0243 Sleep-Wake Patterns during Infancy are Associated with Gut Microbial Community Structure in Toddlerhood

When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.

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Peer Review #2 of "Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects (v0.1)"

10.7287/peerj.6199v0.1/reviews/2 ◽

2019 ◽

Keyword(s):

Community Structure ◽

Microbial Community ◽

Side Effects ◽

Peer Review ◽

Mechanism Of Action ◽

Microbial Community Structure ◽

Gut Microbial Community

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Peer Review #3 of "Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects (v0.1)"

10.7287/peerj.6199v0.1/reviews/3 ◽

2019 ◽

Keyword(s):

Community Structure ◽

Microbial Community ◽

Side Effects ◽

Peer Review ◽

Mechanism Of Action ◽

Microbial Community Structure ◽

Gut Microbial Community

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Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech

10.1101/687418 ◽

2019 ◽

Cited By ~ 3

Author(s):

Emily Ann McClure ◽

Michael C. Nelson ◽

Amy Lin ◽

Joerg Graf

Keyword(s):

Animal Model ◽

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Medicinal Leech ◽

Easy Access ◽

Macrobdella Decora ◽

Hirudo Verbana ◽

Geographic Separation ◽

Gut Microbial Community

ABSTRACTLeeches are found in terrestrial, aquatic, and marine habitats on all continents. Sanguivorous leeches have been used in medicine for millennia. Modern scientific uses include studies of neurons, anticoagulants, and gut microbial symbioses.Hirudo verbana, the European medicinal leech, maintains a gut community dominated by two bacterial symbionts,Aeromonas veroniiandMucinivorans hirudinis, which sometimes account for as much as 97% of the total crop microbiota. The highly simplified gut anatomy and microbiome ofH. verbanamake it an excellent model organism for studying gut microbial dynamics. The North American medicinal leech,Macrobdella decora,is a hirudinid leech native to Canada and the northern U.S.A. In this study we show thatM. decorasymbiont communities are very similar to those inH. verbana.This similarity allowed for an extensive study in which wild caught animals were sampled to determine effects of geographic separation, time of collection, and feeding on the microbiome. Through 16S V4 rRNA deep sequencing we show that: i) theM. decoragut and bladder microbial communities are distinct, ii) theM. decoragut community is affected by feeding and long periods of starvation, and iii) geographic separation does not appear to affect the overall gut microbial community structure. We propose thatM. decorais a replacement forH. verbanafor studies of wild-caught animals and offer evidence for the conservation of annelid symbionts. Successful culturing and comparison of dominant symbionts fromM. decoraandH. verbenawill provide the ability to assess host-symbiont co-evolution in future work.IMPORTANCEBuilding evidence implicates the gut microbiome in regulating animal digestion, nutritional acquisition, immune regulation, development, and even mood regulation. Because of the difficulty of assigning causative relationships in complex gut microbiomes a simplified model for testing hypotheses is necessary. Previous research inHirudo verbanahas suggested this animal as a highly simplified and tractable animal model of gut symbioses. Our data show thatMacrobdella decoramay work just as well asH. verbanawithout the drawback of being an endangered organism and with the added convenience of easy access to field-caught specimens. The similarity of the microbial community structure of species from two different continents reveals the highly-conserved nature of the microbial symbionts in sanguivorous leeches and confirms the medicinal leech as a highly simplified, natural animal model in which to study gut symbioses.

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Peer Review #1 of "Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects (v0.1)"

10.7287/peerj.6199v0.1/reviews/1 ◽

2019 ◽

Keyword(s):

Community Structure ◽

Microbial Community ◽

Side Effects ◽

Peer Review ◽

Mechanism Of Action ◽

Microbial Community Structure ◽

Gut Microbial Community

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Secondary bile acid ursodeoxycholic acid (UDCA) alters weight, the gut microbiota, and the bile acid pool in conventional mice

10.1101/698795 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jenessa A. Winston ◽

Alissa Rivera ◽

Jingwei Cai ◽

Andrew D. Patterson ◽

Casey M. Theriot

Keyword(s):

Community Structure ◽

Bile Acid ◽

Microbial Community ◽

Gut Microbiota ◽

Ursodeoxycholic Acid ◽

Microbial Community Structure ◽

Cecal Content ◽

Bile Acid Pool ◽

Acid Pool ◽

Gut Microbial Community

AbstractUrsodeoxycholic acid (commercially available as Ursodiol) is a naturally occurring bile acid that is used to treat a variety of hepatic and gastrointestinal diseases. Ursodiol can modulate bile acid pools, which have the potential to alter the gut microbiota community structure. In turn, the gut microbial community can modulate bile acid pools, thus highlighting the interconnectedness of the gut microbiota-bile acid-host axis. Despite these interactions, it remains unclear if and how exogenously administered ursodiol shapes the gut microbial community structure and bile acid pool. This study aims to characterize how ursodiol alters the gastrointestinal ecosystem in conventional mice. C57BL/6J wildtype mice were given one of three doses of ursodiol (50, 150, or 450 mg/kg/day) by oral gavage for 21 days. Alterations in the gut microbiota and bile acids were examined including stool, ileal, and cecal content. Bile acids were also measured in serum. Significant weight loss was seen in mice treated with the low and high dose of ursodiol. Alterations in the microbial community structure and bile acid pool were seen in ileal and cecal content compared to pretreatment, and longitudinally in feces following the 21-day ursodiol treatment. In both ileal and cecal content, members of the Lachnospiraceae family significantly contributed to the changes observed. This study is the first to provide a comprehensive view of how exogenously administered ursodiol shapes the gastrointestinal ecosystem. Further studies to investigate how these changes in turn modify the host physiologic response are important.ImportanceUrsodeoxycholic acid (commercially available as ursodiol) is used to treat a variety of hepatic and gastrointestinal diseases. Despite its widespread use, how ursodiol impacts the gut microbial community structure and bile acid pool remains unknown. This study is the first to provide a comprehensive view of how exogenously administered ursodiol shapes the gastrointestinal ecosystem. Ursodiol administration in conventional mice resulted in significant alterations in the gut microbial community structure and bile acid pool, indicating that ursodiol has direct impacts on the gut microbiota-bile acid-host axis which should be considered when this medication is administered.Bile Acid AbbreviationsαMCA – α–Muricholic acid; βMCA –β–Muricholic acid; ωMCA –ω–Muricholic acid; CA – Cholic acid; CDCA – Chenodeoxycholic acid; DCA – Deoxycholic acid; GCDCA – Glycochenodeoxycholic acid; GDCA – Glycodeoxycholic acid; GLCA – Glycolithocholic acid; GUDCA – Glycoursodeoxycholic acid; HCA – Hyodeoxycholic acid; iDCA – Isodeoxycholic acid; iLCA – Isolithocholic acid; LCA – Lithocholic acid; TCA – Taurocholic acid; TCDCA – Taurochenodeoxycholic acid; TDCA – Taurodeoxycholic acid; THCA – Taurohyodeoxycholic acid; TUDCA – Tauroursodeoxycholic acid; TβMCA – Tauro-β-muricholic acid; TωMCA –Tauro ω-muricholic acid; UDCA – Ursodeoxycholic acid.

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