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Background  Chronic recurrent diarrhoea and weight loss is a common problem in captive callitrichids. These symptoms are common clinical features of marmoset wasting syndrome (MWS), a chronic enteric inflammation of unknown aetiology associated with mortality in captive marmosets. The unknown aetiology of the condition presents problems for conservation projects where affected colonies present higher mortality and lower birth rates. Since a role for the microbiome has been established in chronic enteric inflammation of other species it is possible that the intestinal microbiome undergoes similar changes during MWS.    Results  The faecal microbiome of pied tamarins ( Saguinus bicolor ) at Jersey Zoo was determined using 16S rRNA gene amplicon sequencing to compare the composition of the faecal microbiome of tamarins affected by chronic recurrent diarrhoea and weight loss with unaffected individuals. Affected individuals had a higher relative abundance of amplicon sequence variants assigned to  Lactobacillus  and  Helicobacter jaachi  while unaffected individuals had a higher relative abundance of some  Lachnospiraceae  and  Ruminococcaceae .    Conclusions  Although  Helicobacter  has been shown to reside in healthy wild and captive marmosets and tamarins and appears to form part of the normal microbiota, the results of this study raise the prospect that certain species of  Helicobacter  may be associated with chronic, recurrent diarrhoea in captive callitrichids. The presence of  Lactobacillus  may also play a role in the development of MWS. Since depletion of  Lachnospiraceae  and  Ruminococcaceae  have been linked to chronic gastrointestinal inflammation in humans, this feature of the microbiome of affected tamarins provides another avenue of further research in the pathogenesis of MWS.    Supplementary Information  The online version contains supplementary material available at (doi:10.1186/s42523-020-00062-4).

Changes in the faecal microbiome of pied tamarins (Saguinus bicolor) associated with chronic, recurrent diarrhoea and weight loss