1
|
Small CM, Beck EA, Currey MC, Tavalire HF, Bassham S, Cresko WA. Host genomic variation shapes gut microbiome diversity in threespine stickleback fish. mBio 2023; 14:e0021923. [PMID: 37606367 PMCID: PMC10653670 DOI: 10.1128/mbio.00219-23] [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: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment. Furthermore, we measured host genetic variation over 2,000 regions of the stickleback genome, comparing this information and microbiome composition data among fish from very similar and very different genetic backgrounds. Our findings highlight how differences in the host genome influence microbiome diversity and make a case for future manipulative microbiome experiments that use host systems with naturally occurring genetic variation.
Collapse
Affiliation(s)
- Clayton M. Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Mark C. Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hannah F. Tavalire
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| |
Collapse
|
2
|
Frantz SI, Small CM, Cresko WA, Singh ND. Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression. G3 (BETHESDA, MD.) 2023; 13:jkad047. [PMID: 36857313 PMCID: PMC10151400 DOI: 10.1093/g3journal/jkad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/22/2022] [Accepted: 01/07/2023] [Indexed: 03/02/2023]
Abstract
Wolbachia is a maternally transmitted endosymbiotic bacteria that infects a wide variety of arthropod and nematode hosts. The effects of Wolbachia on host biology are far-reaching and include changes in host gene expression. However, previous work on the host transcriptional response has generally been investigated in the context of a single host genotype. Thus, the relative effect of Wolbachia infection versus vs. host genotype on gene expression is unknown. Here, we explicitly test the relative roles of Wolbachia infection and host genotype on host gene expression by comparing the ovarian transcriptomes of 4 strains of Drosophila melanogaster (D. melanogaster) infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation, particularly in comparison to variation in gene expression among strains. However, infection specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide novel understanding of the relative magnitude of the effect of Wolbachia infection on gene expression in the context of host genetic variation and also point to genes that are consistently differentially expressed in response to infection among multiple genotypes.
Collapse
Affiliation(s)
- Sophia I Frantz
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
| | - Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - Nadia D Singh
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
| |
Collapse
|
3
|
Holmes IA, Grundler MC. Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community. Mol Ecol 2023; 32:258-274. [PMID: 36221927 PMCID: PMC9797449 DOI: 10.1111/mec.16733] [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: 07/20/2021] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 12/31/2022]
Abstract
While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.
Collapse
Affiliation(s)
- Iris A. Holmes
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Michael C. Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
| |
Collapse
|
4
|
Beck EA, Bassham S, Cresko WA. Extreme intraspecific divergence in mitochondrial haplotypes makes the threespine stickleback fish an emerging evolutionary mutant model for mito-nuclear interactions. Front Genet 2022; 13:925786. [PMID: 36159975 PMCID: PMC9499175 DOI: 10.3389/fgene.2022.925786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial DNA is primarily maternally inherited in most animals and evolves about 10 times faster than biparentally inherited nuclear DNA. Mitochondrial dysfunction (mt-dys) arises when interactions between the co-evolving mitochondrial and nuclear genomes are perturbed in essential processes like oxidative phosphorylation (OXPHOS). Over time mt-dys can lead to mitochondrial diseases (mt-diseases), which are surprisingly prevalent and include common diseases such as Alzheimer’s, Parkinson’s, and diabetes. Unfortunately, the strong impact that intraspecific mitochondrial and nuclear genetic variation has on mt-disease complicates its study and the development of effective treatments. Animal models have advanced our understanding of mt-disease but their relevance to human conditions is often limited by their relatively low nuclear genetic diversity. Many traditional laboratory models also typically have a single mitochondrial haplotype (mitotype), in stark contrast to over 5,000 mitotypes in humans worldwide. The threespine stickleback fish has an evolutionary history that has made it a favorable evolutionary mutant model (EMM) for studying mito-nuclear interactions and possibly mt-diseases. EMMs are species with naturally evolved states that mimic maladaptive human diseases. In threespine stickleback, a period of isolation followed by introgression of the mitochondrial genome from a sister species resulted in the maintenance of two distinct mitochondrial haplotypes which continue to segregate within many populations of wild stickleback. The existence of two mitogenomes segregating in numerous genetically diverse populations provides a unique system for exploring complex mito-nuclear dynamics. Here we provide the first complete coding region analysis of the two threespine stickleback mitotypes, whose mitogenomic divergence exceeds that of other mammalian models for mitochondrial disease and even that between ancient and modern humans. We find that divergence is not uniform across the mitogenome, but primarily impacts protein coding genes, and significantly impacts proteins in Complex I of OXPHOS. The full characterization of these highly divergent intraspecific mitotypes provides a foundation for the development of threespine stickleback as an EMM for mito-nuclear interactions.
Collapse
Affiliation(s)
- Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, United States
- *Correspondence: Emily A. Beck, ; William A. Cresko,
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, United States
- *Correspondence: Emily A. Beck, ; William A. Cresko,
| |
Collapse
|
5
|
Healey HM, Bassham S, Cresko WA. Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis. Genetics 2022; 220:iyac017. [PMID: 35143654 PMCID: PMC8893252 DOI: 10.1093/genetics/iyac017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/24/2022] [Indexed: 12/02/2022] Open
Abstract
Single-cell RNA sequencing is a powerful technique that continues to expand across various biological applications. However, incomplete 3'-UTR annotations can impede single-cell analysis resulting in genes that are partially or completely uncounted. Performing single-cell RNA sequencing with incomplete 3'-UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single-cell isoform sequencing in tandem with single-cell RNA sequencing can rapidly improve 3'-UTR annotations. Using threespine stickleback fish (Gasterosteus aculeatus), we show that gene models resulting from a minimal embryonic single-cell isoform sequencing dataset retained 26.1% greater single-cell RNA sequencing reads than gene models from Ensembl alone. Furthermore, pooling our single-cell sequencing isoforms with a previously published adult bulk Iso-Seq dataset from stickleback, and merging the annotation with the Ensembl gene models, resulted in a marginal improvement (+0.8%) over the single-cell isoform sequencing only dataset. In addition, isoforms identified by single-cell isoform sequencing included thousands of new splicing variants. The improved gene models obtained using single-cell isoform sequencing led to successful identification of cell types and increased the reads identified of many genes in our single-cell RNA sequencing stickleback dataset. Our work illuminates single-cell isoform sequencing as a cost-effective and efficient mechanism to rapidly annotate genomes for single-cell RNA sequencing.
Collapse
Affiliation(s)
- Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
6
|
Hahn MA, Piecyk A, Jorge F, Cerrato R, Kalbe M, Dheilly NM. Host phenotype and microbiome vary with infection status, parasite genotype, and parasite microbiome composition. Mol Ecol 2022; 31:1577-1594. [PMID: 35000227 DOI: 10.1111/mec.16344] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/09/2021] [Accepted: 12/16/2021] [Indexed: 11/29/2022]
Abstract
A growing literature demonstrates the impact of helminths on their host gut microbiome. We investigated whether the stickleback host microbiome depends on eco-evolutionary variables by testing the impact of exposure to the cestode parasite Schistocephalus solidus with respect to infection success, host genotype, parasite genotype, and parasite microbiome composition. We observed constitutive differences in the microbiome of sticklebacks of different origin, and those differences increased when sticklebacks exposed to the parasite resisted infection. In contrast, the microbiome of successfully infected sticklebacks varied with parasite genotype. More specifically, we revealed that the association between microbiome and immune gene expression increased in infected individuals and varied with parasite genotype. In addition, we showed that S. solidus hosts a complex endo- microbiome and that bacterial abundance in the parasite correlates with expression of host immune genes. Within this comprehensive analysis we demonstrated that (i) parasites contribute to modulating the host microbiome through both successful and unsuccessful infection, (ii) when infection is successful, the host microbiome varies with parasite genotype due to genotype-dependent variation in parasite immunomodulation, and (iii) the parasite-associated microbiome is distinct from its host's and impacts the host immune response to infection.
Collapse
Affiliation(s)
- Megan A Hahn
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Agnes Piecyk
- Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz, Centre for Ocean Research Kiel, Germany
| | - Fátima Jorge
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Robert Cerrato
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Martin Kalbe
- Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz, Centre for Ocean Research Kiel, Germany
| | - Nolwenn M Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.,ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail - Laboratoire de Ploufragan-Plouzané, Unité Génétique Virale de Biosécurité, Ploufragan, France.,UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704, Maisons-Alfort, France
| |
Collapse
|
7
|
Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
Collapse
Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | | |
Collapse
|
8
|
Ou W, Yu G, Zhang Y, Mai K. Recent progress in the understanding of the gut microbiota of marine fishes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:434-448. [PMID: 37073265 PMCID: PMC10077274 DOI: 10.1007/s42995-021-00094-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/12/2021] [Indexed: 05/03/2023]
Abstract
As the significance of the gut microbiota has become increasingly realized, a large number of related studies have emerged. With respect to the gut microbial composition of fish, the predominant gut microbes and core gut microbiota have been reported by many researchers. Our understanding of fish gut microbiota, especially its functional roles, has fallen far behind that of terrestrial vertebrates, although previous studies using gnotobiotic zebrafish models have revealed that the gut microbiota performs a significant role in gut development, nutrient metabolism and immune responses. Given that environmental factors of marine habitats are very different from those of freshwater habitats, a distinct difference may exist in the gut microbiota between freshwater and marine fish. Therefore, this review aims to address the advances in marine fish gut microbiota in terms of methodologies, the gut microbial composition, and gnotobiotic models of marine fish, the important factors (host genotype and three environmental factors: temperature, salinity and diet) that drive marine fish gut microbiota, and significant roles of the gut microbiota in marine fish.
Collapse
Affiliation(s)
- Weihao Ou
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
| | - Guijuan Yu
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
| | - Yanjiao Zhang
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Kangsen Mai
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) and the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| |
Collapse
|
9
|
Abstract
The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.
Collapse
Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, California 94720, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
| |
Collapse
|
10
|
Nguyen CDH, Amoroso G, Ventura T, Minich JJ, Elizur A. Atlantic Salmon (Salmo salar L., 1758) Gut Microbiota Profile Correlates with Flesh Pigmentation: Cause or Effect? MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:786-804. [PMID: 31942646 DOI: 10.1007/s10126-019-09939-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
In Tasmania (Australia), during the marine phase, it has been observed that flesh pigmentation significantly drops in summer, possibly due to high water temperatures (> 20 °C). Although this deleterious effect of summer temperatures has been ascertained, there is a lack of knowledge of the actual mechanisms behind the impaired uptake and/or loss of pigments in Atlantic salmon in a challenging environment. Since the microbial community in the fish intestine significantly changes in relation to the variations of water temperature, this study was conducted to assess how the gut microbiota profile also correlates with the flesh color during temperature fluctuation. We sampled 68 fish at three time points covering the end of summer to winter at a marine farm in Tasmania, Australia. Flesh color was examined in two ways: the average color throughout and the evenness of the color between different areas of the fillet. Using 16S rRNA sequencing of the v3-v4 region, we determined that water temperature corresponded to changes in the gut microbiome both with alpha diversity (Kruskal-Wallis tests P = 0.05) and beta diversity indices (PERMANOVA P = 0.001). Also, there was a significant correlation between the microbiota and the color of the fillet (PERMANOVA P = 0.016). There was a high abundance of Pseudoalteromonadaceae, Enterobacteriaceae, Microbacteriaceae, and Vibrionaceae in the pale individuals. Conversely, carotenoid-synthesizing bacteria families (Bacillaceae, Mycoplasmataceae, Pseudomonas, Phyllobacteriaceae, and Comamonadaceae) were found in higher abundance in individuals with darker flesh color.
Collapse
Affiliation(s)
- Chan D H Nguyen
- GeneCology Research Centre, University of the Sunshine Coast, 4 Locked Bag, Maroochydore, Queensland, 4558, Australia
| | - Gianluca Amoroso
- GeneCology Research Centre, University of the Sunshine Coast, 4 Locked Bag, Maroochydore, Queensland, 4558, Australia
- Petuna Aquaculture, 134 Tarleton Street, East Devonport, Tasmania, 7310, Australia
| | - Tomer Ventura
- GeneCology Research Centre, University of the Sunshine Coast, 4 Locked Bag, Maroochydore, Queensland, 4558, Australia
| | - Jeremiah J Minich
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Abigail Elizur
- GeneCology Research Centre, University of the Sunshine Coast, 4 Locked Bag, Maroochydore, Queensland, 4558, Australia.
| |
Collapse
|
11
|
Kirschman LJ, Khadjinova A, Ireland K, Milligan-Myhre KC. Early life disruption of the microbiota affects organ development and cytokine gene expression in threespine stickleback. Integr Comp Biol 2020; 63:icaa136. [PMID: 32970813 PMCID: PMC10388389 DOI: 10.1093/icb/icaa136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/20/2022] Open
Abstract
The microbiota that inhabits vertebrates exerts strong effects on host physiology and can be crucial to the development of a normal phenotype. This includes development of the immune system, somatic growth and maintenance, and morphogenesis. However, the genetic background of the host can also affect these life history traits. To this end, we investigated the effects of the microbiota on growth, development, and immune gene expression on two populations of threespine stickleback (Gasterosteus aculeatus), one anadromous and one freshwater. We tested the hypotheses that microbial colonization and the genetic background of the host would affect survival, cytokine gene expression, growth, and development. We raised in vitro crosses of stickleback larvae with and without conventional microbiota. We then exposed all these treatments to Vibrio anguillarum, a potential fish pathogen, in a full factorial design. We found stickleback raised without conventional microbiota had smaller swim bladders relative to those raised with conventional microbiota. Stickleback raised with conventional microbiota exhibited small increases in cytokine gene expression. We found no differences in growth or survival regardless of treatment. These results are consistent with other investigations that show microbiota disruption, in early life, can alter host organ and tissue development and immune responses.
Collapse
Affiliation(s)
- Lucas J Kirschman
- Department Biology, Southeast Missouri University, 1 University Plaza, Cape Girardeau, MO 63701, USA
| | | | - Kelly Ireland
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
| | - Kathryn C Milligan-Myhre
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| |
Collapse
|
12
|
Jung Y, Tagele SB, Son H, Ibal JC, Kerfahi D, Yun H, Lee B, Park CY, Kim ES, Kim SJ, Shin JH. Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change. Microorganisms 2020; 8:microorganisms8091265. [PMID: 32825401 PMCID: PMC7569816 DOI: 10.3390/microorganisms8091265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.
Collapse
Affiliation(s)
- YeonGyun Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Setu Bazie Tagele
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Department of Applied Plant Sciences, University of Gondar, Gondar 196, Ethiopia
| | - HyunWoo Son
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Dorsaf Kerfahi
- Department of Biological Sciences, Keimyung University, Daegu 42601, Korea;
| | - Hyunju Yun
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Bora Lee
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Clara Yongjoo Park
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea;
| | - Sang-Jun Kim
- Department of Natural Sciences, Republic of Korea Naval Academy, Changwon 51702, Korea;
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Correspondence: ; Tel.: +82-53-950-5716; Fax: +82-53-953-7233
| |
Collapse
|
13
|
Derome N, Filteau M. A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evol Appl 2020; 13:1298-1319. [PMID: 32684960 PMCID: PMC7359827 DOI: 10.1111/eva.13027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.
Collapse
Affiliation(s)
- Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieUniversité LavalQuébecQCCanada
| | - Marie Filteau
- Département de BiologieUniversité LavalQuébecQCCanada
- Département des Sciences des alimentsInstitut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQCCanada
| |
Collapse
|
14
|
QTL Mapping of Intestinal Neutrophil Variation in Threespine Stickleback Reveals Possible Gene Targets Connecting Intestinal Inflammation and Systemic Health. G3-GENES GENOMES GENETICS 2020; 10:613-622. [PMID: 31843804 PMCID: PMC7003091 DOI: 10.1534/g3.119.400685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selection, via host immunity, is often required to foster beneficial microbial symbionts and suppress deleterious pathogens. In animals, the host immune system is at the center of this relationship. Failed host immune system-microbial interactions can result in a persistent inflammatory response in which the immune system indiscriminately attacks resident microbes, and at times the host cells themselves, leading to diseases such as Ulcerative Colitis, Crohn’s Disease, and Psoriasis. Host genetic variation has been linked to both microbiome diversity and to severity of such inflammatory disease states in humans. However, the microbiome and inflammatory states manifest as quantitative traits, which encompass many genes interacting with one another and the environment. The mechanistic relationships among all of these interacting components are still not clear. Developing natural genetic models of host-microbe interactions is therefore fundamental to understanding the complex genetics of these and other diseases. Threespine stickleback (Gasterosteus aculeatus) fish are a tractable model for attacking this problem because of abundant population-level genetic and phenotypic variation in the gut inflammatory response. Previous work in our laboratory identified genetically divergent stickleback populations exhibiting differences in intestinal neutrophil activity. We took advantage of this diversity to genetically map variation in an emblematic element of gut inflammation - intestinal neutrophil recruitment - using an F2-intercross mapping framework. We identified two regions of the genome associated with increased intestinal inflammation containing several promising candidate genes. Within these regions we found candidates in the Coagulation/Complement System, NFkB and MAPK pathways along with several genes associated with intestinal diseases and neurological diseases commonly accompanying intestinal inflammation as a secondary symptom. These findings highlight the utility of using naturally genetically diverse ‘evolutionary mutant models’ such as threespine stickleback to better understand interactions among host genetic diversity and microbiome variation in health and disease states.
Collapse
|
15
|
Chen X, Fang S, Wei L, Zhong Q. Systematic evaluation of the gut microbiome of swamp eel ( Monopterus albus) by 16S rRNA gene sequencing. PeerJ 2019; 7:e8176. [PMID: 31875148 PMCID: PMC6927349 DOI: 10.7717/peerj.8176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/07/2019] [Indexed: 12/11/2022] Open
Abstract
Background The swamp eel (Monopterus albus) is a commercially important farmed species in China. The dysbiosis and homeostasis of gut microbiota has been suggested to be associated with the swamp eel’s disease pathogenesis and food digestion. Although the contributions of gut microbiome in fish growth and health has been increasingly recognized, little is known about the microbial community in the intestine of the swamp eel (Monopterus albus). Methods The intestinal microbiomes of the five distinct gut sections (midgut content and mucosa, hindgut content and mucosa, and stools) of swamp eel were compared using Illumina MiSeq sequencing of the bacterial 16S rRNA gene sequence and statistical analysis. Results The results showed that the number of observed OTUs in the intestine decreased proximally to distally. Principal coordinate analysis revealed significant separations among samples from different gut sections. There were 54 core OTUs shared by all gut sections and 36 of these core OTUs varied significantly in their abundances. Additionally, we discovered 66 section-specific enriched KEGG pathways. These section-specific enriched microbial taxa (e.g., Bacillus, Lactobacillus) and potential function capacities (e.g., amino acid metabolism, carbohydrate metabolism) might play vital roles in nutrient metabolism, immune modulation and host-microbe interactions of the swamp eel. Conclusions Our results showed that microbial diversity, composition and function capacity varied substantially across different gut sections. The gut section-specific enriched core microbial taxa and function capacities may perform important roles in swamp eel’s nutrient metabolism, immune modulation, and host-microbe interactions. This study should provide insights into the gut microbiome of the swamp eel.
Collapse
Affiliation(s)
- Xuan Chen
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Shaoming Fang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lili Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qiwang Zhong
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
16
|
Zheng Y, Hu G, Wu W, Qiu L, Bing X, Chen J. Time-dependent gut microbiota analysis of juvenile Oreochromis niloticus by dietary supplementation of resveratrol. Arch Microbiol 2019; 202:43-53. [PMID: 31463601 DOI: 10.1007/s00203-019-01712-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/24/2019] [Accepted: 07/31/2019] [Indexed: 02/07/2023]
Abstract
To evaluate the changes in bacterial diversity at various time points under resveratrol supplementation, we aimed to investigate the diversification of gut microbiota and the changes in total genetic diversity. We performed 16S rDNA gene sequencing at different time points (15, 30, and 45 days) to analyze the gut microbiota of tilapia. Fusobacteria, Proteobacteria, and Bacteroidetes (15 days) or Cyanobacteria (30 and 45 days) were found to be the three most abundant phyla. Cyanobacteria (15 and 30 days), Proteobacteria (15 days), Firmicutes and Chlamydiae (30 and 45 days), Planctomycetes (30 days), Bacteroidetes, Actinobacteria, and Fusobacteria (45 days) in the 0.05 g/kg RES group increased as compared to that in the controls. Proteobacteria and Cyanobacteria significantly decreased and increased at 30 and 45 days, respectively, while the reverse pattern was observed at 15 days. The Bacteroidetes:Firmicutes and Proteobacteria:Cyanobacteria ratios were significantly increased (15 and 45 days, P < 0.05) and decreased (30 days, P < 0.05). RES supplementation did not affect the richness and diversity of the gut microbiota in tilapia. Our findings may contribute to the development of strategies for the management of diseases.
Collapse
Affiliation(s)
- Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China
| | - Xuwen Bing
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China.
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China. .,Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture, Beijing, 100141, People's Republic of China.
| |
Collapse
|
17
|
Small CM, Currey M, Beck EA, Bassham S, Cresko WA. Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome. mSystems 2019; 4:e00331-19. [PMID: 31409661 PMCID: PMC6697441 DOI: 10.1128/msystems.00331-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022] Open
Abstract
Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.
Collapse
Affiliation(s)
- Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Mark Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Emily A Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| |
Collapse
|
18
|
Steury RA, Currey MC, Cresko WA, Bohannan BJM. Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback. Genes (Basel) 2019; 10:E484. [PMID: 31248008 PMCID: PMC6678413 DOI: 10.3390/genes10070484] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/27/2022] Open
Abstract
Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation. The few studies that have related population genetic and microbiome variation in wild populations have been constrained by observation-based kinship data or incomplete genomic information. Here we integrate population genomic and microbiome analyses in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.
Collapse
Affiliation(s)
- Robert A Steury
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
| | - Mark C Currey
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
| | - William A Cresko
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
| |
Collapse
|
19
|
The Costs of Living Together: Immune Responses to the Microbiota and Chronic Gut Inflammation. Appl Environ Microbiol 2019; 85:AEM.02147-18. [PMID: 30530709 DOI: 10.1128/aem.02147-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
While the vertebrate microbiota is critical to the normal function of many host traits, hosts may expend a large amount of energy to constrain and interface with their microbiota via their immune system to avoid the high fitness costs associated with gut dysbiosis, pathobionts, and opportunistic pathogens. All jawed vertebrates share mucosal immunity dedicated to isolating the microbiota, and a breakdown of this system can result in chronic gut inflammation. In humans, chronic gut inflammation negatively affects growth and development. There is little information available on the prevalence of chronic gut inflammation in wild animals, but given that animals with different life histories emphasize different immune responses, it follows that wild animals may vary in their susceptibility to chronic gut inflammation, and most animals will experience signaling that can lead to this state. These can be top-down signals originating from sources like the central nervous system or bottom-up signals originating from changes in the gut microbiota. The sources of these signals might include stress, developmental transitions, food restriction, and dietary shifts. Here, we briefly discuss host-microbiota interactions from the perspective of life history theory and ecoimmunology, focusing on the mucosal immune system and chronic gut inflammation. We also include future directions for research and the tools necessary to investigate them.
Collapse
|
20
|
Friberg IM, Taylor JD, Jackson JA. Diet in the Driving Seat: Natural Diet-Immunity-Microbiome Interactions in Wild Fish. Front Immunol 2019; 10:243. [PMID: 30837993 PMCID: PMC6389695 DOI: 10.3389/fimmu.2019.00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/28/2019] [Indexed: 12/18/2022] Open
Abstract
Natural interactions between the diet, microbiome, and immunity are largely unstudied. Here we employ wild three-spined sticklebacks as a model, combining field observations with complementary experimental manipulations of diet designed to mimic seasonal variation in the wild. We clearly demonstrate that season-specific diets are a powerful causal driver of major systemic immunophenotypic variation. This effect occurred largely independently of the bulk composition of the bacterial microbiome (which was also driven by season and diet) and of host condition, demonstrating neither of these, per se, constrain immune allocation in healthy individuals. Nonetheless, through observations in multiple anatomical compartments, differentially exposed to the direct effects of food and immunity, we found evidence of immune-driven control of bacterial community composition in mucus layers. This points to the interactive nature of the host-microbiome relationship, and is the first time, to our knowledge, that this causal chain (diet → immunity → microbiome) has been demonstrated in wild vertebrates. Microbiome effects on immunity were not excluded and, importantly, we identified outgrowth of potentially pathogenic bacteria (especially mycolic-acid producing corynebacteria) as a consequence of the more animal-protein-rich summertime diet. This may provide part of the ultimate explanation (and possibly a proximal cue) for the dramatic immune re-adjustments that we saw in response to diet change.
Collapse
Affiliation(s)
- Ida M Friberg
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Joe D Taylor
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Joseph A Jackson
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| |
Collapse
|
21
|
Hohenlohe PA, Magalhaes IS. The Population Genomics of Parallel Adaptation: Lessons from Threespine Stickleback. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2019_67] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
22
|
Zheng Y, Wu W, Hu G, Qiu L, Meng S, Song C, Fan L, Zhao Z, Bing X, Chen J. Gut microbiota analysis of juvenile genetically improved farmed tilapia (Oreochromis niloticus) by dietary supplementation of different resveratrol concentrations. FISH & SHELLFISH IMMUNOLOGY 2018; 77:200-207. [PMID: 29574130 DOI: 10.1016/j.fsi.2018.03.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 03/05/2018] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Abstract
The genetically improved farmed tilapia (GIFT, Oreochromis niloticus) is cultured widely for production of freshwater fish in China, while streptococcosis, likely related to pathogenic infections, occurs frequently in juvenile, mother, and operated GIFT. The gut microbiota plays an important role in nutrient digestibility in animals, and resveratrol (RES) has been used in feed for different freshwater fish species. Therefore, understanding changes in the tilapia gut microbiota across different concentrations of dietary RES supplementation is extremely important. The gut microbiota population in tilapia at 45 d after supplementation with different concentrations (0, 0.025, 0.05, 0.1 g/kg) of dietary RES was assessed by 16S rDNA gene sequencing. A total of 5445 operational taxonomic units were identified from all samples, and 14 phyla and 81 families were identified from all fecal samples. The bacteria of the phylum Firmicutes were significantly enriched in the 0.025 g/kg RES group when compared with the controls. Proteobacteria, Firmicutes and Cyanobacteria were the most dominant three phyla in all samples. With the increasing concentrations, the proportion of beneficial microbial taxa (Acetobacteraceae and Methylobacteriaceae) increased, whereas the proportion of harmful microbial taxa decreased, eg. Streptococcaceae except for 0.1 g/kg RES groups. RES did not affect the richness and diversity in tilapia gut microbiota. These findings provide information on the diversity and differences in GIFT gut microbiota database, and may contribute to developing strategies for management of diseases and long-term sustainability of O. niloticus culture.
Collapse
Affiliation(s)
- Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China
| | - Zhixiang Zhao
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi, Jiangsu, 214081, PR China
| | - Xuwen Bing
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China; Wuxi Fishery College, Nanjing Agricultural University, Wuxi, Jiangsu, 214081, PR China.
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Evironment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu, 214081, PR China; Wuxi Fishery College, Nanjing Agricultural University, Wuxi, Jiangsu, 214081, PR China; Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture, PR China.
| |
Collapse
|
23
|
Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes. mSystems 2017; 2:mSystems00132-17. [PMID: 29181448 PMCID: PMC5698494 DOI: 10.1128/msystems.00132-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/30/2017] [Indexed: 02/01/2023] Open
Abstract
The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly. The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = −0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies. IMPORTANCE The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
Collapse
|
24
|
Functional Genomics of Host-Microbiome Interactions in Humans. Trends Genet 2017; 34:30-40. [PMID: 29107345 DOI: 10.1016/j.tig.2017.10.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 02/06/2023]
Abstract
The human microbiome has been linked to various host phenotypes and has been implicated in many complex human diseases. Recent genome-wide association studies (GWASs) have used microbiome variation as a complex trait and have uncovered human genetic variants that are associated with the microbiome. Here we summarize results from these studies and illustrate potential regulatory mechanisms by which host genetic variation can interact with microbiome composition. We argue that, similar to human GWASs, it is important to use functional genomics techniques to gain a mechanistic understanding of causal host-microbiome interactions and their role in human disease. We highlight experimental, functional, and computational genomics methodologies for the study of the genomic basis of host-microbiome interactions and describe how these approaches can be utilized to explain how human genetic variation can modulate the effects of the microbiome on the host.
Collapse
|