Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats

Ma, Xiaolei; Brinker, Emily; Graff, Emily C.; Cao, Wenqi; Gross, Amanda L.; Johnson, Aime K.; Zhang, Chao; Martin, Douglas R.; Wang, Xiaozhu

doi:10.1128/spectrum.00837-22

Cited by 27 publications

(19 citation statements)

References 114 publications

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“…Whole‐genome shotgun (WGS) metagenomic sequencing was performed in this study to assess the feline microbiome, as this method is rapidly becoming the new standard for assessing microbiomes across all species. We anticipate that the results will be applicable to 16S rDNA ampliconic sequencing, because a high correlation in taxonomic composition was observed in the feline microbiome using these 2 approaches 15 …”

Section: Discussionmentioning

confidence: 97%

“…The feline reads were extracted using SAMtools (version 1.6) 13 and BEDTools (version 2.30.0) 14 . The remaining microbial reads were aligned to the feline gut metagenomic reference contigs (GCA_022675345.1) 15 with comprehensive taxonomy assignments and microbial gene annotations. Taxonomic abundances were determined in the form of read counts, which were normalized by the total amount of sequences to obtain counts per million mapped reads (CPM) for subsequent metagenomic analyses.…”

Section: Methodsmentioning

confidence: 99%

“…The sample size of 8 was determined based on the rarefaction plots in our previous research on the feline microbiome, 9 to ensure at least 90% of bacterial species and microbial genes in the reference assembly (NCBI Assembly ID JAIZPE000000000) were covered. Two fecal samples were collected from each of the 8 enrolled cats under sedation.…”

Section: Methodsmentioning

confidence: 99%

“…The feline reads were extracted using SAMtools (version 1.6) 13 and BEDTools (version 2.30.0). 14 The remaining microbial reads were aligned to the feline gut metagenomic reference contigs (GCA_022675345.1) 15 with comprehensive taxonomy assignments and microbial gene annotations.…”

Section: Processing and Bioinformatic Analysis Of Metagenomic Datamentioning

confidence: 99%

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Effect of mineral oil as a lubricant to collect feces from cats for microbiome studies

Brinker

Cao

et al. 2022

Veterinary Internal Medicne

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Background Fecal specimens are critical for disease screening, diagnosis, and gut microbiome research. For domestic cats, lubricants are often necessary to obtain a sufficient quantity of sample. However, the effect of lubrication on feline microbiome analysis has not been assessed. Objectives To evaluate if lubrication using mineral oil during cat feces sample collection affects the DNA extraction, metagenomic sequencing yield, and the microbial composition and diversity in subsequent gut microbiome analyses. Animals Eight 6‐year‐old male, neutered, domestic short‐haired cats housed in a research facility. Methods Cohort study. The gut microbiomes were investigated for fecal sample collection with and without lubrication using whole‐genome shotgun metagenomic sequencing. Results Fecal specimens were collected using a fecal loop under sedation without lubrication and with mineral oil lubrication. There were no significant differences between the 2 groups in the microbial DNA yield in ng/mg fecal sample (75.75 [25.8‐125.7] vs 60.72 [33.49‐87.95], P = .95), metagenomic sequencing yield in Gbp (10.31 [6.29‐14.32] vs 13.53 [12.04‐15.02], P = .2), proportion of host contamination (0.1 [0.02‐0.18] vs 0.15 [0‐0.3], P = .84), relative taxonomy abundance (P > .8), or the number of microbial genes covered (408 132 [341 556‐474 708] vs 425 697 [358 505‐492 889], P = .31). Conclusions and Clinical Importance Fecal sampling with mineral oil lubrication did not change the microbial DNA extraction yield, metagenomic sequencing yield, level of host contamination, the microbial composition and diversity in subsequent gut microbiome analyses. Here we reported a proven cat‐friendly protocol for fecal sample collection in clinical and research setting for gut microbiome analyses.

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Section: Discussionmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Processing and Bioinformatic Analysis Of Metagenomic Datamentioning

confidence: 99%

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Effect of mineral oil as a lubricant to collect feces from cats for microbiome studies

Brinker

Cao

et al. 2022

Veterinary Internal Medicne

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“…The operational taxonomic units (OTUs) with 97% similarity were clustered using UPARSE version 7.1 ( , accessed on 3 September 2022), and the taxonomy of each OTU representative sequence was analyzed by RDP Classifier version 2.2 ( , accessed on 3 September 2022) against the 16S rRNA database (Silva v138). The bioinformatics analyses of all the sequenced samples referred to previous studies [ 28 , 29 , 30 ].…”

Section: Methodsmentioning

confidence: 99%

Comparative Analyses of the Gut Microbiota in Growing Ragdoll Cats and Felinae Cats

Sun

et al. 2022

Animals

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Today, domestic cats are important human companion animals for their appearance and favorable personalities. During the history of their domestication, the morphological and genetic portraits of domestic cats changed significantly from their wild ancestors, and the gut microbial communities of different breeds of cats also apparently differ. In the current study, the gut microbiota of Ragdoll cats and Felinae cats were analyzed and compared. Our data indicated that the diversity and richness of the gut microbiota in the Felinae cats were much higher than in the Ragdoll cats. The taxonomic analyses revealed that the most predominant phyla of the feline gut microbiota were Firmicutes, Bacteroidota, Fusobacteriota, Proteobacteria, Actinobacteriota, Campilobacterota, and others, while the most predominant genera were Anaerococcus, Fusobacterium, Bacteroides, Escherichia-Shigella, Finegoldia, Porphyromonas, Collinsella, Lactobacillus, Ruminococcus_gnavus_group, Prevotella, and others. Different microbial communities between the Ragdoll group and the Felinae group were observed, and the compared results demonstrated that the relative abundances of beneficial microbes (such as Lactobacillus, Enterococcus, Streptococcus, Blautia, Roseburia, and so on) in the Ragdoll group were much higher than in the Felinae group. The co-occurrence network revealed that the number of nodes and links in the Felinae group was significantly higher than the Ragdoll group, which meant that the network of the Felinae group was larger and more complex than that of the Ragdoll group. PICRUSt function analyses indicated that the differences in microbial genes might influence the energy metabolism and immune functions of the host. In all, our data demonstrated that the richness and diversity of beneficial microbes in the Ragdoll group were much higher than the Felinae group. Therefore, it is possible to isolate and identify more candidate probiotics in the gut microbiota of growing Ragdoll cats.

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Gastrointestinal Microbiomes

2023

Small Animal Microbiomes and Nutrition

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Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats

Abstract: Obesity affects around 45% of domestic cats, and licensed drugs for treating feline obesity are lacking. Physical exercise and calorie restrictions are commonly used for weight loss but with limited efficacy.

Cited by 27 publications

References 114 publications

Effect of mineral oil as a lubricant to collect feces from cats for microbiome studies

Effect of mineral oil as a lubricant to collect feces from cats for microbiome studies

Comparative Analyses of the Gut Microbiota in Growing Ragdoll Cats and Felinae Cats

Gastrointestinal Microbiomes

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