Available online 7 May 2024, 102862

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The first study of culturing novel Bacteroides from an Alpaca.

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Strains independently isolated from separate breeds of huacaya and suri alpacas.

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Novel species Bacteroides vicugnae, sp. nov. is proposed.

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Relatively few recovered bacteria from non-human, mammalian sources.

ABSTRACT

Two strictly anaerobic, Gram-stain-negative rod-shaped bacterial isolates, A2-P53T and A1-P5, were isolated from an enrichment of fecal material from two alpacas (Vicugna pacos). Based on a comparative 16S rRNA gene sequence analysis, the isolates were assigned to the genus Bacteroides with the highest sequence similarities to Bacteroides koreensis YS-aM39T (A2- P53T 97.7% and A1-P5 97.9%). Additionally, the average nucleotide identity and digital DNA-DNA hybridization values between these isolates and their closest relatives within Bacteroides were less than 92.1% and 49.1%, respectively. The average nucleotide identity between isolates A2-P53T and A1-P5 was 99.9%. The predominant cellular fatty acid for isolates A2-P53T and A1-P5 was C15:0 antesio. The G+C % content of the isolates was 41.7%. Based on biochemical, phylogenetic, genotypic, and chemotaxonomic criteria, these isolates A2-P53T and A1-P5 represent two individual strains of a novel species within the genus Bacteroides for which the name Bacteroides vicugnae sp. nov. is proposed. The type strain of this species is strain A2-P53T (CCUG 77273T=CCM 9377T=NRRL B-65693T).

Section snippetsINTRODUCTION

There is an inherent bacterial cultivation bias towards humans as 400% more bacteria have been isolated from humans than from the rest of the class Mammalia (https://bacdive.dsmz.de). Furthermore, there is a paucity of microbiome data regarding the alpaca (Vicugna pacos), and minimal microbiome studies have been exclusively focused on culture-independent methods [1], [2], [3], [4]. These molecular inventories have provided tremendous insights into the microbial diversity and taxa richness

Bacterial Strains

Strains A2-P53T and A1-P5 were isolated from freshly voided alpaca fecal samples obtained from two domesticated alpacas (a male, suri alpaca and a female, huacaya alpaca), herein denoted by A1 or A2, from the same privately owned alpaca ranch near Newcastle, Oklahoma, USA (35.24 N 97.59 W). The freshly voided fecal samples were collected and immediately placed into an anaerobic jar (oxoid) with an anaerobic gas pack (BD). The jar was placed on ice and transported to the Lawson Microbial

Phylogenetic Analysis

Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strains A2-P53T and A1-P5 were most closely related to Bacteroides koreensis Ys-aM39T (GenBank: KX025133) (97.9/97.7%), Bacteroides ovatus ATCC 8486T (GenBank: DS264555) (97.4/97.6%), and Bacteroides luhongzhouii HF-5141T (GenBank: MK584158) (97.2/96.1%). These values, along with the phylogenetic trees constructed by the Maximum Likelihood method [29] (Fig. 1) and the Neighbor-Joining method [30] (Fig. S1), support the

FUNDING INFORMATION

This research was supported by the Center for Microbial Identification & Taxonomy.

ETHICAL STATEMENT

This article does not contain any studies with animals performed by any of the authors.

REPOSITORIES

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of A2-P53T and A1-P5 are OQ724630 and OQ725027. The GenBank/EMBL/DDBJ accession numbers for the genome sequences of A2-P53T and A1-P5 GCA_034291875.1and GCA_034291865.1 .

Declaration of Competing Interest

The authors declare that they have no indirect or direct conflicts of interest.

ACKNOWLEDGEMENTS

The authors thank Terri and Kerry Bates of the Magnolia Blossom Ranch for allowing us to visit their property and collect samples. We thank Professor Aharon Oren (Hebrew University of Jerusalem, Israel) for helping coin and check the etymology of proposed name.

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