Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon

Devine, Anthony A.; González, Antonio; Speck, K. Elizabeth; Knight, Rob; Helmrath, Michael A.; Lund, P. Kay; Azcárate-Peril, M. Andrea

doi:10.1371/journal.pone.0073140

Cited by 59 publications

(58 citation statements)

References 58 publications

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“…This study demonstrated a marked shift in bacterial species resulting from surgery alone with Clostridium species becoming dominant as well as an increase in ϒ-proteobacteria. The results also confirmed the findings of the previous study with similar populations found in the small bowel and colon after ICR 12 .…”

Section: Introductionsupporting

confidence: 92%

Murine Ileocolic Bowel Resection with Primary Anastomosis

Perry

Borowiec

Dicken

et al. 2014

JoVE

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Intestinal resections are frequently required for treatment of diseases involving the gastrointestinal tract, with Crohn's disease and colon cancer being two common examples. Despite the frequency of these procedures, a significant knowledge gap remains in describing the inherent effects of intestinal resection on host physiology and disease pathophysiology. This article provides detailed instructions for an ileocolic resection with primary end-to-end anastomosis in mice, as well as essential aspects of peri-operative care to maximize post-operative success. When followed closely, this procedure yields a 95% long-term survival rate, no failure to thrive, and minimizes post-operative complications of bowel obstruction and anastomotic leak. The technical challenges of performing the procedure in mice are a barrier to its wide spread use in research. The skills described in this article can be acquired without previous surgical experience. Once mastered, the murine ileocolic resection procedure will provide a reproducible tool for studying the effects of intestinal resection in models of human disease. Video LinkThe video component of this article can be found at

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Section: Introductionsupporting

confidence: 92%

Murine Ileocolic Bowel Resection with Primary Anastomosis

Perry

Borowiec

Dicken

et al. 2014

JoVE

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“…Amplification and sequencing of the V1-V2 region of the bacterial 16S rRNA gene was performed on total DNA from collected samples (n = 307) as previously described (29,30). Briefly, reaction master mixes contained the Qiagen Hotstar HiFidelity Polymerase Kit (Qiagen) with a forward primer composed of the Roche Titanium Fusion Primer A (5′-CCATCTCATCCCTGC-GTGTCTCCGACTCAG-3′), a 10-bp Multiplex Identifier (MID) sequence (Roche), and the universal bacterial primer 8F (5′-AGAGTTTGATCCTGGCT-CAG-3′) (31).…”

Section: Methodsmentioning

confidence: 99%

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals

Azcárate-Peril

Ritter²,

Savaiano

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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194

131

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Directed modulation of the colonic bacteria to metabolize lactose effectively is a potentially useful approach to improve lactose digestion and tolerance. A randomized, double-blind, multisite placebo-controlled trial conducted in human subjects demonstrated that administration of a highly purified (>95%) short-chain galactooligosaccharide (GOS), designated "RP-G28," significantly improved clinical outcomes for lactose digestion and tolerance. In these individuals, stool samples were collected pretreatment (day 0), after GOS treatment (day 36), and 30 d after GOS feeding stopped and consumption of dairy products was encouraged (day 66). In this study, changes in the fecal microbiome were investigated using 16S rRNA amplicon pyrosequencing and high-throughput quantitative PCR. At day 36, bifidobacterial populations were increased in 27 of 30 of GOS subjects (90%), demonstrating a bifidogenic response in vivo. Relative abundance of lactose-fermenting Bifidobacterium, Faecalibacterium, and Lactobacillus were significantly increased in response to GOS. When dairy was introduced into the diet, lactosefermenting Roseburia species increased from day 36 to day 66. The results indicated a definitive change in the fecal microbiome of lactose-intolerant individuals, increasing the abundance of lactosemetabolizing bacteria that were responsive to dietary adaptation to GOS. This change correlated with clinical outcomes of improved lactose tolerance.A limited ability to digest lactose occurs when the intestinal lactase enzyme is reduced in the brush border of the small bowel mucosa. Consumption of dairy foods by lactose-intolerant individuals may result in clinical symptoms including abdominal pain, diarrhea, bloating, flatulence, and abdominal cramping. In these cases, lactose travels through the gastrointestinal tract and is fermented in the colon, producing acetate, carbon dioxide, hydrogen gas, and methane by gas-producing microbes. Approximately 75% of the global human population are lactose maladsorbers (1, 2). In the United States, it is estimated that up to 80 million Americans are at risk for lactose intolerance.Efforts to address lactose intolerance include avoidance of dairy foods, reduction in the lactose content of milk through treatment with microbial lactases, and the use of lactase enzymes to process milk before dairy consumption (3). Savaiano et al. conducted a randomized, double-blind, parallel-group, placebocontrolled study at two sites in the United States (4). A high purity (>95%) galactooligosaccharide (GOS/RP-G28) or a placebo (Sweetose; Tate & Lyle Ingredients) was administered in increasing doses to 62 lactose-intolerant subjects for 36 d. Subjects refrained from consuming lactose during the GOS treatment period. After GOS treatment, subjects reintroduced dairy products into their diets for an additional 30 d and then were challenged for lactose digestion and were evaluated for symptoms improvement via a Likert scale. Subjects consuming GOS trended toward improvement in overall symptoms after 36 d of ...

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“…7,18 Sequencing data were demultiplexed and filtered for quality control. Sequences were then aligned and clustered into operational taxonomic units (OTU) using the QIIME implementation of UCLUST.…”

Section: Methodsmentioning

confidence: 99%

Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery

Becker‐Dreps¹,

Allali²,

Monteagudo³

et al. 2015

The American Society of Tropical Medicine and Hygiene

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Abstract. Understanding how the gut microbiota is affected by diarrhea episodes may help explain alterations in intestinal function among children in low-income settings. This study examined the composition of the gut microbiome of Nicaraguan children both during diarrhea episodes and while free of diarrhea for at least 2 months. Relative abundances of bacterial taxa, phylogenetic diversity, and species richness were determined by 16S amplicon sequencing and compared between paired diarrhea and recovery samples. A total of 66 stools were provided by 25 children enrolled in a 1-year cohort study of diarrhea etiologies. Children in our cohort had a mean age of 21.9 months; 64% were breast-fed, and 10% had received an antibiotic during the diarrhea episode. Overall, phylogenetic diversity and species richness did not differ significantly between diarrhea and recovery stools. However, of children who had a bacterial enteropathogen detected in any diarrhea stool, none experienced an increase in phylogenetic diversity in recovery, whereas of those in whom no bacterial enteropathogens were detected in their diarrhea stool(s), 59% experienced an increase in phylogenetic diversity in recovery (P = 0.008). This preliminary study suggests that recovery of the gut microbiota after a diarrhea episode may take longer time than previously thought and may be pathogen specific.

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Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon

Cited by 59 publications

References 58 publications

Murine Ileocolic Bowel Resection with Primary Anastomosis

Murine Ileocolic Bowel Resection with Primary Anastomosis

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals

Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery

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