Best Practices for Microbiome Study Design in Companion Animal Research

Jarett, Jessica K.; Kingsbury, Dawn D.; Dahlhausen, Katherine E.; Ganz, Holly H.

doi:10.3389/fvets.2021.644836

Cited by 21 publications

(23 citation statements)

References 148 publications

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“…This was counteracted by controlling for most influential gut microbiota environmental (food, lifestyle and living environment) and genetic factors (all dogs were Beagles), as shown in previous human studies [ 36 , 37 ]. In dogs, there is currently a large body of evidence that the diet exerts a significant impact on the gut microbiota in this species [ 38 , 39 ], but there is no data on the genetic influence. This combined with the fact that the breed and the environment were controlled, gives our report a crucial edge, since both factors have been shown to be important in the pathogenesis of AD [ 40 , 41 ].…”

Section: Discussionmentioning

confidence: 99%

Comparison of the Gut Microbiome between Atopic and Healthy Dogs—Preliminary Data

Rostaher

Morsy

Favrot

et al. 2022

Animals

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Human studies show that in addition to skin barrier and immune cell dysfunction, both the cutaneous and the gut microbiota can influence the pathogenesis of atopic diseases. There is currently no data on the gut-skin axis in allergic canines. Therefore, the aim of this study was to assess the bacterial diversity and composition of the gut microbiome in dogs with atopic dermatitis (AD). Stool samples from adult beagle dogs (n = 3) with spontaneous AD and a healthy control group (n = 4) were collected at Days 0 and 30. After the first sampling, allergic dogs were orally dosed on a daily basis with oclacitinib for 30 days, and then re-sampled. Sequencing of the V3–V4 region of the 16S rRNA gene was performed on the Illumina MiSeq platform and the data were analyzed using QIIME2. The atopic dogs had a significantly lower gut microbiota alpha-diversity than healthy dogs (p = 0.033). In healthy dogs, a higher abundance of the families Lachnospiraceae (p = 0.0006), Anaerovoracaceae (p = 0.006) and Oscillospiraceae (p = 0.021) and genera Lachnospira (p = 0.022), Ruminococcustorques group (p = 0.0001), Fusobacterium (p = 0.022) and Fecalibacterium (p = 0.045) was seen, when compared to allergic dogs. The abundance of Conchiformibius (p = 0.01), Catenibacterium spp. (p = 0.007), Ruminococcus gnavus group (p = 0.0574) and Megamonas (p = 0.0102) were higher in allergic dogs. The differences in alpha-diversity and on the compositional level remained the same after 1 month, adding to the robustness of the data. Additionally, we could also show that a 4-week treatment course with oclacitinib was not associated with changes in the gut microbiota diversity and composition in atopic dogs. This study suggests that alterations in the gut microbiota diversity and composition may be associated with canine AD. Large-scale studies preferably associated to a multi-omics approach and interventions targeting the gut microbiota are needed to confirm these results.

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Section: Discussionmentioning

confidence: 99%

Comparison of the Gut Microbiome between Atopic and Healthy Dogs—Preliminary Data

Rostaher

Morsy

Favrot

et al. 2022

Animals

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“…The kinetics required by a dietary change to modify the community structure and activity of gut microbiota and then stabilize, however, has not been well studied. Most dietary intervention studies provide a dietary treatment for 2 to 4 weeks prior to sample collection to allow the microbial community and activity to stabilize [ 20 ]. A limited number of studies have measured short-term microbial dynamics in humans [ 21 – 23 ], but with low subject numbers and a lack of longitudinal sampling times.…”

Section: Introductionmentioning

confidence: 99%

Longitudinal fecal microbiome and metabolite data demonstrate rapid shifts and subsequent stabilization after an abrupt dietary change in healthy adult dogs

Lin

Jha²,

Oba

et al. 2022

anim microbiome

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Background Diet has a large influence on gut microbiota diversity and function. Although previous studies have investigated the effect of dietary interventions on the gut microbiome, longitudinal changes in the gut microbiome, microbial functions, and metabolite profiles post dietary interventions have been underexplored. How long these outcomes require to reach a steady-state, how they relate to one another, and their impact on host physiological changes are largely unknown. To address these unknowns, we collected longitudinal fecal samples following an abrupt dietary change in healthy adult beagles (n = 12, age: 5.16 ± 0.87 year, BW: 13.37 ± 0.68 kg) using a crossover design. All dogs were fed a kibble diet (control) from d1-14, and then fed that same diet supplemented with fiber (HFD) or a protein-rich canned diet (CD) from d15-27. Fresh fecal samples were collected on d13, 16, 20, 24, and 27 for metabolite and microbiome assessment. Fecal microbial diversity and composition, metabolite profiles, and microbial functions dramatically diverged and stabilized within a few days (2 d for metabolites; 6 d for microbiota) after dietary interventions. Fecal acetate, propionate, and total short-chain fatty acids increased after change to HFD, while fecal isobutyrate, isovalerate, total branched-chain fatty acids, phenol, and indole increased after dogs consumed CD. Relative abundance of ~ 100 bacterial species mainly belonging to the Firmicutes, Proteobacteria, and Actinobacteria phyla increased in HFD. These shifts in gut microbiome diversity and composition were accompanied by functional changes. Transition to HFD led to increases in the relative abundance of KEGG orthology (KO) terms related to starch and sucrose metabolism, fatty acid biosynthesis, and amino sugar and nucleotide sugar metabolism, while transition to CD resulted in increased relative abundance of KO terms pertaining to inositol phosphate metabolism and sulfur metabolism. Significant associations among fecal microbial taxa, KO terms, and metabolites were observed, allowing for high-accuracy prediction of diet group by random forest analysis. Conclusions Longitudinal sampling and a multi-modal approach to characterizing the gastrointestinal environment allowed us to demonstrate how drastically and quickly dietary changes impact the fecal microbiome and metabolite profiles of dogs following an abrupt dietary change and identify key microbe-metabolite relationships that allowed for treatment prediction.

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“…After deciding on the study design, necessary measurements based on its specific demands are then collected from the participants. These will further depend on the project goals and limitations of the available equipment or other resources (Jarett et al ., 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Towards standardized and reproducible research in skin microbiomes

Ruuskanen

Vats

Potbhare

et al. 2022

Environmental Microbiology

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Summary Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host‐associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high‐throughput sequencing of sample‐extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.

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Best Practices for Microbiome Study Design in Companion Animal Research

Cited by 21 publications

References 148 publications

Comparison of the Gut Microbiome between Atopic and Healthy Dogs—Preliminary Data

Comparison of the Gut Microbiome between Atopic and Healthy Dogs—Preliminary Data

Longitudinal fecal microbiome and metabolite data demonstrate rapid shifts and subsequent stabilization after an abrupt dietary change in healthy adult dogs

Towards standardized and reproducible research in skin microbiomes

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