What are the consequences of the disappearing microbiota?

Department of Medicine and the Department of Microbiology, New York University Langone Medical Center, New York, New York 10017, USA.
Nature Reviews Microbiology (Impact Factor: 23.57). 11/2009; 7(12):887-94. DOI: 10.1038/nrmicro2245
Source: PubMed


Humans and our ancestors have evolved since the most ancient times with a commensal microbiota. The conservation of indicator species in a niche-specific manner across all of the studied human population groups suggests that the microbiota confer conserved benefits on humans. Nevertheless, certain of these organisms have pathogenic properties and, through medical practices and lifestyle changes, their prevalence in human populations is changing, often to an extreme degree. In this Essay, we propose that the disappearance of these ancestral indigenous organisms, which are intimately involved in human physiology, is not entirely beneficial and has consequences that might include post-modern conditions such as obesity and asthma.

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    • "Infants go from the womb to abruptly encountering the full microbial diversity of their new ex-utero environment. Early microbial colonization impacts the long-term adult microbial ecosystem (Biasucci et al., 2008), and is likely a critical ecological window that influences health trajectory throughout life (Blaser & Falkow, 2009;Dominguez-bello et al., 2011;Scholtens et al., 2012;Cho et al., 2012). Infant fecal samples are commonly studied to investigate the impacts of factors such as breastfeeding on the development of the gut microbiota and subsequent health effects. "
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    ABSTRACT: Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.
    Full-text · Article · Jan 2016 · PeerJ
    • "S. pneumoniae and H. influenzae are more likely to cocolonize with one another than independently, suggesting these species have a cooperative relationship ; in contrast, colonization with these species is associated with lower prevalence of S. aureus[1]. Negative associations between carriage of S. pneumoniae and S. aureus led to concerns that pneumococcal conjugate vaccine (PCV) could have unintended consequences, such as increasing carriage or disease caused by S. aureus123. However, it remains unclear whether observed patterns in cocolonization result from true interspecies interactions or confounding epidemiological risk factors. "
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    ABSTRACT: Background: Co-colonization by Streptococcus pneumoniae and Haemophilus influenzae among children has been noted in numerous studies, as has an inverse relationship involving colonization with these species and Staphylococcus aureus. Interactions among these pathogens could mediate unanticipated outcomes of clinical interventions, including changes in H. influenzae and S. aureus disease incidence following pneumococcal vaccine introduction. However, it remains unclear whether co-colonization patterns represent true interspecies interactions or owe to confounding factors. Methods: We investigated polymicrobial carriage using longitudinal data from 369 Bedouin children and 400 Jewish children in Israel enrolled in a 7-valent pneumococcal conjugate vaccine (PCV7) trial. Children were swabbed ten times between two and 30 months of age. Results: The pathogens followed distinct age and seasonal distributions, however polymicrobial carriage associations persisted after controlling for these and other confounding factors. Receipt of PCV7 resulted in pneumococcal serotype replacement but did not impact total carriage of S. pneumoniae, H. influenzae, or S. aureus. Conclusions: The fact that S. pneumoniae, H. influenzae, and S. aureus polymicrobial carriage patterns do not owe to confounding by age and season supports the idea of active interspecies interactions. However, pneumococcal serotype replacement may prevent changes in H. influenzae and S. aureus carriage among PCV7 recipients.
    No preview · Article · Dec 2015 · The Journal of Infectious Diseases
    • "The early iterations of the hygiene hypothesis suggested that lack of exposure to microbial life in infancy results in immunological shifts in immune balance, with suppression of Th1 and exaggeration of Th2 immunity, which is associated with production of pro-inflammatory cytokines, IgE, and eosinophilic infiltrates . More recently, this hypothesis has been expanded to consider the effects of early alterations in gut microbiota as a driving " engine " for the immune alterations that lead to allergy (Blaser and Falkow, 2009;Bendiks and Kopp, 2013). Such effects, due to influences, such as Caesarean delivery, antibiotics, and lack of breastfeeding, interact with the developing immune system of the infant through alteration in immune-microbial cross talk, impairing normal tolerance. "
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    ABSTRACT: This review describes current understandings about the nature of the very low birth weight infant (VLBW) gut microbiome. VLBW infants often experience disruptive pregnancies and births, and prenatal factors can influence the maturity of the gut and immune system, and disturb microbial balance and succession. Many VLBWs experience rapid vaginal or Caesarean births. After birth these infants often have delays in enteral feeding, and many receive little or no mother's own milk. Furthermore the stressors of neonatal life in the hospital environment, common use of antibiotics, invasive procedures and maternal separation can contribute to dysbiosis. These infants experience gastrointestinal dysfunction, sepsis, transfusions, necrotizing enterocolitis, oxygen toxicity, and other pathophysiological consditions that affect the normal microbiota. The skin is susceptible to dysbiosis, due to its fragility and contact with NICU organisms. Dysbiosis in early life may resolve but little is known about the timing of the development of the signature gut microbiome in VLBWs. Dysbiosis has been associated with a number of physical and behavioral problems, including autism spectrum disorders, allergy and asthma, gastrointestinal disease, obesity, depression, and anxiety. Dysbiosis may be prevented or ameliorated in part by prenatal care, breast milk feeding, skin to skin contact, use of antibiotics only when necessary, and vigilance during infancy and early childhood. Birth Defects Research (Part C), 2015. © 2015 Wiley Periodicals, Inc.
    No preview · Article · Dec 2015 · Birth Defects Research Part C Embryo Today Reviews
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