Gastrointestinal helminth infection likely affects the gut microbiome, in turn affecting host health. To investigate the effect of intestinal parasite status on the gut microbiome, parasitic infection surveys were conducted in communities in Nan Province, Thailand. In total, 1047 participants submitted stool samples for intestinal parasite examination, and 391 parasite-positive cases were identified, equating to an infection prevalence of 37.3%. Intestinal protozoan species were less prevalent (4.6%) than helminth species. The most prevalent parasite was the minute intestinal fluke Haplorchis taichui (35.9%). Amplicon sequencing of 16S rRNA was conducted to investigate the gut microbiome profiles of H. taichui-infected participants compared with those of parasite-free participants. Prevotella copri was the dominant bacterial operational taxonomic unit (OTU) in the study population. The relative abundance of three bacterial taxa, Ruminococcus, Roseburia faecis and Veillonella parvula, was significantly increased in the H. taichui-infected group. Parasite-negative group had higher bacterial diversity (α diversity) than the H. taichui-positive group. In addition, a significant difference in bacterial community composition (β diversity) was found between the two groups. The results suggest that H. taichui infection impacts the gut microbiome profile by reducing bacterial diversity and altering bacterial community structure in the gastrointestinal tract.

Chigger mites (Trombiculidae) are temporary habitat-specific ectoparasites that often occur on rodents. Little ecological data are available on chiggers associated with rodents in South Africa. The study aims were to (1) record the chigger species associated with rodents in the savanna, (2) assess if chigger species display parasitope preference on the rodent body and (3) compare the distribution of chigger species in natural, agricultural and urban habitats. Rodents (n = 314) belonging to eight genera were trapped in the savanna biome during 2014 and 2015. Twelve chigger species, of which five are recently described species, were recorded from 161 rodent hosts. The data include three new country locality records. Microtrombicula mastomyia was the most prevalent species across sampling seasons and habitat types. Significant parasitope preference was recorded for two species, with the ear, face and tail base some of the preferred attachment sites. Sampling season and habitat type had a significant effect on chigger communities with summer and agricultural habitats recording the highest species richness, while the highest species diversity was recorded in natural habitats. The study contributes to our current knowledge regarding rodent-associated chigger diversity and distribution in South Africa and further highlights the importance of environmental characteristics in shaping chigger communities.

DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. DNA barcoding found new applications in disease ecology, conservation parasitology, environmental parasitology and in paleoparasitology. New technologies such as next-generation sequencing and matrix-assisted laser desorption–ionization time-of-flight have made it now possible to investigate large samples of specimens. By allowing the investigation of parasites at the interface between environment, biodiversity, animal and human health, barcoding and biobanking have important policy outcomes as well as ethics and legal implications. The special issue ‘Advances and challenges in the barcoding of parasites, vectors and reservoirs’ illustrates some recent advances and proposes new avenues for research in barcoding in parasitology.

Pneumocystis organisms are airborne-transmitted fungal parasites that infect the lungs of numerous mammalian species with strong host specificity. In this study, we investigated the genetic diversity and host specificity of Pneumocystis organisms infecting Southeast Asian murid rodents through PCR amplification of two mitochondrial genes and tested the co-phylogeny hypothesis among these fungi and their rodent hosts. Pneumocystis DNA was detected in 215 of 445 wild rodents belonging to 18 Southeast Asian murid species. Three of the Pneumocystis lineages retrieved in our phylogenetic trees correspond to known Pneumocystis species, but some of the remaining lineages may correspond to new undescribed species. Most of these Pneumocystis species infect several rodent species or genera and some sequence types are shared among several host species and genera. These results indicated a weaker host specificity of Pneumocystis species infecting rodents than previously thought. Our co-phylogenetic analyses revealed a complex evolutionary history among Pneumocystis and their rodent hosts. Even if a significant global signal of co-speciation has been detected, co-speciation alone is not sufficient to explain the observed co-phylogenetic pattern and several host switches are inferred. These findings conflict with the traditional view of a prolonged process of co-evolution and co-speciation of Pneumocystis and their hosts.

A dataset of bacterial diversity found in mites was compiled from 193 publications (from 1964 to January 2015). A total of 143 mite species belonging to the 3 orders (Mesostigmata, Sarcoptiformes and Trombidiformes) were recorded and found to be associated with approximately 150 bacteria species (in 85 genera, 51 families, 25 orders and 7 phyla). From the literature, the intracellular symbiont Cardinium, the scrub typhus agent Orientia, and Wolbachia (the most prevalent symbiont of arthropods) were the dominant mite-associated bacteria, with approximately 30 mite species infected each. Moreover, a number of bacteria of medical and veterinary importance were also reported from mites, including species from the genera Rickettsia, Anaplasma, Bartonella, Francisella, Coxiella, Borrelia, Salmonella, Erysipelothrix and Serratia. Significant differences in bacterial infection patterns among mite taxa were identified. These data will not only be useful for raising awareness of the potential for mites to transmit disease, but also enable a deeper understanding of the relationship of symbionts with their arthropod hosts, and may facilitate the development of intervention tools for disease vector control. This review provides a comprehensive overview of mite-associated bacteria and is a valuable reference database for future research on mites of agricultural, veterinary and/or medical importance.