Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

Asnicar, Francesco; Manara, Serena; Zolfo, Moreno; Truong, Duy Tin; Scholz, Matthias; Armanini, Federica; Ferretti, Pamela; Gorfer, Valentina; Pedrotti, Anna; Tett, Adrian; Segata, Nicola

doi:10.1128/msystems.00164-16

Cited by 369 publications

(291 citation statements)

References 85 publications

(126 reference statements)

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“…It will be similarly crucial to associate the presence of strains or subclades of microbial species with immune or chronic disease phenotypes even in the absence of acute infection. The same types of approaches can also start to unravel how members of the microbiome without overt phenotypes are transmitted among hosts, e.g., in vertical mother-to-infant transmission (Milani et al 2015;Asnicar et al 2017) or horizontal orofecal routes . This is of particular interest in the context of interventions such as probiotics or fecal microbiome transplants, in which strain tracking is necessary to identify successful receipt or engraftment of the intended microbes (Li et al 2016).…”

Section: Discussionmentioning

confidence: 99%

Microbial strain-level population structure and genetic diversity from metagenomes

et al. 2017

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Among the human health conditions linked to microbial communities, phenotypes are often associated with only a subset of strains within causal microbial groups. Although it has been critical for decades in microbial physiology to characterize individual strains, this has been challenging when using culture-independent high-throughput metagenomics. We introduce StrainPhlAn, a novel metagenomic strain identification approach, and apply it to characterize the genetic structure of thousands of strains from more than 125 species in more than 1500 gut metagenomes drawn from populations spanning North and South American, European, Asian, and African countries. The method relies on per-sample dominant sequence variant reconstruction within species-specific marker genes. It identified primarily subject-specific strain variants (<5% inter-subject strain sharing), and we determined that a single strain typically dominated each species and was retained over time (for >70% of species). Microbial population structure was correlated in several distinct ways with the geographic structure of the host population. In some cases, discrete subspecies (e.g., for Eubacterium rectale and Prevotella copri) or continuous microbial genetic variations (e.g., for Faecalibacterium prausnitzii) were associated with geographically distinct human populations, whereas few strains occurred in multiple unrelated cohorts. We further estimated the genetic variability of gut microbes, with Bacteroides species appearing remarkably consistent (0.45% median number of nucleotide variants between strains), whereas P. copri was among the most plastic gut colonizers. We thus characterize here the population genetics of previously inaccessible intestinal microbes, providing a comprehensive strain-level genetic overview of the gut microbial diversity.

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Section: Discussionmentioning

confidence: 99%

Microbial strain-level population structure and genetic diversity from metagenomes

et al. 2017

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“…Based on the taxonomic profile of the infant gut, it is clear that vaginal microbiota, consisting mostly of lactobacilli (Ravel et al 2011), cannot account for the majority of infant gut species. The same is true for breast milk, as the overlap with infant gut taxa is minor (Asnicar et al 2017). The most likely source of bacteria to the infant is the mother's gut, which contains most of the species present in the infant gut, albeit at different relative abundances (Bäckhed et al 2015;Asnicar et al 2017).…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 93%

Selective maternal seeding and environment shape the human gut microbiome

et al. 2018

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Vertical transmission of bacteria from mother to infant at birth is postulated to initiate a life-long host-microbe symbiosis, playing an important role in early infant development. However, only the tracking of strictly defined unique microbial strains can clarify where the intestinal bacteria come from, how long the initial colonizers persist, and whether colonization by other strains from the environment can replace existing ones. Using rare single nucleotide variants in fecal metagenomes of infants and their family members, we show strong evidence of selective and persistent transmission of maternal strain populations to the vaginally born infant and their occasional replacement by strains from the environment, including those from family members, in later childhood. Only strains from the classes Actinobacteria and Bacteroidia, which are essential components of the infant microbiome, are transmitted from the mother and persist for at least 1 yr. In contrast, maternal strains of Clostridia, a dominant class in the mother's gut microbiome, are not observed in the infant. Caesarean-born infants show a striking lack of maternal transmission at birth. After the first year, strain influx from the family environment occurs and continues even in adulthood. Fathers appear to be more frequently donors of novel strains to other family members than receivers. Thus, the infant gut is seeded by selected maternal bacteria, which expand to form a stable community, with a rare but stable continuing strain influx over time.

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“…Research indicates that there is vertical transmission of microbiota from mother to infant. Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii are among those that are transmitted (Asnicar et al, 2017). In fact, infant gut microbial communities are dominated by bifidobacteria .…”

Section: Infant Gut Microbiome and Oxytocinmentioning

confidence: 99%

Calming Cycle Theory and the Co-Regulation of Oxytocin

Welch

Ludwig

2017

Psychodynamic Psychiatry

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Abstract:The biological functions of oxytocin in attachment and bonding between mother and infant in parturition and breastfeeding and between adults have been studied extensively. However, most current authors have proposed that infant attachment to the mother is learned through operant conditioning mechanisms via the infant's brain and central nervous system. We propose that oxytocin levels in the mother and infant are co-regulated by emotional connection or disconnection, and that the autonomic co-conditioning learning mechanism can be exploited to change a negative physiological and behavioral response between mother and infant into a positive one. Lack of efficacy and scalability of child development therapies that have come out of the attachment theoretical framework have prompted calls for new ideas. Here, we review calming cycle theory, which takes a new view of the emotional relationship of mother and infant, and predicts ways to positively intervene when problems arise. The theory builds upon the research and ideas of Pavlov and his followers and proposes that subcortical Pavlovian co-conditioning of the autonomic nervous systems of mother and infant is the key to maintaining emotional connection between the two and to shaping emotional behavior of the infant into adulthood. We review evidence in support of calming cycle theory from a randomized controlled trial of Family Nurture Intervention (FNI), which is designed to overcome adverse emotional, behavioral, and developmental outcomes in prematurely born infants. Finally, we discuss the role of visceral oxytocin and emotional behavior, and that the conditional motherinfant relationship may affect behavioral changes through anti-inflammatory gut-brain stem vagal signaling.

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Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

Cited by 369 publications

References 85 publications

Microbial strain-level population structure and genetic diversity from metagenomes

Microbial strain-level population structure and genetic diversity from metagenomes

Selective maternal seeding and environment shape the human gut microbiome

Calming Cycle Theory and the Co-Regulation of Oxytocin

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