Patterned progression of bacterial populations in the premature infant gut

Rosa, Patricio S. La; Warner, Barbara B.; Zhou, Yanjiao; Weinstock, George M.; Sodergren, Erica; Hall-Moore, Carla; Stevens, Harold J.; Bennett, William E.; Shaikh, Nurmohammad; Linneman, Laura; Hoffmann, Julie; Hamvas, Aaron; Deych, Elena; Shands, Berkley; Shannon, William D.; Tarr, Phillip I.

doi:10.1073/pnas.1409497111

Cited by 473 publications

(606 citation statements)

References 47 publications

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“…Relevant studies in broilers have confirmed increasing bacterial diversity and succession with age, and the current findings are in agreement with this (21,24,29). The increased diversification and succession of the bacterial community structure reflect the development of the immature cecal microflora toward a more mature and stable flora, a characteristic demonstrated in the juveniles of many species, including mice and humans (30,31). Host physiology has been shown to have an impact on the development of the gastrointestinal microbiota (32).…”

Section: Resultssupporting

confidence: 85%

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation

Corrigan

Leeuw²,

Penaud-Frézet

et al. 2015

Appl Environ Microbiol

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cThis study focused on identifying reproducible effects of dietary supplementation with a mannan oligosaccharide (MOS) on the broiler cecal bacterial community structure and function in a commercial production setting. Two separate trials, each with a control and a supplemented group, were carried out in the same commercial location and run concurrently. Approximately 10,000 birds from the same commercial hatchery were mirror imaged into each of four commercial broiler sheds and fed either a control or supplemented diet. Cecal contents were obtained on days 7, 21, and 35 posthatch from 12 randomly caught broilers from each group. Bacterial pyrosequencing was performed on all samples, with approximately 250,000 sequences obtained per treatment per time point. The predominant phyla identified at all three time points in both trials were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Tenericutes, representing >99% of all sequences. MOS supplementation altered the bacterial community composition from 7 days supplementation through 35 days supplementation. Bacteroidetes appeared to be replacing Firmicutes as a result of supplementation, with the most noticeable effects after 35 days. The effects of supplementation were reproducible across both trials. PICRUSt was used to identify differences between the functional potentials of the bacterial communities as a result of MOS supplementation. Using level 3 KEGG ortholog function predictions, differences between control and supplemented groups were observed, with very strong segregation noted on day 35 posthatch in both trials. This indicated that alterations of bacterial communities as a result of MOS are likely to alter the functional capability of the cecum. The gastrointestinal microbiota plays a vital role in nutritional, physiological, and protective functions in animals (1). An understanding and a description of the intestinal microbial communities in broilers are important for the development of new feed additives and the appropriate manipulation of diets to improve broiler performance, health, and welfare (2). The intestinal microbiota has a major impact on the bioavailability and bioactivity of dietary components by consuming, storing, and circulating nutrients effectively, while also impacting the host's ability to resist infection, thereby making an essential contribution to host health and performance (3). Poor intestinal health in poultry is associated with increased susceptibility to infectious disease and colonization by pathogens (4). Bacterial-disease outbreaks impose significant constraints on poultry production, adversely impacting the poultry industry by reducing animal welfare and productivity through disease, poor digestion, and poor nutrient absorption. This, in turn, can lead to significant losses for the farmer and can increase the potential for the contamination of poultry products marketed for human consumption (5).Traditionally, antibiotics have been used in poultry feed at subtherapeutic levels to prevent clinical and subclini...

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Section: Resultssupporting

confidence: 85%

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation

Corrigan

Leeuw²,

Penaud-Frézet

et al. 2015

Appl Environ Microbiol

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“…1,2 Following birth, the infant gut microbiota undergoes a patterned maturation process. [3][4][5] This process begins with a few taxa, but this population inexorably expands in content and concentration until it approaches an adultlike microbial configuration dominated by Bacteroidetes and Firmicutes. 3,[6][7][8] Perturbation of the gut microbiota during this key developmental window can have lasting effects on host physiology and disease risk.…”

Section: Introductionmentioning

confidence: 99%

“…4,20,27,[32][33][34] Until recently, similar efforts to characterize the preterm infant gut reservoir of antibiotic resistance genes (the resistome) have been largely culture or PCR-based. While these methods can provide a high level overview of the resistome, they underestimate diversity, are limited to previously known resistance genes, and are only semi-quantitative.…”

Section: Introductionmentioning

confidence: 99%

Antibiotic perturbation of the preterm infant gut microbiome and resistome

Gasparrini¹,

Crofts²,

Gibson³

et al. 2016

Gut Microbes

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The gut microbiota plays important roles in nutrient absorption, immune system development, and pathogen colonization resistance. Perturbations early in life may be detrimental to host health in the short and the long-term. Antibiotics are among the many factors that influence the development of the microbiota. Because antibiotics are heavily administered during the first critical years of gut microbiota development, it is important to understand the effects of these interventions. Infants, particularly those born prematurely, represent an interesting population because they receive early and often extensive antibiotic therapy in the first months after birth.Gibson et al. recently demonstrated that antibiotic therapy in preterm infants can dramatically affect the gut microbiome. While meropenem, ticarcillin-clavulanate, and cefotaxime treatments were associated with decreased species richness, gentamicin and vancomycin had variable effects on species richness. Interestingly, the direction of species richness response could be predicted based on the abundance of 2 species and 2 genes in the microbiome prior to gentamicin or vancomycin treatment. Nonetheless, all antibiotic treatments enriched the presence of resistance genes and multidrug resistant organisms. Treatment with different antibiotics further resulted in unique population shifts of abundant organisms and selection for different sets of resistance genes. In this addendum, we provide an extended discussion of these recent findings, and outline important future directions for elucidating the interplay between antibiotics and preterm infant gut microbiota development.

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“…This technique has been applied to gastrointestinal disorders such as Crohn's disease, ulcerative colitis, and necrotizing entercolitis (13)(14)(15). In the setting of oncology, preliminary investigations of gut microbiome changes in colorectal cancer have been reported (16).…”

Section: Introductionmentioning

confidence: 99%

Stool Bacteriomic Profiling in Patients with Metastatic Renal Cell Carcinoma Receiving Vascular Endothelial Growth Factor–Tyrosine Kinase Inhibitors

Pal

et al. 2015

Clinical Cancer Research

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Purpose: Diarrhea occurs in approximately half of patients with metastatic renal cell carcinoma (mRCC) receiving vascular endothelial growth factor–tyrosine kinase inhibitors (VEGF-TKI). We evaluated the relationship between VEGF-TKI–related diarrhea and stool microbiota. Experimental Design: Stool samples were collected from 20 mRCC patients receiving VEGF-TKIs. 16S rRNA sequencing was used to characterize the stool bacteriomic profiling of patients. Assay validation with Salmonella typhimurium spike-in experiments suggested greatest speciation with use of the V5 region. Results: Higher levels of Bacteroides spp. and lower levels of Prevotella spp. were found in patients with diarrhea. In addition, patients receiving VEGF-TKIs with mRCC appeared to have less relative abundance of Bifidobacterium spp. as compared with previous reports based on healthy subjects. Conclusions: We have thus demonstrated interplay between microbiota and VEGF-TKI–induced diarrhea. Further studies are warranted to evaluate the potential causative role of preexisting dysbiosis in VEGF-TKI–related diarrhea. Clin Cancer Res; 21(23); 5286–93. ©2015 AACR.

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Patterned progression of bacterial populations in the premature infant gut

Cited by 473 publications

References 47 publications

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation

Antibiotic perturbation of the preterm infant gut microbiome and resistome

Stool Bacteriomic Profiling in Patients with Metastatic Renal Cell Carcinoma Receiving Vascular Endothelial Growth Factor–Tyrosine Kinase Inhibitors

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