Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut

From BugSigDB
Reviewed Marked as Reviewed by Chloe on 2024-4-30
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Parris DJ, Morgan MM, Stewart FJ
Journal
Applied and environmental microbiology
Year
2019
Keywords:
digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics
Diet is a major determinant of intestinal microbiome composition. While studies have evaluated microbiome responses to diet variation, less is understood about how the act of feeding influences the microbiome, independent of diet type. Here, we use the clownfish Premnas biaculeatus, a species reared commonly in ornamental marine aquaculture, to test how the diversity, predicted gene content, and gene transcription of the microbiome vary over a 2-day diurnal period with a single daily feeding event. This study used fish fed four times daily, once daily, or every 3 days prior to the diurnal period, allowing us also to test how feeding frequency affected microbiome diversity. The amount of time between feedings had no effect on baseline diversity of the microbiome. In contrast, the act of feeding itself caused a significant short-term change in the microbiome, with microbiome diversity, predicted gene content, and gene transcription varying significantly between time points immediately before and 1.5 hours postfeeding. Variation was driven by abundance shifts involving exact sequence variants (ESVs), with one ESV identified as Photobacterium sp. increasing from <0.5% of sequences immediately prefeeding to 34% at 1.5 h postfeeding. Other ESVs from a range of microbial groups also increased dramatically after feeding, with the majority also detected in the food. One ESV identified as Clostridium perfringens represented up to 55% of sequences but did not vary significantly over the diurnal period and was not detected in the food. Postfeeding samples were enriched in transcripts and predicted genes for social interactions, cell motility, and coping with foreign DNA, whereas time points farther from feeding were enriched in genes of diverse catabolic and biosynthetic functions. These results confirm feeding as a significant destabilizing force in clownfish intestinal microbiomes, likely due to both input of cells attached to food and stimulation of resident microbes. Microbes such as Photobacterium may episodically transition from environmental reservoirs to growth in the gut, likely in association with food particles. This transition may be facilitated by functions for navigating a new environment and interacting with neighboring microbes and host cells. Other taxa, such as Clostridium, are comparatively stable intestinal members and less likely to be affected by passing food. Conclusions about microbiome ecology may therefore differ based on when samples were collected relative to the last feeding.IMPORTANCE Despite extensive study of intestinal microbiome diversity and the role of diet type in structuring gut microbial communities, we know very little about short-term changes in the intestinal microbiome as a result of feeding alone. Sampling microbiomes over a feeding cycle will allow us to differentiate opportunistic, feeding-responsive microbes from resident, potentially commensal members of the gut community. Also, since feeding has the potential to alter microbiome structure, sampling at different points relative to the last feeding event will likely yield different conclusions about microbiome composition and function. This variation should be addressed in comparative microbiome studies. Our study contributes to knowledge of short-term changes in the gut microbiome associated with feeding events.

Experiment 1


Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/03/06

Curator: Muqtadirat

Revision editor(s): Muqtadirat, Victoria

Subjects

Location of subjects
Georgia
Host species Species from which microbiome was sampled. Contact us to have more species added.
Premnas biaculeatus
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Digestive tract Alimentary canal,Alimentary tract,Digestive canal,Digestive tube,Enteric tract,Gut,Gut tube,Digestive tract,digestive tract
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Diet Dietary,Diets,Diet,diet
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-fed group at 1100 h
Group 1 name Corresponds to the case (exposed) group for case-control studies
Post-fed group at 1230 h
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The post-fed group consists of fish fed at 1230 hours. (1.5 hours postfeeding)
Group 0 sample size Number of subjects in the control (unexposed) group
17
Group 1 sample size Number of subjects in the case (exposed) group
18

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
Statistical test
ANCOM
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/03/06

Curator: Muqtadirat

Revision editor(s): Muqtadirat, Victoria

Source: Supplemental Table S2

Description: The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.

Abundance in Group 1: increased abundance in Post-fed group at 1230 h

NCBI Quality ControlLinks
Alcaligenaceae
Anoxybacillus
Arcobacter
Azoarcus
Bacillales
Bacillus
Bacteroidales
Balneolaceae
Beijerinckiaceae
Cetobacterium
Chromatiaceae
Citrobacter
Cryomorphaceae
Erwinia
Eubacteriales
Geobacillus
Hydrogenophaga
Jeotgalicoccus
Lactobacillaceae
Lactobacillales
Lactobacillus
Lactococcus
Leuconostoc
Moritella
Nocardiopsaceae
Opitutia
Paracoccus
Pasteurellaceae
Peptostreptococcaceae
Peptostreptococcus
Photobacterium
Planococcaceae
Prevotella
Proteus
Pseudidiomarina
Psychrilyobacter
Psychrobacter
Psychromonas
Roseinatronobacter
Sporanaerobacter
Sporosarcina
Staphylococcaceae
Staphylococcus
Streptococcus
Tepidimicrobium
Thermus
Ureibacillus
Vagococcus
Veillonellaceae
Vibrionaceae
Virgibacillus
Lysobacteraceae
Yersinia
MarinicellaceaeMarinicellaceae

Revision editor(s): Muqtadirat, Victoria

Signature 2

Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/03/07

Curator: Muqtadirat

Revision editor(s): Muqtadirat, Victoria

Source: Supplemental Table S2

Description: The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.

Abundance in Group 1: decreased abundance in Post-fed group at 1230 h

NCBI Quality ControlLinks
Alteromonadales

Revision editor(s): Muqtadirat, Victoria

Experiment 2


Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/05

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Post-fed group at 1400 h
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The post-fed group consists of fish fed at 1400 hours. (3 hours post-feeding)

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/11

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Table S2

Description: The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.

Abundance in Group 1: increased abundance in Post-fed group at 1400 h

NCBI Quality ControlLinks
Photobacterium
Vibrionaceae
Arcobacter
Paracoccus
Psychromonas
Staphylococcus
Lactobacillus
Psychrobacter
Cetobacterium
Streptococcus
Bacillus
Lactococcus
Geobacillus
Thermus
MarinicellaceaeMarinicellaceae
Pasteurellaceae
Bacillales
Hydrogenophaga
Citrobacter
Alcaligenaceae
Tepidimicrobium
Lactobacillales
Opitutia
Planococcaceae
Staphylococcaceae
Cryomorphaceae
Peptostreptococcaceae
Prevotella
Lysobacteraceae
Veillonellaceae
Proteus
Anoxybacillus
Peptostreptococcus
Chromatiaceae
Vagococcus
Leuconostoc
Jeotgalicoccus
Erwinia
Bacteroidales
Yersinia
Moritella
Psychrilyobacter
Lactobacillaceae
Virgibacillus
Eubacteriales
Sporosarcina
Nocardiopsaceae
Balneolaceae
Ureibacillus
Azoarcus
Pseudidiomarina
Roseinatronobacter
Sporanaerobacter
Beijerinckiaceae

Revision editor(s): Victoria

Signature 2

Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/12

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Table S2

Description: The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.

Abundance in Group 1: decreased abundance in Post-fed group at 1400 h

NCBI Quality ControlLinks
Alteromonadales

Revision editor(s): Victoria

Experiment 3


Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/06

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Post-fed group at 1600 h
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The post-fed group consists of fish fed at 1600 hours. (5 hours postfeeding)

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/12

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Table S2

Description: The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.

Abundance in Group 1: increased abundance in Post-fed group at 1600 h

NCBI Quality ControlLinks
Yersinia
Bacteroidales
Erwinia
Jeotgalicoccus
Leuconostoc
Vagococcus
Chromatiaceae
Peptostreptococcus
Anoxybacillus
Proteus
Veillonellaceae
Lysobacteraceae
Prevotella
Peptostreptococcaceae
Staphylococcaceae
Planococcaceae
Opitutia
Lactobacillales
Bacillales
Tepidimicrobium
Alcaligenaceae
Citrobacter
Hydrogenophaga
Pasteurellaceae
MarinicellaceaeMarinicellaceae
Thermus
Geobacillus
Lactococcus
Bacillus
Streptococcus
Cetobacterium
Psychrobacter
Lactobacillus
Staphylococcus
Psychromonas
Paracoccus
Arcobacter
Vibrionaceae
Photobacterium
Moritella
Psychrilyobacter
Lactobacillaceae
Virgibacillus
Eubacteriales
Sporosarcina
Nocardiopsaceae
Balneolaceae
Ureibacillus
Azoarcus
Pseudidiomarina
Roseinatronobacter
Sporanaerobacter
Beijerinckiaceae

Revision editor(s): Victoria

Signature 2

Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/12

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Table S2

Description: The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.

Abundance in Group 1: decreased abundance in Post-fed group at 1600 h

NCBI Quality ControlLinks
Cryomorphaceae
Alteromonadales

Revision editor(s): Victoria

Experiment 4


Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/06

Curator: Victoria

Revision editor(s): Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Post-fed group at 2000 h
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The post-fed group consists of fish fed at 2000 hours. (9 hours post-feeding)
Group 1 sample size Number of subjects in the case (exposed) group
17

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/12

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Table S2

Description: The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.

Abundance in Group 1: increased abundance in Post-fed group at 2000 h

NCBI Quality ControlLinks
Alcaligenaceae
Anoxybacillus
Arcobacter
Azoarcus
Bacillales
Bacillus
Bacteroidales
Balneolaceae
Beijerinckiaceae
Cetobacterium
Chromatiaceae
Citrobacter
Erwinia
Eubacteriales
Geobacillus
Hydrogenophaga
Jeotgalicoccus
Lactobacillaceae
Lactobacillales
Lactobacillus
Lactococcus
Leuconostoc
Moritella
Nocardiopsaceae
Paracoccus
Pasteurellaceae
Peptostreptococcaceae
Peptostreptococcus
Photobacterium
Planococcaceae
Prevotella
Proteus
Pseudidiomarina
Psychrilyobacter
Psychrobacter
Psychromonas
Roseinatronobacter
Sporanaerobacter
Sporosarcina
Staphylococcaceae
Staphylococcus
Tepidimicrobium
Thermus
Ureibacillus
Vagococcus
Veillonellaceae
Vibrionaceae
Virgibacillus
Yersinia
Lysobacteraceae

Revision editor(s): Victoria

Signature 2

Reviewed Marked as Reviewed by Chloe on 2024-4-30

Curated date: 2024/04/12

Curator: Victoria

Revision editor(s): Victoria

Source: Supplemental Table S2

Description: The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.

Abundance in Group 1: decreased abundance in Post-fed group at 2000 h

NCBI Quality ControlLinks
Alteromonadales
Cryomorphaceae
Opitutia
Streptococcus
MarinicellaceaeMarinicellaceae

Revision editor(s): Victoria