - Helen Tammert
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Institute of TechnologyUniversity of TartuTartuEstonia
| | - Carmen Kivistik
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
| | - Kairi Käiro
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
| | - Veljo Kisand
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Institute of TechnologyUniversity of TartuTartuEstonia
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Nanes Sarfati D, Xue Y, Song ES, Byrne A, Le D, Darmanis S, Quake SR, Burlacot A, Sikes J, Wang B. Coordinated wound responses in a regenerative animal-algal holobiont. Nat Commun 2024; 15:4032. [PMID: 38740753 DOI: 10.1038/s41467-024-48366-2] [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: 06/20/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Animal regeneration involves coordinated responses across cell types throughout the animal body. In endosymbiotic animals, whether and how symbionts react to host injury and how cellular responses are integrated across species remain unexplored. Here, we study the acoel Convolutriloba longifissura, which hosts symbiotic Tetraselmis sp. green algae and can regenerate entire bodies from tissue fragments. We show that animal injury causes a decline in the photosynthetic efficiency of the symbiotic algae, alongside two distinct, sequential waves of transcriptional responses in acoel and algal cells. The initial algal response is characterized by the upregulation of a cohort of photosynthesis-related genes, though photosynthesis is not necessary for regeneration. A conserved animal transcription factor, runt, is induced after injury and required for acoel regeneration. Knockdown of Cl-runt dampens transcriptional responses in both species and further reduces algal photosynthetic efficiency post-injury. Our results suggest that the holobiont functions as an integrated unit of biological organization by coordinating molecular networks across species through the runt-dependent animal regeneration program.
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Affiliation(s)
| | - Yuan Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Eun Sun Song
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | | | - Daniel Le
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Adrien Burlacot
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - James Sikes
- Department of Biology, University of San Francisco, San Francisco, CA, USA.
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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10
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Habteweld A, Kantor M, Kantor C, Handoo Z. Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors. FRONTIERS IN PLANT SCIENCE 2024; 15:1377453. [PMID: 38745927 PMCID: PMC11091308 DOI: 10.3389/fpls.2024.1377453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.
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Affiliation(s)
- Alemayehu Habteweld
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD, United States
| | - Mihail Kantor
- Plant Pathology and Environmental Microbiology Department, Pennsylvania State University, University Park, PA, United States
| | - Camelia Kantor
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, United States
| | - Zafar Handoo
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD, United States
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11
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Whiting-Fawcett F, Blomberg AS, Troitsky T, Meierhofer MB, Field KA, Puechmaille SJ, Lilley TM. A Palearctic view of a bat fungal disease. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024:e14265. [PMID: 38616727 DOI: 10.1111/cobi.14265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/02/2024] [Accepted: 01/20/2024] [Indexed: 04/16/2024]
Abstract
The fungal infection causing white-nose disease in hibernating bats in North America has resulted in dramatic population declines of affected species, since the introduction of the causative agent Pseudogymnoascus destructans. The fungus is native to the Palearctic, where it also infects several bat species, yet rarely causes severe pathology or the death of the host. Pseudogymnoascus destructans infects bats during hibernation by invading and digesting the skin tissue, resulting in the disruption of torpor patterns and consequent emaciation. Relations among pathogen, host, and environment are complex, and individuals, populations, and species respond to the fungal pathogen in different ways. For example, the Nearctic Myotis lucifugus responds to infection by mounting a robust immune response, leading to immunopathology often contributing to mortality. In contrast, the Palearctic M. myotis shows no significant immunological response to infection. This lack of a strong response, resulting from the long coevolution between the hosts and the pathogen in the pathogen's native range, likely contributes to survival in tolerant species. After more than 15 years since the initial introduction of the fungus to North America, some of the affected populations are showing signs of recovery, suggesting that the fungus, hosts, or both are undergoing processes that may eventually lead to coexistence. The suggested or implemented management methods of the disease in North America have encompassed, for example, the use of probiotics and fungicides, vaccinations, and modifying the environmental conditions of the hibernation sites to limit the growth of the pathogen, intensity of infection, or the hosts' responses to it. Based on current knowledge from Eurasia, policy makers and conservation managers should refrain from disrupting the ongoing evolutionary processes and adopt a holistic approach to managing the epizootic.
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Affiliation(s)
- F Whiting-Fawcett
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - A S Blomberg
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - T Troitsky
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - M B Meierhofer
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - K A Field
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
| | - S J Puechmaille
- Institut des Sciences de l'Évolution Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - T M Lilley
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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Schwob G, Cabrol L, Saucède T, Gérard K, Poulin E, Orlando J. Unveiling the co-phylogeny signal between plunderfish Harpagifer spp. and their gut microbiomes across the Southern Ocean. Microbiol Spectr 2024; 12:e0383023. [PMID: 38441978 PMCID: PMC10986581 DOI: 10.1128/spectrum.03830-23] [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: 11/01/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Understanding the factors that sculpt fish gut microbiome is challenging, especially in natural populations characterized by high environmental and host genomic complexity. However, closely related hosts are valuable models for deciphering the contribution of host evolutionary history to microbiome assembly, through the underscoring of phylosymbiosis and co-phylogeny patterns. Here, we propose that the recent diversification of several Harpagifer species across the Southern Ocean would allow the detection of robust phylogenetic congruence between the host and its microbiome. We characterized the gut mucosa microbiome of 77 individuals from four field-collected species of the plunderfish Harpagifer (Teleostei, Notothenioidei), distributed across three biogeographic regions of the Southern Ocean. We found that seawater physicochemical properties, host phylogeny, and geography collectively explained 35% of the variation in bacterial community composition in Harpagifer gut mucosa. The core microbiome of Harpagifer spp. gut mucosa was characterized by a low diversity, mostly driven by selective processes, and dominated by a single Aliivibrio Operational Taxonomic Unit (OTU) detected in more than 80% of the individuals. Nearly half of the core microbiome taxa, including Aliivibrio, harbored co-phylogeny signal at microdiversity resolution with host phylogeny, indicating an intimate symbiotic relationship and a shared evolutionary history with Harpagifer. The clear phylosymbiosis and co-phylogeny signals underscore the relevance of the Harpagifer model in understanding the role of fish evolutionary history in shaping the gut microbiome assembly. We propose that the recent diversification of Harpagifer may have led to the diversification of Aliivibrio, exhibiting patterns that mirror the host phylogeny. IMPORTANCE Although challenging to detect in wild populations, phylogenetic congruence between marine fish and its microbiome is critical, as it highlights intimate associations between hosts and ecologically relevant microbial symbionts. Our study leverages a natural system of closely related fish species in the Southern Ocean to unveil new insights into the contribution of host evolutionary trajectory on gut microbiome assembly, an underappreciated driver of the global marine fish holobiont. Notably, we unveiled striking evidence of co-diversification between Harpagifer and its microbiome, demonstrating both phylosymbiosis of gut bacterial communities and co-phylogeny of some specific bacterial symbionts, mirroring the host diversification patterns. Given Harpagifer's significance as a trophic resource in coastal areas and its vulnerability to climatic and anthropic pressures, understanding the potential evolutionary interdependence between the hosts and its microbiome provides valuable microbial candidates for future monitoring, as they may play a pivotal role in host species acclimatization to a rapidly changing environment.
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Affiliation(s)
- Guillaume Schwob
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
| | - Léa Cabrol
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France, Marseille, France
| | - Thomas Saucède
- UMR 6282 Biogeosciences, University Bourgogne Franche-Comté, CNRS, EPHE, Dijon, France
| | - Karin Gérard
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Laboratory of Antarctic and Subantarctic Marine Ecosystems, Faculty of Sciences, University of Magallanes, Punta Arenas, Chile
- Cape Horn International Center, Puerto Williams, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
| | - Julieta Orlando
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
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13
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Wiley KS, Gregg AM, Fox MM, Lagishetty V, Sandman CA, Jacobs JP, Glynn LM. Contact with caregivers is associated with composition of the infant gastrointestinal microbiome in the first 6 months of life. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24858. [PMID: 37804008 PMCID: PMC10922139 DOI: 10.1002/ajpa.24858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/18/2023] [Accepted: 09/24/2023] [Indexed: 10/08/2023]
Abstract
OBJECTIVES Little is known about how physical contact at birth and early caregiving environments influence the colonization of the infant gastrointestinal microbiome. We investigated how infant contact with caregivers at birth and within the first 2 weeks of life relates to the composition of the gastrointestinal microbiome in a sample of U.S. infants (n = 60). METHODS Skin-to-skin and physical contact with caregivers at birth and early caregiving environments were surveyed at 2 weeks postpartum. Stool samples were collected from infants at 2 weeks, 2, 6, and 12 months of age and underwent 16S rRNA sequencing as a proxy for the gastrointestinal microbiome. Associations between early caregiving environments and alpha and beta diversity, and differential abundance of bacteria at the genus level were assessed using PERMANOVA, and negative binomial mixed models in DEseq2. RESULTS Time in physical contact with caregivers explained 10% of variation in beta diversity at 2 weeks' age. The number of caregivers in the first few weeks of life explained 9% of variation in beta diversity at 2 weeks and the number of individuals in physical contact at birth explained 11% of variation in beta diversity at 6 months. Skin-to-skin contact on the day of birth was positively associated with the abundance of eight genera. Infants held for by more individuals had greater abundance of eight genera. DISCUSSION Results reveal a potential mechanism (skin-to-skin and physical contact) by which caregivers influence the infant gastrointestinal microbiome. Our findings contribute to work exploring the social transmission of microbes.
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Affiliation(s)
- Kyle S Wiley
- Department of Anthropology, UCLA, Los Angeles, California, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, California, USA
| | - Andrew M Gregg
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Molly M Fox
- Department of Anthropology, UCLA, Los Angeles, California, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, California, USA
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Curt A Sandman
- Department of Psychiatry and Human Behavior, UC Irvine, Irvine, California, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Laura M Glynn
- Department of Psychology, Chapman University, Orange, California, USA
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Efremova J, Mazzella V, Mirasole A, Teixidó N, Núñez-Pons L. Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170171. [PMID: 38246375 DOI: 10.1016/j.scitotenv.2024.170171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
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Affiliation(s)
- Jana Efremova
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
| | - Valerio Mazzella
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Alice Mirasole
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Núria Teixidó
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy; Laboratoire d'Océanographie de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
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15
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Burgunter-Delamare B, Shetty P, Vuong T, Mittag M. Exchange or Eliminate: The Secrets of Algal-Bacterial Relationships. PLANTS (BASEL, SWITZERLAND) 2024; 13:829. [PMID: 38592793 PMCID: PMC10974524 DOI: 10.3390/plants13060829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Algae and bacteria have co-occurred and coevolved in common habitats for hundreds of millions of years, fostering specific associations and interactions such as mutualism or antagonism. These interactions are shaped through exchanges of primary and secondary metabolites provided by one of the partners. Metabolites, such as N-sources or vitamins, can be beneficial to the partner and they may be assimilated through chemotaxis towards the partner producing these metabolites. Other metabolites, especially many natural products synthesized by bacteria, can act as toxins and damage or kill the partner. For instance, the green microalga Chlamydomonas reinhardtii establishes a mutualistic partnership with a Methylobacterium, in stark contrast to its antagonistic relationship with the toxin producing Pseudomonas protegens. In other cases, as with a coccolithophore haptophyte alga and a Phaeobacter bacterium, the same alga and bacterium can even be subject to both processes, depending on the secreted bacterial and algal metabolites. Some bacteria also influence algal morphology by producing specific metabolites and micronutrients, as is observed in some macroalgae. This review focuses on algal-bacterial interactions with micro- and macroalgal models from marine, freshwater, and terrestrial environments and summarizes the advances in the field. It also highlights the effects of temperature on these interactions as it is presently known.
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Affiliation(s)
- Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
| | - Prateek Shetty
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Trang Vuong
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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16
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Piccini C, Martínez de la Escalera G, Segura AM, Croci C, Kruk C. The Microcystis-microbiome interactions: origins of the colonial lifestyle. FEMS Microbiol Ecol 2024; 100:fiae035. [PMID: 38499447 PMCID: PMC10996927 DOI: 10.1093/femsec/fiae035] [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: 01/04/2024] [Revised: 02/21/2024] [Accepted: 03/16/2024] [Indexed: 03/20/2024] Open
Abstract
Species of the Microcystis genus are the most common bloom-forming toxic cyanobacteria worldwide. They belong to a clade of unicellular cyanobacteria whose ability to reach high biomasses during blooms is linked to the formation of colonies. Colonial lifestyle provides several advantages under stressing conditions of light intensity, ultraviolet light, toxic substances and grazing. The progression from a single-celled organism to multicellularity in Microcystis has usually been interpreted as individual phenotypic responses of the cyanobacterial cells to the environment. Here, we synthesize current knowledge about Microcystis colonial lifestyle and its role in the organism ecology. We then briefly review the available information on Microcystis microbiome and propose that changes leading from single cells to colonies are the consequence of specific and tightly regulated signals between the cyanobacterium and its microbiome through a biofilm-like mechanism. The resulting colony is a multi-specific community of interdependent microorganisms.
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Affiliation(s)
- Claudia Piccini
- Departamento de Microbiología, Centro de Investigación en Ciencias Ambientales, Instituto de Investigaciones Biológicas Clemente Estable. Av. Italia 3318, Montevideo 11600, Uruguay
| | - Gabriela Martínez de la Escalera
- Departamento de Microbiología, Centro de Investigación en Ciencias Ambientales, Instituto de Investigaciones Biológicas Clemente Estable. Av. Italia 3318, Montevideo 11600, Uruguay
| | - Angel M Segura
- Modelización Estadística de Datos e Inteligencia Artificial, Centro Universitario Regional del Este, Universidad de la República. Ruta nacional Nº9 intersección con ruta Nº15, Uruguay
| | - Carolina Croci
- Departamento de Microbiología, Centro de Investigación en Ciencias Ambientales, Instituto de Investigaciones Biológicas Clemente Estable. Av. Italia 3318, Montevideo 11600, Uruguay
| | - Carla Kruk
- Modelización Estadística de Datos e Inteligencia Artificial, Centro Universitario Regional del Este, Universidad de la República. Ruta nacional Nº9 intersección con ruta Nº15, Uruguay
- Sección Limnología, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República. Iguá 4225, Montevideo 11400, Uruguay
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17
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Raza W, Jiang G, Eisenhauer N, Huang Y, Wei Z, Shen Q, Kowalchuk GA, Jousset A. Microbe-induced phenotypic variation leads to overyielding in clonal plant populations. Nat Ecol Evol 2024; 8:392-399. [PMID: 38195997 DOI: 10.1038/s41559-023-02297-1] [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: 12/23/2022] [Accepted: 12/06/2023] [Indexed: 01/11/2024]
Abstract
Overyielding, the high productivity of multispecies plant communities, is commonly seen as the result of plant genetic diversity. Here we demonstrate that biodiversity-ecosystem functioning relationships can emerge in clonal plant populations through interaction with microorganisms. Using a model clonal plant species, we found that exposure to volatiles of certain microorganisms led to divergent plant phenotypes. Assembling communities out of plants associated with different microorganisms led to transgressive overyielding in both biomass and seed yield. Our results highlight the importance of belowground microbial diversity in plant biodiversity research and open new avenues for precision ecosystem management.
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Affiliation(s)
- Waseem Raza
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, the Netherlands
| | - Gaofei Jiang
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Yishuo Huang
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhong Wei
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.
| | - Qirong Shen
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - George A Kowalchuk
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, the Netherlands
| | - Alexandre Jousset
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.
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18
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Hyder M, Lodhi AM, Wang Z, Bukero A, Gao J, Mao R. Wolbachia Interactions with Diverse Insect Hosts: From Reproductive Modulations to Sustainable Pest Management Strategies. BIOLOGY 2024; 13:151. [PMID: 38534421 DOI: 10.3390/biology13030151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
Effective in a variety of insect orders, including dipteran, lepidopteran, and hemipteran, Wolbachia-based control tactics are investigated, noting the importance of sterile and incompatible insect techniques. Encouraging approaches for controlling Aedes mosquitoes are necessary, as demonstrated by the evaluation of a new SIT/IIT combination and the incorporation of SIT into Drosophila suzukii management. For example, Wolbachia may protect plants from rice pests, demonstrating its potential for agricultural biological vector management. Maternal transmission and cytoplasmic incompatibility dynamics are explored, while Wolbachia phenotypic impacts on mosquito and rice pest management are examined. The importance of host evolutionary distance is emphasised in recent scale insect research that addresses host-shifting. Using greater information, a suggested method for comprehending Wolbachia host variations in various contexts emphasises ecological connectivity. Endosymbionts passed on maternally in nematodes and arthropods, Wolbachia are widely distributed around the world and have evolved both mutualistic and parasitic traits. Wolbachia is positioned as a paradigm for microbial symbiosis due to advancements in multiomics, gene functional assays, and its effect on human health. The challenges and opportunities facing Wolbachia research include scale issues, ecological implications, ethical conundrums, and the possibility of customising strains through genetic engineering. It is thought that cooperative efforts are required to include Wolbachia-based therapies into pest management techniques while ensuring responsible and sustainable ways.
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Affiliation(s)
- Moazam Hyder
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Abdul Mubeen Lodhi
- Department Plant Protection, Sindh Agriculture University, Tandojam 70080, Pakistan
| | - Zhaohong Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Aslam Bukero
- Department of Entomology, Sindh Agriculture University, Tandojam 70080, Pakistan
| | - Jing Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Runqian Mao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
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Tanger IS, Stefanschitz J, Schwert Y, Roth O. The source of microbial transmission influences niche colonization and microbiome development. Proc Biol Sci 2024; 291:20232036. [PMID: 38320611 PMCID: PMC10846951 DOI: 10.1098/rspb.2023.2036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
Early life microbial colonizers shape and support the immature vertebrate immune system. Microbial colonization relies on the vertical route via parental provisioning and the horizontal route via environmental contribution. Vertical transmission is mostly a maternal trait making it hard to determine the source of microbial colonization in order to gain insight into the establishment of the microbial community during crucial development stages. The evolution of unique male pregnancy in pipefishes and seahorses enables the disentanglement of both horizontal and vertical transmission, but also facilitates the differentiation of maternal versus paternal provisioning ranging from egg development, to male pregnancy and early juvenile development. Using 16S rRNA amplicon sequencing and source-tracker analyses, we revealed how the distinct origins of transmission (maternal, paternal and horizontal) shaped the juvenile internal and external microbiome establishment in the broad-nosed pipefish Syngnathus typhle. Our data suggest that transovarial maternal microbial contribution influences the establishment of the juvenile gut microbiome whereas paternal provisioning mainly shapes the juvenile external microbiome. The identification of juvenile key microbes reveals crucial temporal shifts in microbial development and enhances our understanding of microbial transmission routes, colonization dynamics and their impact on lifestyle evolution.
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Affiliation(s)
- Isabel S. Tanger
- GEOMAR, Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Düsternbrookerweg 20, 24105 Kiel, Germany
- Zoological Institute, Marine Evolutionary Biology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Julia Stefanschitz
- GEOMAR, Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Düsternbrookerweg 20, 24105 Kiel, Germany
| | - Yannick Schwert
- Zoological Institute, Marine Evolutionary Biology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Olivia Roth
- GEOMAR, Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Düsternbrookerweg 20, 24105 Kiel, Germany
- Zoological Institute, Marine Evolutionary Biology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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20
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Nguyen JB, Marshall CW, Cook CN. The buzz within: the role of the gut microbiome in honeybee social behavior. J Exp Biol 2024; 227:jeb246400. [PMID: 38344873 DOI: 10.1242/jeb.246400] [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] [Indexed: 02/15/2024]
Abstract
Gut symbionts influence the physiology and behavior of their host, but the extent to which these effects scale to social behaviors is an emerging area of research. The use of the western honeybee (Apis mellifera) as a model enables researchers to investigate the gut microbiome and behavior at several levels of social organization. Insight into gut microbial effects at the societal level is critical for our understanding of how involved microbial symbionts are in host biology. In this Commentary, we discuss recent findings in honeybee gut microbiome research and synthesize these with knowledge of the physiology and behavior of other model organisms to hypothesize how host-microbe interactions at the individual level could shape societal dynamics and evolution.
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Affiliation(s)
- J B Nguyen
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - C W Marshall
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - C N Cook
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
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21
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González-Pech RA, Li VY, Garcia V, Boville E, Mammone M, Kitano H, Ritchie KB, Medina M. The Evolution, Assembly, and Dynamics of Marine Holobionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:443-466. [PMID: 37552896 DOI: 10.1146/annurev-marine-022123-104345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.
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Affiliation(s)
- Raúl A González-Pech
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vivian Y Li
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vanessa Garcia
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Elizabeth Boville
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Marta Mammone
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina, Beaufort, South Carolina, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
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22
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Yan K, Lu DS, Ding CJ, Wang Y, Tian YR, Su XH, Dong YF, Wang YP. Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168216. [PMID: 37923276 DOI: 10.1016/j.scitotenv.2023.168216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R2 = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry.
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Affiliation(s)
- Kun Yan
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - De Shan Lu
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Chang Jun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yan Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Yong Ren Tian
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Xiao Hua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | | | - Yan Ping Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China.
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23
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Dosi A, Meziti A, Tounta E, Koemtzopoulos K, Komnenou A, Dendrinos P, Kormas K. Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation. Microbiol Spectr 2024; 12:e0280523. [PMID: 38084980 PMCID: PMC10783143 DOI: 10.1128/spectrum.02805-23] [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: 07/09/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.
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Affiliation(s)
- Aggeliki Dosi
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Eleni Tounta
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Kimon Koemtzopoulos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Anastasia Komnenou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
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24
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Boem F, Greslehner GP, Konsman JP, Chiu L. Minding the gut: extending embodied cognition and perception to the gut complex. Front Neurosci 2024; 17:1172783. [PMID: 38260022 PMCID: PMC10800657 DOI: 10.3389/fnins.2023.1172783] [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: 02/23/2023] [Accepted: 10/30/2023] [Indexed: 01/24/2024] Open
Abstract
Scientific and philosophical accounts of cognition and perception have traditionally focused on the brain and external sense organs. The extended view of embodied cognition suggests including other parts of the body in these processes. However, one organ has often been overlooked: the gut. Frequently conceptualized as merely a tube for digesting food, there is much more to the gut than meets the eye. Having its own enteric nervous system, sometimes referred to as the "second brain," the gut is also an immune organ and has a large surface area interacting with gut microbiota. The gut has been shown to play an important role in many physiological processes, and may arguably do so as well in perception and cognition. We argue that proposals of embodied perception and cognition should take into account the role of the "gut complex," which considers the enteric nervous, endocrine, immune, and microbiota systems as well as gut tissue and mucosal structures. The gut complex is an interface between bodily tissues and the "internalized external environment" of the gut lumen, involved in many aspects of organismic activity beyond food intake. We thus extend current embodiment theories and suggest a more inclusive account of how to "mind the gut" in studying cognitive processes.
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Affiliation(s)
- Federico Boem
- Section Philosophy, University of Twente, Enschede, Netherlands
| | | | - Jan Pieter Konsman
- IMMUNOlogy from CONcepts and ExPeriments to Translation, CNRS UMR, University of Bordeaux, Bordeaux, France
| | - Lynn Chiu
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
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25
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Wang Y, Gao P, Qin W, Li H, Zheng J, Meng L, Li B. Gut microbiota variation across generations regarding the diet and life stage in Harmonia axyridis (Coleoptera: Coccinellidae). INSECT SCIENCE 2024. [PMID: 38183402 DOI: 10.1111/1744-7917.13310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 01/08/2024]
Abstract
We attempt to determine the effect of the dietary switch from a native to non-native prey on the gut microbiota in the predaceous ladybird Harmonia axyridis larvae and adults and examine how the dietary effect may vary across generations. We fed H. axyridis with different diets, native aphid Megoura japonica (Matsumura) versus non-native mealybug Phenacoccus solenopsis (Tinsley), for 5 generations and sequenced microbes in the gut of the 3rd instar larvae and adults of the 1st, 3rd, and 5th generations. In addition, we identified microbes in M. japonica and P. solenopsis. The 2 prey species differed in microbial community as measured by abundances of prevalent microbial genera and diversity. In H. axyridis, abundances of some prevalent microbial genera differed between the 2 diets in the 1st and 3rd generations, but the difference disappeared in the 5th generation; this tendency is more obvious in adults than in larvae. Overall, gut microbial assemblages became gradually cohesive over generations. Microbial diversity differed between diets in the 1st and 3rd generations but became similar in the 5th generation. Major prevalent gut microbial genera are predicted to be associated with metabolic functions of H. axyridis and associated genera are more abundant for consuming the mealybug than the aphid. Our findings from this study suggest that the gut microbiota in H. axyridis is flexible in response to the dietary switch, but tends toward homogeneity in microbial composition over generations.
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Affiliation(s)
- Yansong Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ping Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Wenquan Qin
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hongran Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jie Zheng
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ling Meng
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Baoping Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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26
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Rinaldi G, Paz Meseguer C, Cantacessi C, Cortés A. Form and Function in the Digenea, with an Emphasis on Host-Parasite and Parasite-Bacteria Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1454:3-45. [PMID: 39008262 DOI: 10.1007/978-3-031-60121-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
This review covers the general aspects of the anatomy and physiology of the major body systems in digenetic trematodes, with an emphasis on new knowledge of the area acquired since the publication of the second edition of this book in 2019. In addition to reporting on key recent advances in the morphology and physiology of tegumentary, sensory, neuromuscular, digestive, excretory, and reproductive systems, and their roles in host-parasite interactions, this edition includes a section discussing the known and putative roles of bacteria in digenean biology and physiology. Furthermore, a brief discussion of current trends in the development of novel treatment and control strategies based on a better understanding of the trematode body systems and associated bacteria is provided.
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Affiliation(s)
- Gabriel Rinaldi
- Department of Life Sciences, Edward Llwyd Building, Aberystwyth University, Aberystwyth, UK
| | - Carla Paz Meseguer
- Department of Pharmacy and Pharmaceutical Technology and Parasitology, School of Pharmacy and Food Sciences, Universitat de València, Valencia, Spain
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alba Cortés
- Department of Pharmacy and Pharmaceutical Technology and Parasitology, School of Pharmacy and Food Sciences, Universitat de València, Valencia, Spain.
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27
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Mazel F, Pitteloud C, Guisan A, Pellissier L. Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets. ISME COMMUNICATIONS 2024; 4:ycad013. [PMID: 38374896 PMCID: PMC10875604 DOI: 10.1093/ismeco/ycad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Camille Pitteloud
- Département de la mobilité, du territoire et de l'environnement, Service des forêts, de la nature et du paysage, Sion 1950, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne 1015, Switzerland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
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28
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O'Neill AM, Cavagnero KJ, Seidman JS, Zaramela L, Chen Y, Li F, Nakatsuji T, Cheng JY, Tong YL, Do TH, Brinton SL, Hata TR, Modlin RL, Gallo RL. Genetic and Functional Analyses of Cutibacterium Acnes Isolates Reveal the Association of a Linear Plasmid with Skin Inflammation. J Invest Dermatol 2024; 144:116-124.e4. [PMID: 37478901 PMCID: PMC11137742 DOI: 10.1016/j.jid.2023.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/19/2023] [Accepted: 05/04/2023] [Indexed: 07/23/2023]
Abstract
Cutibacterium acnes is a commensal bacterium on the skin that is generally well-tolerated, but different strain types have been hypothesized to contribute to the disease acne vulgaris. To understand how some strain types might contribute to skin inflammation, we generated a repository of C. acnes isolates from skin swabs of healthy subjects and subjects with acne and assessed their strain-level identity and capacity to stimulate cytokine release. Phylotype II K-type strains were more frequent on healthy and nonlesional skin of subjects with acne than those isolated from lesions. Phylotype IA-1 C-type strains were increased on lesional skin compared with those on healthy skin. The capacity to induce cytokines from cultured monocyte-derived dendritic cells was opposite to this action on sebocytes and keratinocytes and did not correlate with the strain types associated with the disease. Whole-genome sequencing revealed a linear plasmid in high-inflammatory isolates within similar strain types that had different proinflammatory responses. Single-cell RNA sequencing of mouse skin after intradermal injection showed that strains containing this plasmid induced a higher inflammatory response in dermal fibroblasts. These findings revealed that C. acnes strain type is insufficient to predict inflammation and that carriage of a plasmid could contribute to disease.
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Affiliation(s)
- Alan M O'Neill
- Department of Dermatology, University of California San Diego, La Jolla, California, USA
| | - Kellen J Cavagnero
- Department of Dermatology, University of California San Diego, La Jolla, California, USA
| | - Jason S Seidman
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Livia Zaramela
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Yang Chen
- Department of Dermatology, University of California San Diego, La Jolla, California, USA; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Fengwu Li
- Department of Dermatology, University of California San Diego, La Jolla, California, USA
| | - Teruaki Nakatsuji
- Department of Dermatology, University of California San Diego, La Jolla, California, USA
| | - Joyce Y Cheng
- Department of Dermatology, University of California San Diego, La Jolla, California, USA
| | - Yun L Tong
- Department of Dermatology, University of California San Diego, La Jolla, California, USA
| | - Tran H Do
- Division of Dermatology, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Samantha L Brinton
- Department of Dermatology, University of California San Diego, La Jolla, California, USA
| | - Tissa R Hata
- Department of Dermatology, University of California San Diego, La Jolla, California, USA
| | - Robert L Modlin
- Division of Dermatology, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Richard L Gallo
- Department of Dermatology, University of California San Diego, La Jolla, California, USA.
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Dapa T, Xavier KB. Effect of diet on the evolution of gut commensal bacteria. Gut Microbes 2024; 16:2369337. [PMID: 38904092 PMCID: PMC11195494 DOI: 10.1080/19490976.2024.2369337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
The gut microbiota, comprising trillions of diverse microorganisms inhabiting the intestines of animals, forms a complex and indispensable ecosystem with profound implications for the host's well-being. Its functions include contributing to developing the host's immune response, aiding in nutrient digestion, synthesizing essential compounds, acting as a barrier against pathogen invasion, and influencing the development or regression of various pathologies. The dietary habits of the host directly impact this intricate community of gut microbes. Diet influences the composition and function of the gut microbiota through alterations in gene expression, enzymatic activity, and metabolome. While the impact of diet on gut ecology is well-established, the investigation into the relationship between dietary consumption and microbial genotypic diversity has been limited. This review provides an overview of the relationship between diet and gut microbiota, emphasizing the impact of host nutrition on both short- and long-term evolution in the mammalian gut. It is evident that the evolution of the gut microbiota occurs even on short timescales through the acquisition of novel mutations, within the gut bacteria of individual hosts. Consequently, we discuss the importance of considering alterations in bacterial genomic diversity when analyzing microbiota-dependent effects on host physiology. Future investigations into the various microbiota-related traits shall greatly benefit from a deeper understanding of commensal bacterial evolutionary adaptation.
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Affiliation(s)
- Tanja Dapa
- Andalusian Center for Developmental Biology (CABD), Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University/CSIC/Junta de Andalucía, Seville, Spain
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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30
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Baranova MN, Pilipenko EA, Gabibov AG, Terekhov SS, Smirnov IV. Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains. Int J Mol Sci 2023; 25:537. [PMID: 38203702 PMCID: PMC10779147 DOI: 10.3390/ijms25010537] [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: 11/29/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.
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Affiliation(s)
- Margarita N. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Ekaterina A. Pilipenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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31
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Troitsky TS, Laine VN, Lilley TM. When the host's away, the pathogen will play: the protective role of the skin microbiome during hibernation. Anim Microbiome 2023; 5:66. [PMID: 38129884 PMCID: PMC10740296 DOI: 10.1186/s42523-023-00285-1] [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: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
The skin of animals is enveloped by a symbiotic microscopic ecosystem known as the microbiome. The host and microbiome exhibit a mutualistic relationship, collectively forming a single evolutionary unit sometimes referred to as a holobiont. Although the holobiome theory highlights the importance of the microbiome, little is known about how the skin microbiome contributes to protecting the host. Existing studies focus on humans or captive animals, but research in wild animals is in its infancy. Specifically, the protective role of the skin microbiome in hibernating animals remains almost entirely overlooked. This is surprising, considering the massive population declines in hibernating North American bats caused by the fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome. Hibernation offers a unique setting in which to study the function of the microbiome because, during torpor, the host's immune system becomes suppressed, making it susceptible to infection. We conducted a systematic review of peer-reviewed literature on the protective role of the skin microbiome in non-human animals. We selected 230 publications that mentioned pathogen inhibition by microbes residing on the skin of the host animal. We found that the majority of studies were conducted in North America and focused on the bacterial microbiome of amphibians infected by the chytrid fungus. Despite mentioning pathogen inhibition by the skin microbiome, only 30.4% of studies experimentally tested the actual antimicrobial activity of symbionts. Additionally, only 7.8% of all publications studied defensive cutaneous symbionts during hibernation. With this review, we want to highlight the knowledge gap surrounding skin microbiome research in hibernating animals. For instance, research looking to mitigate the effects of white-nose syndrome in bats should focus on the antifungal microbiome of Palearctic bats, as they survive exposure to the Pseudogymnoascus destructans -pathogen during hibernation. We also recommend future studies prioritize lesser-known microbial symbionts, such as fungi, and investigate the effects of a combination of anti-pathogen microbes, as both areas of research show promise as probiotic treatments. By incorporating the protective skin microbiome into disease mitigation strategies, conservation efforts can be made more effective.
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Affiliation(s)
- T S Troitsky
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - V N Laine
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - T M Lilley
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
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32
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Griem-Krey H, Petersen C, Hamerich IK, Schulenburg H. The intricate triangular interaction between protective microbe, pathogen and host determines fitness of the metaorganism. Proc Biol Sci 2023; 290:20232193. [PMID: 38052248 PMCID: PMC10697802 DOI: 10.1098/rspb.2023.2193] [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: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
The microbiota shapes host biology in numerous ways. One example is protection against pathogens, which is likely critical for host fitness in consideration of the ubiquity of pathogens. The host itself can affect abundance of microbiota or pathogens, which has usually been characterized in separate studies. To date, however, it is unclear how the host influences the interaction with both simultaneously and how this triangular interaction determines fitness of the host-microbe assemblage, the so-called metaorganism. To address this current knowledge gap, we focused on a triangular model interaction, consisting of the nematode Caenorhabditis elegans, its protective symbiont Pseudomonas lurida MYb11 and its pathogen Bacillus thuringiensis Bt679. We combined the two microbes with C. elegans mutants with altered immunity and/or microbial colonization, and found that (i) under pathogen stress, immunocompetence has a larger influence on metaorganism fitness than colonization with the protective microbe; (ii) in almost all cases, MYb11 still improves fitness; and (iii) disruption of p38 MAPK signalling, which contributes centrally to immunity against Bt679, completely reverses the protective effect of MYb11, which further reduces nematode survival and fitness upon infection with Bt679. Our study highlights the complex interplay between host, protective microbe and pathogen in shaping metaorganism biology.
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Affiliation(s)
- Hanne Griem-Krey
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel 24118, Germany
| | - Carola Petersen
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel 24118, Germany
| | - Inga K. Hamerich
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel 24118, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel 24118, Germany
- Antibiotic resistance group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
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Cheddadi R, Yeramilli V, Martin C. From Mother to Infant, from Placenta to Gut: Understanding Varied Microbiome Profiles in Neonates. Metabolites 2023; 13:1184. [PMID: 38132866 PMCID: PMC10745069 DOI: 10.3390/metabo13121184] [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: 11/03/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
The field of human microbiome and gut microbial diversity research has witnessed a profound transformation, driven by advances in omics technologies. These advancements have unveiled essential connections between microbiome alterations and severe conditions, prompting the development of new frameworks through epidemiological studies. Traditionally, it was believed that each individual harbored unique microbial communities acquired early in life, evolving over the course of their lifetime, with little acknowledgment of any prenatal microbial development, but recent research challenges this belief. The neonatal microbiome's onset, influenced by factors like delivery mode and maternal health, remains a subject of intense debate, hinting at potential intrauterine microbial processes. In-depth research reveals associations between microbiome profiles and specific health outcomes, ranging from obesity to neurodevelopmental disorders. Understanding these diverse microbiome profiles is essential for unraveling the intricate relationships between the microbiome and health outcomes.
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Affiliation(s)
- Riadh Cheddadi
- Department of Surgery, Division of Pediatric Surgery, Washington University School of Medicine, Saint Louis, MO 63110, USA (C.M.)
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Andargie YE, Lee G, Jeong M, Tagele SB, Shin JH. Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere. FRONTIERS IN PLANT SCIENCE 2023; 14:1301698. [PMID: 38116158 PMCID: PMC10728675 DOI: 10.3389/fpls.2023.1301698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.
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Affiliation(s)
- Yohannes Ebabuye Andargie
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
- Next Generation Sequencing (NGS) Core Facility, Kyungpook National University, Daegu, Republic of Korea
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35
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Rolshausen G, Dal Grande F, Otte J, Schmitt I. Lichen holobionts show compositional structure along elevation. Mol Ecol 2023; 32:6619-6630. [PMID: 35398946 DOI: 10.1111/mec.16471] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/25/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Holobionts are dynamic ecosystems that may respond to abiotic drivers with compositional changes. Uncovering elevational diversity patterns within these microecosystems can further our understanding of community-environment interactions. Here, we assess how the major components of lichen holobionts-fungal hosts, green algal symbionts, and the bacterial community-collectively respond to an elevational gradient. We analyse populations of two lichen symbioses, Umbilicaria pustulata and U. hispanica, along an elevational gradient spanning 2100 altitudinal metres and covering three major biomes. Our study shows (i) discontinuous genomic variation in fungal hosts with one abrupt genomic differentiation within each of the two host species, (ii) altitudinally structured bacterial communities with pronounced turnover within and between hosts, and (iii) altitude-specific presence of algal symbionts. Alpha diversity of bacterial communities decreased with increasing elevation. A marked turnover in holobiont diversity occurred across two altitudinal belts: at 11°C-13°C average annual temperature (here: 800-1200 m a.s.l.), and at 7°C-9°C average annual temperature (here: 1500-1800 m a.s.l.). The two observed zones mark a clustering of distribution limits and community shifts. The three ensuing altitudinal classes, that is, the most frequent combinations of species in holobionts, approximately correspond to the Mediterranean, cool-temperate, and alpine climate zones. We conclude that multitrophic microecosystems, such as lichen holobionts, respond with concerted compositional changes to climatic factors that also structure communities of macroorganisms, for example, vascular plants.
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Affiliation(s)
- Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Center for Wildlife Genetics, Senckenberg Research Institute, Gelnhausen, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Departement of Biological Sciences, Goethe University, Frankfurt am Main, Germany
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36
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van der Loos LM, D'hondt S, Engelen AH, Pavia H, Toth GB, Willems A, Weinberger F, De Clerck O, Steinhagen S. Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient. Mol Ecol 2023; 32:6260-6277. [PMID: 35395701 DOI: 10.1111/mec.16462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/21/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.
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Affiliation(s)
- Luna M van der Loos
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sofie D'hondt
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Aschwin H Engelen
- Marine Microbial Ecology & Biotechnology, CCMAR, University of Algarve, Faro, Portugal
| | - Henrik Pavia
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Gunilla B Toth
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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Di Cesare F, Calgaro M, Ghini V, Squarzanti DF, De Prisco A, Visciglia A, Zanetta P, Rolla R, Savoia P, Amoruso A, Azzimonti B, Vitulo N, Tenori L, Luchinat C, Pane M. Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals. J Proteome Res 2023; 22:3866-3878. [PMID: 37970754 PMCID: PMC10696601 DOI: 10.1021/acs.jproteome.3c00548] [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: 08/29/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 11/17/2023]
Abstract
Probiotics are live microorganisms that confer health benefits when administered in adequate amounts. They are used to promote gut health and alleviate various disorders. Recently, there has been an increasing interest in the potential effects of probiotics on human physiology. In the presented study, the effects of probiotic treatment on the metabolic profiles of human urine and serum using a nuclear magnetic resonance (NMR)-based metabonomic approach were investigated. Twenty-one healthy volunteers were enrolled in the study, and they received two different dosages of probiotics for 8 weeks. During the study, urine and serum samples were collected from volunteers before and during probiotic supplementation. The results showed that probiotics had a significant impact on the urinary and serum metabolic profiles without altering their phenotypes. This study demonstrated the effects of probiotics in terms of variations of metabolite levels resulting also from the different probiotic posology. Overall, the results suggest that probiotic administration may affect both urine and serum metabolomes, although more research is needed to understand the mechanisms and clinical implications of these effects. NMR-based metabonomic analysis of biofluids is a powerful tool for monitoring host-gut microflora dynamic interaction as well as for assessing the individual response to probiotic treatment.
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Affiliation(s)
- Francesca Di Cesare
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Matteo Calgaro
- Department
of Biotechnology, University of Verona, Strada le Grazie, 15, Verona 37134, Italy
| | - Veronica Ghini
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Diletta Francesca Squarzanti
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
- Center
for Translational Research on Autoimmune and Allergic Diseases (CAAD),
Department of Health Sciences (DiSS), University
of Piemonte Orientale (UPO), Corso Trieste, 15, Novara 28100, Italy
| | | | | | - Paola Zanetta
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
- Center
for Translational Research on Autoimmune and Allergic Diseases (CAAD),
Department of Health Sciences (DiSS), University
of Piemonte Orientale (UPO), Corso Trieste, 15, Novara 28100, Italy
| | - Roberta Rolla
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
| | - Paola Savoia
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
| | - Angela Amoruso
- Probiotical
Research Srl, Via Enrico
Mattei, 3, Novara 28100, Italy
| | - Barbara Azzimonti
- Department
of Health Sciences (DiSS), University of
Piemonte Orientale (UPO), Via Solaroli, 17, Novara 28100, Italy
- Center
for Translational Research on Autoimmune and Allergic Diseases (CAAD),
Department of Health Sciences (DiSS), University
of Piemonte Orientale (UPO), Corso Trieste, 15, Novara 28100, Italy
| | - Nicola Vitulo
- Department
of Biotechnology, University of Verona, Strada le Grazie, 15, Verona 37134, Italy
| | - Leonardo Tenori
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
| | - Claudio Luchinat
- Consorzio
Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, Firenze 50019, Italy
- Giotto
Biotech S.r.l., Via Madonna
del Piano, 6, Sesto Fiorentino, Firenze 50019, Italy
| | - Marco Pane
- Probiotical
Research Srl, Via Enrico
Mattei, 3, Novara 28100, Italy
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Molina L, Rajchenberg M, de Errasti A, Vogel B, Coetzee MPA, Aime MC, Pildain MB. Sapwood mycobiome varies across host, plant compartment and environments in Nothofagus forests from Northern Patagonia. Mol Ecol 2023; 32:6599-6618. [PMID: 36345145 DOI: 10.1111/mec.16771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 10/21/2022] [Accepted: 10/31/2022] [Indexed: 11/10/2022]
Abstract
Global forests are increasingly being threatened by altered climatic conditions and increased attacks by pests and pathogens. The complex ecological interactions among pathogens, microbial communities, tree hosts and the environment are important drivers of forest dynamics. Little is known about the ecology of forest pathology and related microbial communities in temperate forests of the southern hemisphere. In this study, we used next-generation sequencing to characterize sapwood-inhabiting fungal communities in North Patagonian Nothofagus forests and assessed patterns of diversity of taxa and ecological guilds across climatic, site and host variables (health condition and compartment) as a contribution to Nothofagus autecology. The diversity patterns inferred through the metabarcoding analysis were similar to those obtained through culture-dependent approaches. However, we detected additional heterogeneity and greater richness with culture-free methods. Host species was the strongest driver of fungal community structure and composition, while host health status was the weakest. The relative impacts of site, season, plant compartment and health status were different for each tree species; these differences can be interpreted as a matter of water availability. For Nothofagus dombeyi, which is distributed across a wide range of climatic conditions, site was the strongest driver of community composition. The microbiome of N. pumilio varied more with season and temperature, a relevant factor for forest conservation in the present climate change scenario. Both species carry a number of potential fungal pathogens in their sapwood, whether they exhibit symptoms or not. Our results provide insight into the diversity of fungi associated with the complex pathobiome of the dominant Nothofagus species in southern South America.
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Affiliation(s)
- Lucía Molina
- Fitopatología y Microbiología Aplicada, Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esquel, Argentina
| | - Mario Rajchenberg
- Fitopatología y Microbiología Aplicada, Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esquel, Argentina
| | - Andrés de Errasti
- Fitopatología y Microbiología Aplicada, Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esquel, Argentina
| | - Braian Vogel
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esquel, Argentina
- Centro de Estudios Ambientales Integrados (CEAI) Facultad de Ingeniería, Universidad Nacional de la Patagonia San Juan Bosco Sede Esquel, Pretoria, Argentina
| | - Martin P A Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Mary Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - María Belén Pildain
- Fitopatología y Microbiología Aplicada, Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP), Esquel, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esquel, Argentina
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Chalifour BN, Elder LE, Li J. Diversity of gut microbiome in Rocky Mountainsnail across its native range. PLoS One 2023; 18:e0290292. [PMID: 38011083 PMCID: PMC10681204 DOI: 10.1371/journal.pone.0290292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 08/07/2023] [Indexed: 11/29/2023] Open
Abstract
The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.
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Affiliation(s)
- Bridget N. Chalifour
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Leanne E. Elder
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, United States of America
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40
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Sadeghi J, Chaganti SR, Johnson TB, Heath DD. Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome. MICROBIOME 2023; 11:258. [PMID: 37981701 PMCID: PMC10658978 DOI: 10.1186/s40168-023-01697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/11/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation. RESULTS We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. CONCLUSIONS Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, USA
| | - Timothy B Johnson
- Ontario Ministry of Natural Resources and Forestry, Glenora Fisheries Station, Picton, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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41
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Lachmansingh DA, Lavelle A, Cryan JF, Clarke G. Microbiota-Gut-Brain Axis and Antidepressant Treatment. Curr Top Behav Neurosci 2023. [PMID: 37962812 DOI: 10.1007/7854_2023_449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In the treatment of depressive disorders, conventional antidepressant therapy has been the mainstay of clinical management, along with well-established nonpharmacological interventions such as various kinds of psychotherapy. Over the last 2 decades, there has been considerable interest in the role of the gastrointestinal system and its microbiota on brain function, behavior, and mental health. Components of what is referred to as the microbiota-gut-brain axis have been uncovered, and further research has elicited functional capabilities such as "gut-brain modules." Some studies have found associations with compositional alterations of gut microbiota in patients with depressive disorders and individuals experiencing symptoms of depression. Regarding the pathogenesis and neurobiology of depression itself, there appears to be a multifactorial contribution, in addition to the theories involving deficits in catecholaminergic and monoamine neurotransmission. Interestingly, there is evidence to suggest that antidepressants may play a role in modulating the gut microbiota, thereby possibly having an impact on the microbiota-gut-brain axis in this manner. The development of prebiotics, probiotics, and synbiotics has led to studies investigating not only their impact on the microbiota but also their therapeutic value in mental health. These psychobiotics have the potential to be used as therapeutic adjuncts in the treatment of depression. Regarding future directions, and in an attempt to further understand the role of the microbiota-gut-brain axis in depression, more studies such as those involving fecal microbiota transplantation will be required. In addition to recent findings, it is also suggested that more research will have to be undertaken to elicit whether specific strains of gut organisms are linked to depression. In terms of further investigation of the therapeutic potential of prebiotics, probiotics, and synbiotics as adjuncts to antidepressant treatment, we also expect there to be more research targeting specific microorganisms, as well as a strong focus on the effects of specific prebiotic fibers from an individualized (personalized) point of view.
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Affiliation(s)
- David Antoine Lachmansingh
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Aonghus Lavelle
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
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Shankregowda AM, Siriyappagouder P, Kuizenga M, Bal TMP, Abdelhafiz Y, Eizaguirre C, Fernandes JMO, Kiron V, Raeymaekers JAM. Host habitat rather than evolutionary history explains gut microbiome diversity in sympatric stickleback species. Front Microbiol 2023; 14:1232358. [PMID: 37901806 PMCID: PMC10601471 DOI: 10.3389/fmicb.2023.1232358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Host-associated microbiota can influence host phenotypic variation, fitness and potential to adapt to local environmental conditions. In turn, both host evolutionary history and the abiotic and biotic environment can influence the diversity and composition of microbiota. Yet, to what extent environmental and host-specific factors drive microbial diversity remains largely unknown, limiting our understanding of host-microbiome interactions in natural populations. Here, we compared the intestinal microbiota between two phylogenetically related fishes, the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius) in a common landscape. Using amplicon sequencing of the V3-V4 region of the bacterial 16S rRNA gene, we characterised the α and β diversity of the microbial communities in these two fish species from both brackish water and freshwater habitats. Across eight locations, α diversity was higher in the nine-spined stickleback, suggesting a broader niche use in this host species. Habitat was a strong determinant of β diversity in both host species, while host species only explained a small fraction of the variation in gut microbial composition. Strong habitat-specific effects overruled effects of geographic distance and historical freshwater colonisation, suggesting that the gut microbiome correlates primarily with local environmental conditions. Interestingly, the effect of habitat divergence on gut microbial communities was stronger in three-spined stickleback than in nine-spined stickleback, possibly mirroring the stronger level of adaptive divergence in this host species. Overall, our results show that microbial communities reflect habitat divergence rather than colonisation history or dispersal limitation of host species.
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Affiliation(s)
| | | | - Marijn Kuizenga
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thijs M. P. Bal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | | | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [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: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Venegas L, López P, Derome N, Yáñez JM. Leveraging microbiome information for animal genetic improvement. Trends Genet 2023; 39:721-723. [PMID: 37516623 DOI: 10.1016/j.tig.2023.07.004] [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: 04/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023]
Abstract
There is growing evidence that the microbiome influences host phenotypic variation. Incorporating information about the holobiont - the host and its microbiome - into genomic prediction models may accelerate genetic improvements in farmed animal populations. Importantly, these models must account for the indirect effects of the host genome on microbiome-mediated phenotypes.
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Affiliation(s)
- Lucas Venegas
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Paulina López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - José M Yáñez
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Millennium Nucleus of Austral Invasive Salmonids, INVASAL, Concepción, Chile.
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Calvert J, McTaggart A, Carvalhais LC, Rensink S, Dennis PG, Drenth A, Shivas R. Divergent rainforest tree microbiomes between phases of the monsoon cycle, host plants and tissues. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:860-870. [PMID: 37647418 DOI: 10.1111/plb.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.
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Affiliation(s)
- J Calvert
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - A McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - L C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - S Rensink
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - P G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - A Drenth
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - R Shivas
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
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Pinnow N, Chibani CM, Güllert S, Weiland-Bräuer N. Microbial community changes correlate with impaired host fitness of Aurelia aurita after environmental challenge. Anim Microbiome 2023; 5:45. [PMID: 37735458 PMCID: PMC10515101 DOI: 10.1186/s42523-023-00266-4] [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: 03/30/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change globally endangers certain marine species, but at the same time, such changes may promote species that can tolerate and adapt to varying environmental conditions. Such acclimatization can be accompanied or possibly even be enabled by a host's microbiome; however, few studies have so far directly addressed this process. Here we show that acute, individual rises in seawater temperature and salinity to sub-lethal levels diminished host fitness of the benthic Aurelia aurita polyp, demonstrated by up to 34% reduced survival rate, shrinking of the animals, and almost halted asexual reproduction. Changes in the fitness of the polyps to environmental stressors coincided with microbiome changes, mainly within the phyla Proteobacteria and Bacteroidota. The absence of bacteria amplified these effects, pointing to the benefit of a balanced microbiota to cope with a changing environment. In a future ocean scenario, mimicked by a combined but milder rise of temperature and salinity, the fitness of polyps was severely less impaired, together with condition-specific changes in the microbiome composition. Our results show that the effects on host fitness correlate with the strength of environmental stress, while salt-conveyed thermotolerance might be involved. Further, a specific, balanced microbiome of A. aurita polyps supports the host's acclimatization. Microbiomes may provide a means for acclimatization, and microbiome flexibility can be a fundamental strategy for marine animals to adapt to future ocean scenarios and maintain biodiversity and ecosystem functioning.
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Affiliation(s)
- Nicole Pinnow
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Cynthia M Chibani
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Simon Güllert
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
- Current address: Sysmex Inostics GmbH, Falkenried 88, 20251, Hamburg, Germany
| | - Nancy Weiland-Bräuer
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
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Narciso A, Barra Caracciolo A, De Carolis C. Overview of Direct and Indirect Effects of Antibiotics on Terrestrial Organisms. Antibiotics (Basel) 2023; 12:1471. [PMID: 37760767 PMCID: PMC10525971 DOI: 10.3390/antibiotics12091471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotics (ABs) have made it possible to treat bacterial infections, which were in the past untreatable and consequently fatal. Regrettably, their use and abuse among humans and livestock led to antibiotic resistance, which has made them ineffective in many cases. The spread of antibiotic resistance genes (ARGs) and bacteria is not limited to nosocomial environments, but also involves water and soil ecosystems. The environmental presence of ABs and ARGs is a hot topic, and their direct and indirect effects, are still not well known or clarified. A particular concern is the presence of antibiotics in agroecosystems due to the application of agro-zootechnical waste (e.g., manure and biosolids), which can introduce antibiotic residues and ARGs to soils. This review provides an insight of recent findings of AB direct and indirect effects on terrestrial organisms, focusing on plant and invertebrates. Possible changing in viability and organism growth, AB bioaccumulation, and shifts in associated microbiome composition are reported. Oxidative stress responses of plants (such as reactive oxygen species production) to antibiotics are also described.
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Affiliation(s)
- Alessandra Narciso
- Water Research Institute, National Research Council (IRSA-CNR), SP 35d, km 0.7 Montelibretti, 00010 Rome, Italy; (A.N.); (C.D.C.)
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Anna Barra Caracciolo
- Water Research Institute, National Research Council (IRSA-CNR), SP 35d, km 0.7 Montelibretti, 00010 Rome, Italy; (A.N.); (C.D.C.)
| | - Chiara De Carolis
- Water Research Institute, National Research Council (IRSA-CNR), SP 35d, km 0.7 Montelibretti, 00010 Rome, Italy; (A.N.); (C.D.C.)
- Department of Environmental Biology, La Sapienza’ University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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Embacher J, Zeilinger S, Kirchmair M, Rodriguez-R LM, Neuhauser S. Wood decay fungi and their bacterial interaction partners in the built environment – A systematic review on fungal bacteria interactions in dead wood and timber. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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49
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Steininger H, Moltzau-Anderson J, Lynch SV. Contributions of the early-life microbiome to childhood atopy and asthma development. Semin Immunol 2023; 69:101795. [PMID: 37379671 DOI: 10.1016/j.smim.2023.101795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/13/2023] [Indexed: 06/30/2023]
Abstract
The rapid rise in atopy and asthma in industrialized nations has led to the identification of early life environmental factors that promote these conditions and spurred research into how such exposures may mediate the trajectory to childhood disease development. Over the past decade, the human microbiome has emerged as a key determinant of human health. This is largely due to the increasing appreciation for the myriad of non-mutually exclusive mechanisms by which microbes tune and train host immunity. Microbiomes, particularly those in early life, are shaped by extrinsic and intrinsic factors, including many of the exposures known to influence allergy and asthma risk. This has led to the over-arching hypothesis that such exposures mediate their effect on childhood atopy and asthma by altering the functions and metabolic productivity of microbiomes that shape immune function during this critical developmental period. The capacity to study microbiomes at the genetic and molecular level in humans from the pre-natal period into childhood with well-defined clinical outcomes, offers an unprecedented opportunity to identify early-life and inter-generational determinants of atopy and asthma outcomes. Moreover, such studies provide an integrative microbiome research framework that can be applied to other chronic inflammatory conditions. This review attempts to capture key studies in the field that offer insights into the developmental origins of childhood atopy and asthma, providing novel insights into microbial mediators of maladaptive immunity and chronic inflammatory disease in childhood.
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Affiliation(s)
- Holly Steininger
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA
| | - Jacqueline Moltzau-Anderson
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA.
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50
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Kashung S, Bhardwaj P, Saikia M, Mazumdar-Leighton S. Midgut serine proteinases participate in dietary adaptations of the castor (Eri) silkworm Samia ricini Anderson transferred from Ricinus communis to an ancestral host, Ailanthus excelsa Roxb. FRONTIERS IN INSECT SCIENCE 2023; 3:1169596. [PMID: 38469493 PMCID: PMC10926435 DOI: 10.3389/finsc.2023.1169596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 07/10/2023] [Indexed: 03/13/2024]
Abstract
Dietary change influenced the life-history traits, nutritional utilization, and midgut serine proteinases in the larvae of the domesticated polyphagous S. ricini, transferred from R. communis (common name: castor; family Euphorbiaceae; the host plant implicated in its domestication) to A. excelsa (common name: Indian tree of heaven; family Simaroubaceae; an ancestral host of wild Samia species). Significantly higher values for fecundity and body weight were observed in larvae feeding on R. communis (Scr diet), and they took less time to reach pupation than insects feeding on A. excelsa (Scai diet). Nevertheless, the nutritional index for efficiency of conversion of digested matter (ECD) was similar for larvae feeding on the two plant species, suggesting the physiological adaptation of S. ricini (especially older instars) to an A. excelsa diet. In vitro protease assays and gelatinolytic zymograms using diagnostic substrates and protease inhibitors revealed significantly elevated levels (p ≤ 0.05) of digestive trypsins, which may be associated with the metabolic costs influencing slow growth in larvae feeding on A. excelsa. RT-PCR with semidegenerate serine proteinase gene-specific primers, and cloning and sequencing of 3' cDNA ends identified a large gene family comprising at least two groups of putative chymotrypsins (i.e., Sr I and Sr II) resembling invertebrate brachyurins/collagenases with wide substrate specificities, and five groups of putative trypsins (i.e., Sr III, Sr IV, Sr V, Sr VII, and Sr VIII). Quantitative RT-PCR indicated that transcripts belonging to the Sr I, Sr III, Sr IV, and Sr V groups, especially the Sr IV group (resembling achelase I from Lonomia achelous), were expressed differentially in the midguts of fourth instars reared on the two plant species. Sequence similarity indicated shared lineages with lepidopteran orthologs associated with expression in the gut, protein digestion, and phytophagy. The results obtained are discussed in the context of larval serine proteinases in dietary adaptations, domestication, and exploration of new host plant species for commercial rearing of S. ricini.
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