The wild mammalian microbiome

Lead Research Organisation: Royal Veterinary College
Department Name: Pathology and Pathogen Biology

Abstract

The vertebrate gut teems with a vast, diverse community of bacteria that outnumber the cells of their host by at least an order of magnitude, the so-called gut microbiota. Recent advances in molecular biology have revolutionised research into these bacterial communities, and demonstrated their pervasive effects on host biology, health and disease. At the same time, their tremendous variability has come to light - they vary enormously across species, among individuals, and within individuals over time. Such variation demands an explanation, yet our current understanding of the ecological and evolutionary processes responsible remains limited. A key obstacle in this respect is that so far, microbiota research has focused heavily on just two model organisms - humans and laboratory mice, leaving a gap in knowledge about what shapes gut microbial communities in natural vertebrate populations. I outline a research programme that addresses this need, by developing wild small mammals as a novel system for microbiota research, and using them to address several key questions about which we currently know rather little: (1) Why do individuals within a single population show distinct gut microbial profiles, and what processes drive changes in these communities over time within individuals? (2) How exactly are gut microbes and other gut-dwelling organisms transmitted among hosts within a population - do their social interactions or shared use of space play a significant role in this process? (3) What ecological and evolutionary processes underlie variation across species in their gut microbiota?

To address the first two questions, I will use a common British rodent - the wood mouse - as a model study system. Wood mice are ideal for this purpose: in the wild, a large number of individuals can be uniquely marked and monitored throughout their lives in a relatively small area, with repeated sampling of their gut microbiota and fine-scale characterisation of their local habitat. Also, manipulative experiments both in the wild and in captivity are possible with this species. To address the first question, I will use a combination of detailed field observations and controlled experiments to build a comprehensive picture of the processes shaping within-population variation in gut microbial communities. Observational data on key hypothesized factors including genetic relatedness, diet, habitat, gut parasites, age and reproductive status will allow me to estimate their relative contribution to microbiota variation within and among individuals. I will also use a large-scale drug treatment experiment in wild mice to directly test how the presence of another key group of gut inhabitants - parasitic helminths, affects the microbiota. Finally, I will perform a "diet shift" experiment in captive wood mice, to test how changes in natural food groups shape the gut microbiota. To address the second question, I will use a novel 'social network' based approach in the same wild wood mouse population used above, to examine how animal social contacts and space use drive the transmission of gut microbes and gut parasites. Finally, to answer the third question, I will perform a multi-species study using wild small mammals (mice, voles and shrews) that co-occur across several different habitat types in Europe. This study will test for the first time whether a host's evolutionary heritage or their current environmental conditions (habitat and diet), dominate in shaping their microbiota.

This research will provide fundamental insight into the ecological and evolutionary processes affecting the mammalian gut microbiota, and thereby advance our knowledge about how and why these communities, which are so critical to host health, vary in nature. It will also fill an important gap in knowledge about how gut-dwelling organisms are transmitted among animals, with relevance to the control of infectious disease.

Planned Impact

I identify four major groups that will benefit from this work.

(1) The academic community
As detailed in 'Academic Beneficiaries' this research will be of key interest to academic researchers from a range of disciplines, including microbial ecologists, infectious disease biologists and mammal ecologists. I will ensure my research achieves impact in these academic fields by publishing primary research in high impact journals (open access whenever possible), writing opinion pieces and commentaries, presenting my work at relevant conferences, and organising a workshop. The latter will facilitate the exchange of ideas and approaches between microbiota researchers working on both model and non-model organisms and forge new research directions capitalising on the strengths of different systems.

(2) Postgraduate and undergraduate students
I anticipate a significant student interest in my research. The wood mouse project I would use in objectives 1 and 2 has already proved popular among Imperial MSc and MRes students for research projects. Aurelio Malo has supervised 15 Master's projects on this system since setting it up, and I anticipate similar popularity going forward. I will engage postgraduate and undergraduate students to carry out their own research projects. Through their involvement, these students will benefit from training in microbial and disease ecology, field techniques and statistical analyses, as well as transferable skills in project and data management.

(3) The general public
Gut microbes and parasites/pathogens pervade everyone's lives, with vast numbers colonizing all animals including humans. With continual revelations about the complexity of these communities and their diverse effects on host biology, our symbiotic communities certainly capture the public's interest. Other aspects of this work are also likely to stimulate public interest, including insight into the social lives of familiar wild species, and how social interactions affect pathogen spread (currently a hot topic, for example with recent media spotlight on bovine TB). Through actively pursuing media coverage of published work, having an accessible website and blog, as well as outreach activities at public science events, I will maximise the impact my research has on public understanding and enjoyment of science.

(4) Disease control community
This work is relevant to and has potential to inform public health programmes. Millions of pounds are spent each year on deworming as part of disease control programmes in humans and livestock. The Neglected Tropical Disease (NTD) community has set ambitious goals (e.g. the London Declaration on NTDs) to control or eliminate helminths from human populations, largely through mass treatment programmes. Current strategies essentially ignore within-host community ecology: there is little consideration of how deworming may alter these communities, and the potential implications for successful disease control. Part of this proposal addresses exactly this question using wild mice as a model system, and the results will provide a test case on this key issue. I will ensure my research broadens awareness in this area by (i) communicating results at conferences attended by end-users in disease control, (ii) organising a symposium focusing on these issues at one such conference, and (iii) writing commentaries that highlight key questions and findings in this area, with collaborators in the human NTD world established through my current position.

Related Projects

Project Reference Relationship Related To Start End Award Value
NE/L011867/1 06/09/2014 30/09/2015 £555,514
NE/L011867/2 Transfer NE/L011867/1 01/10/2015 31/03/2019 £442,660
NE/L011867/3 Transfer NE/L011867/2 01/04/2019 30/09/2021 £153,186
 
Description NBAF pilot scheme
Amount £13,836 (GBP)
Funding ID NBAF969 
Organisation Natural Environment Research Council 
Department NERC Biomolecular Analysis Facility (NBAF)
Sector Public
Country United Kingdom
Start 07/2016 
End 07/2017
 
Description NC3Rs Project Grant
Amount £284,634 (GBP)
Funding ID NC/R001103/1 
Organisation National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2017 
End 04/2019
 
Description NERC
Amount £42,040 (GBP)
Funding ID BRIS/100/05/17 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 12/2017 
End 07/2018
 
Title Comparative rodent microbiota dataset 
Description I have collected samples from a range of rodent species in Lithuania and sequenced the microbiome using 16S sequencing, for the third objective of my fellowship proposal. The dataset awaits analysis. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? No  
Impact F1000 recommended article in Ecology Letters, see publications; dataset in European Research Archive: PRJEB30121 
 
Title Diet shift-microbiome dataset 
Description A complete set of data on how diet shifts influence the microbiome of wood mice in captivity 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact None yet 
 
Title Wytham wild rodent ecology and microbiome dataset 
Description We are building a long-term dataset of wild mouse ecology (longitudinal sampling every fortnight since 2015) and microbiome samples, to address questions in my NERC fellowship. The first 2 years of sampling and data are now complete. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact None yet 
 
Description Collaboration with Alan Wilson - zebra microbiome 
Organisation Royal Veterinary College (RVC)
Department Structure and Motion Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution I have sequenced a pilot set of faecal samples from Plains Zebra, in order to characterise their gut microbiome. We are both developing ideas for grant applications on this new system.
Collaborator Contribution Alan's group conducted fieldwork to collect samples from Zebra in Botswana
Impact None yet. Collaboration is multi-disciplinary - involving engineers, biomathematicians/biophysicists and ecologists.
Start Year 2017
 
Description Collaboration with Amy Pedersen and Adrian Smith: Helminth-microbiota interactions 
Organisation University of Edinburgh
Department School of Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution I am collaborating with Amy and her PhD student, as well as Adrian Smith at Oxford to characterise gut microbiome changes in response to helminth infection in the wood mouse. I am contributing financially and in terms of expertise for the microbiome sequencing.
Collaborator Contribution Amy's group performed the experiments, using the captive wood mouse colony she runs in Edinburgh, is carrying out the lab work, and paid for DNA extractions. Adrian's group contribute in terms of expertise, particularly in library preparations for NGS.
Impact None yet - samples being processed
Start Year 2016
 
Description Collaboration with Amy Pedersen and Adrian Smith: Helminth-microbiota interactions 
Organisation University of Oxford
Department Department of Zoology
Country United Kingdom 
Sector Academic/University 
PI Contribution I am collaborating with Amy and her PhD student, as well as Adrian Smith at Oxford to characterise gut microbiome changes in response to helminth infection in the wood mouse. I am contributing financially and in terms of expertise for the microbiome sequencing.
Collaborator Contribution Amy's group performed the experiments, using the captive wood mouse colony she runs in Edinburgh, is carrying out the lab work, and paid for DNA extractions. Adrian's group contribute in terms of expertise, particularly in library preparations for NGS.
Impact None yet - samples being processed
Start Year 2016
 
Description Collaboration with Andrea Graham and Jackie Leung, Princeton 
Organisation Princeton University
Country United States 
Sector Academic/University 
PI Contribution We have written a review article together. Myself and Jackie researched and wrote the paper, Andrea provided critical comment
Collaborator Contribution Jackie helped prepare and write the paper, both contributed intellectually and Andrea comments on drafts
Impact Review article published in Frontiers Microbiol
Start Year 2015
 
Description Collaboration with Arild Husby 
Organisation University of Helsinki
Country Finland 
Sector Academic/University 
PI Contribution Provision of samples collected from the project to characterise genetic relatedness among population members
Collaborator Contribution Arild's student carried out the genotyping wet lab work and analysis to assign parentage, and analyse how this related to microbiome composition
Impact Assignment of parentage relationships in our two wood mouse study populations - at Silwood Park and Wytham Woods
Start Year 2018
 
Description Collaboration with Jens Walter 
Organisation University of Alberta
Country Canada 
Sector Academic/University 
PI Contribution Jens used some samples from my comparative rodent microbiome project for his studies of Lactobacillus reuteri biology in rodents, leading to publication of a paper "The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract" in ISME J.
Collaborator Contribution Jens received samples, isolated bacteria and characterised their genotype to assess Lactobacillus reuteri diversity across rodent species, and their in vivo interactions. His group drove the project and wrote the paper, which I commented on and edited.
Impact One paper published in ISME Journal "The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract"
Start Year 2015
 
Description Collaboration with Lindsay Hall: wild rodent Bifidobacteria 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution Lindsay, her PhD student and I initiated a collaboration to characterise whole genomes of Bifidobacteria strains from wild rodents. We supply faecal samples from fieldwork and intellectual input.
Collaborator Contribution Lindsay's group perform lab work to grow the bacteria, sequence the genomes and analyse them, and fund this side of the collaboration.
Impact None yet. Samples being sequenced
Start Year 2017
 
Description Collaboration with Philip Hugenholz, Jan Bradley and Kathryn Else 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution To date, my input has been intellectual and scientific expertise and samples. I contacted Philip to collaborate and investigate bacterial metagenomics within some of my wild rodent faecal samples. I had found an interesting result that a particular group of bacteria he works on (family S24-7) were driving host species-specificity in the comparative rodent microbiome dataset associated with this award.
Collaborator Contribution Philip and his postdoc are now going to characterise bacterial genomes within a set of the samples I collected. I will ship them DNA and they will carry out labwork, bioinformatics and analysis to characterise bacterial genomes within these samples.
Impact None yet
Start Year 2018
 
Description Collaboration with Philip Hugenholz, Jan Bradley and Kathryn Else 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution To date, my input has been intellectual and scientific expertise and samples. I contacted Philip to collaborate and investigate bacterial metagenomics within some of my wild rodent faecal samples. I had found an interesting result that a particular group of bacteria he works on (family S24-7) were driving host species-specificity in the comparative rodent microbiome dataset associated with this award.
Collaborator Contribution Philip and his postdoc are now going to characterise bacterial genomes within a set of the samples I collected. I will ship them DNA and they will carry out labwork, bioinformatics and analysis to characterise bacterial genomes within these samples.
Impact None yet
Start Year 2018
 
Description Collaboration with Philip Hugenholz, Jan Bradley and Kathryn Else 
Organisation University of Queensland
Department School of Chemistry and Molecular Biosciences
Country Australia 
Sector Academic/University 
PI Contribution To date, my input has been intellectual and scientific expertise and samples. I contacted Philip to collaborate and investigate bacterial metagenomics within some of my wild rodent faecal samples. I had found an interesting result that a particular group of bacteria he works on (family S24-7) were driving host species-specificity in the comparative rodent microbiome dataset associated with this award.
Collaborator Contribution Philip and his postdoc are now going to characterise bacterial genomes within a set of the samples I collected. I will ship them DNA and they will carry out labwork, bioinformatics and analysis to characterise bacterial genomes within these samples.
Impact None yet
Start Year 2018
 
Description Curiosity Carnival 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact I talked about small mammal research at the Wytham Woods Curiosity Carnival, telling members of the General Public what we do
Year(s) Of Engagement Activity 2017
 
Description Silwood BUGS! Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I ran a "Bugs in the body" stall with a Microbiome theme for visiting schoolchildren at an Imperial (Silwood Park) local event called "BUGS!" day. Many schoolchildren and members of the public stopped by and learned about the microbes in their bodies via interactive games, and the event was very well received overall.
Year(s) Of Engagement Activity 2015
URL http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/eventssummary/event_4-6-2015-10-11-47
 
Description UNIQ summer school 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Engagement / talk to UNIQ summer school students in the woods, about fieldwork and our NERC- and NC3Rs- funded research.
The students came to the woods, had a talk about wild rodent fieldwork, and our research, saw various species of captured rodent, and asked questions, as well as having a tour of the university woodland.
the UNIQ programme is designed to give students from disadvantaged backgrounds a chance to visit Oxford and learn about what a degree at the unversity would be like, and the kinds of research going on.
Year(s) Of Engagement Activity 2018