Royal Netherlands Institute for Sea Research

It takes guts!

It takes guts to boost your resilience against climate change

Food webs are altering under climate change and many animals have needed to switch to alternative food sources due to changes in their prey resources. This obviously requires flexible foraging adaptations. We hypothesize that changes in the gut microbiome are critical in such diets shifts, especially when animals switch from a carnivorous to an herbivorous diet or vice versa. Here we examine the gut microbial community of a migratory shorebird in decline, the red knot (Calidris canutus), which has shown a radical diet shift from shellfish to seagrass rhizomes caused by a climate-induced bill shortening and changes in food supply.


We will combine the expertise available at NIOZ regarding the foraging ecology of migratory shorebirds with the expertise available at UU about the gut microbiomes.

    Jan van Gils, Aldert Zomer

Project description


Food webs are altering under climate change, where animals often need to switch to alternative food sources when their main prey has become unavailable1. This obviously requires flexible foraging adaptations. While focus has been on the easily observed changes in behavior that come with changes in diet, such as changes in habitat choice, the unseen changes inside the animal, specifically changes in the gut microbiome, are pretty much unrecorded but may be of utmost importance. In fact, the so-called ‘hologenome’ concept2 states that animals are better able to adapt to rapid environmental changes by altering their gut microbiome rather than slowly changing through their own genome. Most likely, changes in the gut microbiome are critical in adaptive diets shifts, especially when animals switch from a carnivorous to an herbivorous diet or vice versa. As the organisms in the microbiome degrade difficult to digest compounds (e.g. celluloses) and produce more accessible products such as fatty acids, shifts from a carnivorous diet towards an herbivorous diet is only possible if the microbiome adapts.

A case and point is the red knot, a well-studied shorebird3, that is in strong decline4. This species is shifting its diet from shellfish to seagrass on its West-African wintering grounds, partly due to changes in body size5 and to changes in the food supply6. Here we hypothesize that this change to a predominantly herbivorous diet is only feasible through a concomitant change in the bird’s microbiome. This hypothesis is of conservation concern, as it predicts that birds which do not acquire the necessary microbiome fail to make the required diet switch.

Changes in the gut microbiome are a requirement for animals making radical diet shifts, like red knots shifting from a shellfish-based diet to a seagrass-based diet (left inset). Climate change is shuffling food webs, and we need to understand how well consumers can adapt to new potential prey sources.

To investigate this hypothesis, we aim to investigate the relationship between the gut microbiome community and foraging performance using the red knot as our model forager.

More specific objectives are to:

  • Obj. 1 Investigate the inter-individual correlation between the degree of herbivory and the diversity composition of the gut microbiome.
  • Obj. 2 Investigate the functional content of the microbiome by sequence-based metagenomics before and after a diet shift.
  • Obj. 3 Study cause and effect – does the microbiome composition follow the diet, and/or vice versa?
  • Obj. 4 Assess foraging performance on different food types in relation to different microbiome compositions.


This work will be a mix of descriptive (Obj. 1) and experimental (Obj. 2, 3 and 4) work carried out at our study site in Banc d’Arguin, Mauritania, where the majority of the nominate subspecies of the red knot overwinters. Each winter, NIOZ organizes a ‘catching expedition’ to Banc d’Arguin where 100-200 red knots are caught for the purpose of demographic monitoring.

The descriptive work will link the diet of birds caught from the wild to their gut microbiome. One of the ideal features of the food web in Banc d’Arguin is the distinct stable isotope (SI) ratios of δ13C and δ15N of three major food types (mollusks, seagrass, and a mildly toxic bivalve), enabling reconstruction of the red knot diet composition on the basis of tissue samples (blood and feathers, revealing diet over time scales of weeks and months, respectively)5. The results of a pilot study conducted in 2018 look very promising (right inset in graphic on p. 1), with 11 birds exhibiting a clear trend between their degree of herbivory (based on blood SI ratios) and the community composition of their microbiome. This analysis will be extended to approximately 300 birds, targeting 100 birds caught per year during three winter-expeditions. Blood samples will be taken for SI analyses, while fecal swab samples will be taken for microbial diversity analyses (16S rRNA gene). Sequencing data will be processed with bioinformatic tools already developed by the group.

The experimental work will take place on captive red knots (with which we have ample experience7-9) offered either a shellfish-based or a seagrass-based diet and changes in gut microbial diversity (16S rRNA gene at DNA level), activity (16S rRNA at RNA level), and functionality (metagenomics) will be monitored which will be linked to the relative composition of carbohydrates, protein and fat in the two food types. Furthermore, changes in digestive efficiency will be quantified by relating food intake to excreta production at regular moments (this includes measurements on digestive efficiency on shellfish in the group of birds on a long-term seagrass diet, and vice versa).

An additional experiment in captivity will manipulate the gut microbiome by transferring the microbiome from one animal to the other via fecal microbiota transfer10 (i.e. from a typical seagrass-eater to a typical shellfish eater and vice versa). Subsequently, the response in food intake and digestive efficiency will be quantified at regular moments.

At the end of both experiments, when the birds are fully adjusted to their new diet and/or gut microbiome (presumably a period of a couple of weeks), the birds will be released. By attaching a radio transmitter to their back, we will be able to find them back in the field11. We will then measure whether the manipulated diet and/or microbiome affects their intake rate (telescope observations), digestive efficiency (fecal analyses), diet (fecal analyses) and foraging patch choice in the wild.

The research team

This is a highly multidisciplinary proposal combining elements of animal ecology, microbiology and global change biology. The team members work in three very different but complimentary departments. JvG (NIOZ-COS) is a leading expert on global-scale marine trophodynamics of migrant shorebirds. LV (NIOZ-MMB) is a microbial ecologist specializing in using molecular methods to examine microbial diversity and physiology. AZ (UU-Veterinary Medicine) is specialized in animal microbiome research and genomic epidemiology. JW (UU-Veterinary Medicine) is veterinary microbiologist examining the effects of interventions on the microbiome in healthy and diseased animals. Quarterly meetings will help ensure a successful and productive cooperation. We will benefit from tight international connections, notably between JvG and BH (UoW, Australia), who studies the role of microbial symbionts in shaping animal performance, and the cascading effects for the provision of ecosystem services12.

Connection to the themes

  • Sustainable functioning of coastal and shelf seas. Shorebirds play an important role as top consumers in coastal marine ecosystems. Our research on the effects of climate change on shifting consumer resource interactions contributes directly to this theme which aims at understanding the human impact on ecosystem functioning. If we elucidate the critical role that gut microorganisms play in coping with (forced) diet switches, we may be better able to understand why some species, populations, or individuals, cope better than others with rapid, human-induced changes to marine (or terrestrial) ecosystems.
  • Ocean of discovery. By exploring major unknowns in a.o. microbial life, our proposal also fits well to this theme. We are only at the beginning of revealing the intricate interactions between gut bacteria and their hosts, and the interdisciplinary blend of microbiology and avian foraging ecology will reveal exciting new, fundamental knowledge important to advancing both of these fields.


  1. Evans & Moustakas Ecol Inform 47, 61-66 (2018).
  2. Zilber-Rosenberg & Rosenberg FEMS Microbiol Rev 32, 723-735 (2008).
  3. Piersma & van Gils The Flexible Phenotype (Oxford University Press, 2011).
  4. Oudman et al. Bird Conserv Intl 30, 618-633 (2020).
  5. van Gils et al. Science 352, 819-821 (2016).
  6. van Gils et al. Proc R Soc B 280, 20130861 (2013).
  7. van Gils & Ahmedou Salem PLoS ONE 10, e0140221 (2015).
  8. Oudman et al. Am Nat 183, 650-659 (2014).
  9. de Fouw et al. Anim Behav 115, 55-67 (2016).
  10. Ericsson & Franklin ILAR J 56, 205-217 (2015).
  11. Oudman et al. J Anim Ecol 85, 1378-1388 (2016).
  12. Hoye & Fenton J Anim Ecol 87, 315-319 (2018).
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Foraging red knot in Mauritania, Jan van de Kam

Connected themes

  • Sustainable Functioning of Coastal and Shelf Seas
  • Ocean of Discovery
NIOZ project page
Job opening: PhD position