Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities

Lewis, Zachery T.; Bokulich, Nicholas A.; Kalanetra, Karen M.; Ruíz-Moyano, Santiago; Underwood, Mark A.; Mills, David A.

doi:10.1016/j.anaerobe.2012.12.005

Cited by 22 publications

(24 citation statements)

References 44 publications

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“…A Bifidobacterium -specific terminal restriction fragment length polymorphism assay was performed as previously described73. DNA from feces was PCR amplified using primers NBIF389 (5′-74-GCCTTCGGGTTGTAAAC) and NBIF1018 REV (GACCATGCACCACCTGTG).…”

Section: Methodsmentioning

confidence: 99%

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota

Davis

Lewis

Krishnan

et al. 2017

Sci Rep

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174

198

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Human milk oligosaccharides (HMOs) play an important role in the health of an infant as substrate for beneficial gut bacteria. Little is known about the effects of HMO composition and its changes on the morbidity and growth outcomes of infants living in areas with high infection rates. Mother’s HMO composition and infant gut microbiota from 33 Gambian mother/infant pairs at 4, 16, and 20 weeks postpartum were analyzed for relationships between HMOs, microbiota, and infant morbidity and growth. The data indicate that lacto-N-fucopentaose I was associated with decreased infant morbidity, and 3′-sialyllactose was found to be a good indicator of infant weight-for-age. Because HMOs, gut microbiota, and infant health are interrelated, the relationship between infant health and their microbiome were analyzed. While bifidobacteria were the dominant genus in the infant gut overall, Dialister and Prevotella were negatively correlated with morbidity, and Bacteroides was increased in infants with abnormal calprotectin. Mothers nursing in the wet season (July to October) produced significantly less oligosaccharides compared to those nursing in the dry season (November to June). These results suggest that specific types and structures of HMOs are sensitive to environmental conditions, protective of morbidity, predictive of growth, and correlated with specific microbiota.

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Section: Methodsmentioning

confidence: 99%

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota

Davis

Lewis

Krishnan

et al. 2017

Sci Rep

Self Cite

174

198

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“…[4] [5] Bacilli-specific TRFLP (Bac-TRFLP) and Bifidobacteria-specific TRFLP (Bif-TRFLP) were performed as previously outlined. [6, 7] PCR products were analyzed by electrophoresis and purified using the QIAquick PCR Purification Kit (Qiagen, Valencia, CA). All 16S-TRFLP amplicons were digested using the enzymes AluI, MspI, HaeIII, and HhaI.…”

Section: Dna Extractionmentioning

confidence: 99%

A Comparison of Two Probiotic Strains of Bifidobacteria in Premature Infants

Underwood

Kalanetra

Bokulich

et al. 2013

The Journal of Pediatrics

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112

121

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Objective To determine the impact of two probiotic bifidobacteria on the fecal microbiota of premature infants fed either human milk or formula. Study design In the first of two phase 1 clinical trials, twelve premature infants receiving formula feedings were randomly assigned to receive either Bifidobacterium longum ssp infantis or Bifidobacterium animalis ssp lactis in increasing doses over a five week period. In the second, nine premature infants receiving their mother’s milk received each of the two bifidobacteria for two weeks separated by a one week wash out period. Serial stool specimens from each infant were analyzed by terminal restriction fragment length polymorphism and quantitative polymerase chain reaction for bacterial composition. Results Among the formula-fed infants, there was a greater increase in fecal bifidobacteria among infants receiving B. infantis than those receiving B. lactis. This difference was most marked at a dose of 1.4 × 109 cfu twice daily (p < 0.05). Bacterial diversity improved over dose/time in those infants receiving B. infantis. Among the human milk-fed infants, greater increases in fecal bifidobacteria and decreases in γ-Proteobacteria followed administration of B. infantis than B. lactis. The B. longum group (which includes B. infantis but not B. lactis) was the dominant bifidobacteria among the human milk-fed infants, regardless of the probiotic administered. Conclusions B. infantis was more effective at colonizing the fecal microbiota than B. lactis in both formula-fed and human milk-fed premature infants. The combination of human milk plus B. infantis resulted in the highest fecal levels of bifidobacteria.

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“…In addition, 3 methods were used to identify members of the genus Bifidobacterium: (1) a terminal restriction fragment length polymorphism (T-RFLP) assay 24 was used to determine the relative abundance of Bifidobacterium species, (2) Bifidobacterium 16S rDNA copy numbers (per gram of stool) were measured by quantitative polymerase chain reaction (qPCR), and (3) the Bifidobacterium longum subspecies infantis and longum were identified by polymerase chain reaction (PCR). Methods are described in the Supplemental Information and Supplemental Table 4.…”

Section: Bacterial Dna Methodsmentioning

confidence: 99%

Stool Microbiota and Vaccine Responses of Infants

Huda

Lewis²,

Kalanetra³

et al. 2014

Pediatrics

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338

331

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WHAT'S KNOWN ON THIS SUBJECT:Oral vaccine responses are low in children from less-developed countries perhaps as a result of intestinal dysbiosis. New high-throughput DNA-based methods allow characterization of intestinal microbiota as a predictor of vaccine responses.WHAT THIS STUDY ADDS: High abundance of stool Actinobacteria, including Bifidobacterium, was associated with higher responses to oral and parenteral vaccines and a larger thymus in Bangladeshi infants. Conversely, high abundance of Clostridiales, Enterobacteriales, and Pseudomonadales was associated with neutrophilia and lower vaccine responses. abstract OBJECTIVE: Oral vaccine efficacy is low in less-developed countries, perhaps due to intestinal dysbiosis. This study determined if stool microbiota composition predicted infant oral and parenteral vaccine responses. METHODS:The stool microbiota of 48 Bangladeshi infants was characterized at 6, 11, and 15 weeks of age by amplification and sequencing of the 16S ribosomal RNA gene V4 region and by Bifidobacterium-specific, quantitative polymerase chain reaction. Responses to oral polio virus (OPV), bacille Calmette-Guérin (BCG), tetanus toxoid (TT), and hepatitis B virus vaccines were measured at 15 weeks by using vaccine-specific T-cell proliferation for all vaccines, the delayed-type hypersensitivity skin-test response for BCG, and immunoglobulin G responses using the antibody in lymphocyte supernatant method for OPV, TT, and hepatitis B virus. Thymic index (TI) was measured by ultrasound.RESULTS: Actinobacteria (predominantly Bifidobacterium longum subspecies infantis) dominated the stool microbiota, with Proteobacteria and Bacteroidetes increasing by 15 weeks. Actinobacteria abundance was positively associated with T-cell responses to BCG, OPV, and TT; with the delayed-type hypersensitivity response; with immunoglobulin G responses; and with TI. B longum subspecies infantis correlated positively with TI and several vaccine responses. Bacterial diversity and abundance of Enterobacteriales, Pseudomonadales, and Clostridiales were associated with neutrophilia and lower vaccine responses.CONCLUSIONS: Bifidobacterium predominance may enhance thymic development and responses to both oral and parenteral vaccines early in infancy, whereas deviation from this pattern, resulting in greater bacterial diversity, may cause systemic inflammation (neutrophilia) and lower vaccine responses. Vaccine responsiveness may be improved by promoting intestinal bifidobacteria and minimizing dysbiosis early in infancy.

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Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities

Cited by 22 publications

References 44 publications

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota

A Comparison of Two Probiotic Strains of Bifidobacteria in Premature Infants

Stool Microbiota and Vaccine Responses of Infants

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