Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community Composition

AbstractCharacterization of the gut microbiome may aid understanding and management of natural and experimental disease states in research animals, thereby promoting reproducibility. In this study, the rectal bacterial communities of three separate common marmoset (Callithrix jacchus) breeding colonies were defined using 16S rRNA sequencing of rectal swab samples. Study animals originated from two German colonies and a United States colony (JHU). The two German cohorts, previously fed the same diet, were imported into the JHU facility; they were then isolated, transitioned onto JHU diet, and then moved into rooms housing JHU animals. To dissect the contributions of diet and integration in shaping the rectal bacterial community, samples were collected from German origin marmosets upon JHU arrival (baseline), following diet transition (100 d), and following cohousing (390 d). Baseline and 390 d samples were collected from stably maintained JHU marmosets. Bacterial community composition was distinct between all three cohorts at baseline, suggesting that factors other than primary diet confer significant differences between captive populations. Beta-diversity of the animals from the two German colonies converged by 100 d but remained distinct from JHU sample beta-diversity throughout the 390-d study, indicating that diet had greater influence on bacterial community composition than did housing animals within the same room. Our results demonstrate substantial differences in gut bacteria between different captive marmoset colonies, with persistence of these differences following husbandry standardization and housing integration. Goals of rigor and reproducibility in research underscore the need to consider microbial differences between marmosets of diverse origin.ImportanceCharacterizing gut microbial populations is expected to promote health and enhance research reproducibility in animal studies. As use of common marmosets as animal models of human diseases expands, evaluating the marmoset gut bacterial community will be critical for interpreting research findings, especially as marmosets are prone to gastrointestinal inflammation. In this study, using 16S rRNA sequencing of rectal swab samples, we compared bacterial community among three captive colonies of marmosets at baseline and following importation of cohorts from two of the colonies into the third colony. Diet history had sustained influence on bacterial community composition, while housing the animals within the same room over a period of eight months did not appear to be a major factor. These persistent differences in marmoset gut bacterial community highlight the need for careful consideration of animal origin as a variable in marmoset research studies.

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Isolation of actinomycetes from Nile tilapia (Oreochromis niloticus) cultivated in semi-intensive systems from Morelos, Mexico central zone

Latin American Journal of Aquatic Research ◽

10.3856/vol48-issue5-fulltext-2500 ◽

2020 ◽

Vol 48 (5) ◽

pp. 758-767

Author(s):

Rocio Parra-Laca ◽

Laura Hernández-Andrade ◽

Gary García-Espinosa ◽

Elizabeth Loza-Rubio

Keyword(s):

16S Rrna ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Central Zone ◽

16S Rrna Sequencing ◽

Sequencing Analysis ◽

Nile Tilapia Oreochromis Niloticus ◽

Rrna Sequencing ◽

16S Rrna Sequencing Analysis

The production of Nile tilapia (Oreochromis niloticus) has good technological development; however, today, it is still necessary to make it more efficient. One way to increase efficiency is to prevent disease and improve the food conversion factor. Since previous investigations of tilapia microbiota detected a high proportion of organisms belonging to the order Actinomycetes, this study was to isolate, identify, and describe the species of bacteria microbiota belonging to the cultured Nile tilapia. These were done with Nile tilapia grown in a warm sub-humid climate during spring and summer seasons. The biopsy of different organs was performed for bacteriological culture and 16S rRNA sequencing analysis. From the 180 tissue samples, 49 isolates of the order Actinomycetes were obtained, representing ten species from seven genera: Microbacterium, Brevibacterium, Cellulomonas, Corynebacterium, Kocuria, Actinomyces, and Micrococcus. In spring, Microbacterium dominated, accounting for 74% of the total population. In the summer, lower diversity was observed, with 39% represented by Microbacterium. 16S rRNA sequencing analysis enabled the classification of Actinomyces neuii and Microbacterium lacticum as Kocuria varians and Agromyces indicus; the classification of Microbacterium imperiale as Rhodococcus and Micrococcus luteus was confirmed. No sequences of K. varians have been reported in fish. Microbacterium dextranoliticum showed high similarity to environmental samples. Here is the first study that analyzes the bacteria population in tilapia at the genetic level with an ecosystem approach, present in healthy cultured tilapia, indicating their beneficial associations with the host, making them candidates as probiotics, among other possible functions, applicable in tilapia cultivation.

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16S rRNA sequencing analysis of the correlation between the intestinal microbiota and body-mass of grass carp (Ctenopharyngodon idella)

Comparative Biochemistry and Physiology Part D Genomics and Proteomics ◽

10.1016/j.cbd.2020.100699 ◽

2020 ◽

Vol 35 ◽

pp. 100699

Author(s):

Shen-Tong Wang ◽

Xin-Zhan Meng ◽

Jia-Hua Zhang ◽

Ya-Fan Dai ◽

YuBang Shen ◽

...

Keyword(s):

16S Rrna ◽

Body Mass ◽

Intestinal Microbiota ◽

Grass Carp ◽

16S Rrna Sequencing ◽

Ctenopharyngodon Idella ◽

Sequencing Analysis ◽

Rrna Sequencing ◽

Grass Carp Ctenopharyngodon Idella ◽

16S Rrna Sequencing Analysis

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A Case ofGranulicatella adiacensSepticemia Identified by 16S rRNA Sequencing Analysis

Korean Journal of Clinical Microbiology ◽

10.5145/kjcm.2008.11.1.63 ◽

2008 ◽

Vol 11 (1) ◽

pp. 63 ◽

Cited By ~ 1

Author(s):

Kyeong Seob Shin ◽

Bo Ra Son ◽

Hye Won Jeong

Keyword(s):

16S Rrna ◽

16S Rrna Sequencing ◽

Sequencing Analysis ◽

Rrna Sequencing ◽

16S Rrna Sequencing Analysis

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Biotransformation of Flavonoids by Newly Isolated and Characterized Lactobacillus pentosus NGI01 Strain from Kimchi

Microorganisms ◽

10.3390/microorganisms9051075 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1075

Author(s):

Chan-Mi Park ◽

Gyoung-Min Kim ◽

Gun-Su Cha

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

16S Rrna ◽

16S Rrna Sequencing ◽

Sequencing Analysis ◽

Lactobacillus Pentosus ◽

Flavonoid Aglycones ◽

Food Industries ◽

Rrna Sequencing ◽

16S Rrna Sequencing Analysis

Lactic acid bacteria (LAB) are generally recognized as safe (GRAS) microorganisms. This study aimed to identify novel LAB strains that can transform flavonoids into aglycones to improve bioavailability. We isolated 34 LAB strains from kimchi. The biotransformation activity of these 34 LAB strains was investigated based on α-L-rhamnosidase and β-D-glucosidase activities. Among them, 10 LAB strains with high activities were identified by 16S rRNA sequencing analysis. All tested LAB strains converted hesperidin to hesperetin (12.5–30.3%). Of these, only the Lactobacillus pentosus NGI01 strain produced quercetin from rutin (3.9%). The optimal biotransformation conditions for the L. pentosus NGI01 producing hesperetin and quercetin were investigated. The highest final product concentrations of hesperetin and quercetin were 207 and 78 μM, respectively. Thus, the L. pentosus NGI01 strain can be a biocatalyst for producing flavonoid aglycones in the chemical and food industries.

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