Chronic clinical signs of upper respiratory tract disease associate with gut and respiratory microbiomes in a cohort of domestic felines

Abstract

Feline upper respiratory tract disease (FURTD), often caused by infections etiologies, is a multifactorial syndrome affecting feline populations worldwide. Because of its highly transmissible nature, infectious FURTD is most prevalent anywhere cats are housed in groups such as animal shelters, and is associated with negative consequences such as decreasing adoption rates, intensifying care costs, and increasing euthanasia rates. Understanding the etiology and pathophysiology of FURTD is thus essential to best mitigate the negative consequences of this disease. Clinical signs of FURTD include acute respiratory disease, with a small fraction of cats developing chronic sequelae. It is thought that nasal mucosal microbiome changes play an active role in the development of acute clinical signs, but it remains unknown if the microbiome may play a role in the development and progression of chronic clinical disease. To address the knowledge gap surrounding how microbiomes link to chronic FURTD, we asked if microbial community structure of upper respiratory and gut microbiomes differed between cats with chronic FURTD signs and clinically normal cats. We selected 8 households with at least one cat exhibiting chronic clinical FURTD, and simultaneously collected samples from cohabitating clinically normal cats. Microbial community structure was assessed via 16S rDNA sequencing of both gut and nasal microbiome communities. Using a previously described ecophylogenetic method, we identified 136 and 89 microbial features within gut and nasal microbiomes respectively that significantly associated with presence of active FURTD clinical signs in cats with a history of chronic signs. Overall, we find that nasal and gut microbial community members associate with the presence of chronic clinical course, but more research is needed to confirm our observations.

Identification of rare microbial colonizers of plastic materials incubated in a coral reef environment

“…The vast majority of the ASVs returned neighbors that were of environmental and/or metagenomic origin and did not have taxonomy assignments. To account for this, we opted to use a method of taxonomic agglomeration called Cladal Taxonomic Annotations (CTA), which ( Zalasiewicz et al, 2017 ) applies known taxonomic annotations of reference tips to propagate information about taxonomy to ancestral internal nodes within the phylogenetic tree and then ( Barnes et al, 2009 ) subsequently assigns taxonomic labels to unknown ASVs by using the taxonomic label of the most recent common ancestor ( Supplementary Figure S7 ; Gaulke et al, 2018 ; McLaren and Callahan, 2021 ; Arnold et al, 2022 ). Given the novelty of the CTA method we first labeled all figures with taxonomic annotations obtained using RDP NBC if available, and then only subsequently annotated unknown nodes with CTA.…”

“…The ASVs which failed to be taxonomic annotated were subjected to a novel taxonomic annotation approach called Cladal Taxonomic Annotation (CTA), which expands on our previous work ( Gaulke et al, 2018 ; Sharpton et al, 2021 ; Arnold et al, 2022 ). We used the All Species Living Tree Project (LTP) type strain 16S sequences and taxonomy (v. LTP_06_2022) as reference for our phylogenetic tree generation ( Pruesse et al, 2012 ).…”

Whole-Genome Deep Sequencing of the Healthy Adult Nasal Microbiome

“…FURTD, often caused by infectious etiologies, is a multifactorial syndrome that affects feline populations. The eco-phylogenetic method identified 136 and 89 microbial features within the gut and nasal microbiomes, significantly associated with active FURTD clinical signs [58]. Nasal and gut microbial community members are associated with a chronic clinical course [59].…”

Whole-Genome Deep Sequencing of the Healthy Adult Nasal Microbiome

“…Using the ecophylogenetic method, 136 and 89 microbial features were identified within the gut and nasal microbiomes, which were significantly associated with active FURTD clinical signs. [58] Nasal and gut microbial community members are associated with a chronic clinical course. [59] Studies have shown that endogenous microbiome dysbiosis can affect mucosal health and disease severity.…”