Dynamics of the infant microbiomes onset: exploring the gut and the oral microbiota in full-term and pre-term infants in the frame of mother’s milk microbial ecosystem

The gut microbiota assembly during the very first days of life plays a pivotal role in the education of the immune system and in the building of a healthy status later in life. Besides the mode of delivery, also the feeding type and the gestational age have an impact on the gut microbiota composition. For this reason, by means of next-generation sequencing of the 16S rRNA gene on Illumina MiSeq, we characterized and compared the intestinal bacterial community in 2 cohorts of infants, 1 constituted by 36 healthy breast-fed infants born full-term and the other constituted by 21 infants born moderate to late pre-term (32 to 37 weeks) receiving different types of feeding (mother breast milk, human breast milk from donor and formula). The first cohort was sampled at 20th day of life, whilst the second one was sampled longitudinally from birth to 30th day of life. In addition, also the infant’s saliva and the mother’s milk were sampled and sequenced. The characterization of the 3 ecosystems in full-term infants led to the hypothesis that the mother milk, together with the microorganisms that reside in the baby’s mouth, may act as seeding community and may participate to infant gut microbiota assembly. On the other hand, in the moderately-to late pre-term cohort, the extreme diversity of the infant’s clinical history provokes a tremendous inter-individual variability. Nevertheless, milk and saliva microbiological structures resembled the ones of full-term cohort. The gut microbiota instead presented a very different composition and it is plausible that its establishment is strongly influenced by the infant’s clinical history and environmental bacteria than the mutual relationship with the mother

From lifetime to evolution: Timescales of human gut microbiota adaptation

Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societie

Microbial Community Dynamics in Mother’s Milk and Infant’s Mouth and Gut in Moderately Preterm Infants

Mother’s own milk represents the optimal source for preterm infant nutrition, as it promotes immune defenses and gastrointestinal function, protects against necrotizing enterocolitis, improves long-term clinical outcome and is hypothesized to drive gut microbiota assembly. Preterm infants at birth usually do not receive their mother’s milk directly from the breast, because active suckling and coordination between suckling, swallowing and breathing do not develop until 32–34 weeks gestational age, but actual breastfeeding is usually possible as they grow older. Here, we enrolled moderately preterm infants (gestational age 32–34 weeks) to longitudinally characterize mothers’ milk and infants’ gut and oral microbiomes, up to more than 200 days after birth, through 16S rRNA sequencing. This peculiar population offers the chance to disentangle the differential contribution of human milk feeding per se vs. actual breastfeeding in the development of infant microbiomes, that have both been acknowledged as crucial contributors to short and long-term infant health status. In this cohort, the milk microbiome composition seemed to change following the infant’s latching to the mother’s breast, shifting toward a more diverse microbial community dominated by typical oral microbes, i.e., Streptococcus and Rothia. Even if all infants in the present study were fed human milk, features typical of healthy, full term, exclusively breastfed infants, i.e., high percentages of Bifidobacterium and low abundances of Pseudomonas in fecal and oral samples, respectively, were detected in samples taken after actual breastfeeding started. These findings underline the importance of encouraging not only human milk feeding, but also an early start of actual breastfeeding in preterm infants, since the infant’s latching to the mother’s breast might constitute an independent factor helping the health-promoting assembly of the infant gut microbiome

Modulation of gut microbiota dysbioses in type 2 diabetic patients by macrobiotic Ma-Pi 2 diet

The study was carried out with internal funding

ViromeScan: a new tool for metagenomic viral community profiling

BACKGROUND: Bioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype. RESULTS: ViromeScan is an innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. The tool uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites. CONCLUSIONS: ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples from reads of other microorganisms. This implies that users can fully characterize the microbiome, including bacteria and viruses, by shotgun metagenomic sequencing followed by different bioinformatic pipelines. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2446-3) contains supplementary material, which is available to authorized users

The gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile

The changing physiology and lifestyle of elderly people affect the gut microbiota composition, the changes of which can, in turn, affect the health maintenance of the ageing host. In a co-evolutionary vision of the relationship between gut microbiota and ageing as an adaptive process of the human superorganism, long-living individuals who get to "successfully" age might be the ones whose microbiota manages to continuously re-establish a mutualistic relationship with the host, adapting to the progressive endogenous and environmental changes. The study of the gut microbiota of long-living people might provide insights on whether and how the gut microbiota can contribute to health maintenance and survival. Here, we provide the state of the art on the study of the gut microbiota in ageing and longevity, with particular attention to the perspective and direction this peculiar field of the microbiota research should take, in order to be a starting point for future mechanistic, pharmacological and clinical studies in ageing research. In particular, longevous people having different genetic, environmental, and cultural background must be analyzed and compared in the attempt to describe "universal" longevity dynamics, useful to unravel how the gut microbial ecosystem can help in expanding human healthspan

Variation of Carbohydrate-Active Enzyme Patterns in the Gut Microbiota of Italian Healthy Subjects and Type 2 Diabetes Patients

The human gut microbiota (GM) has been associated, to date, with various complex functions, essentials for the host health. Among these, it is certainly worth noting the degradation of the so-called microbiota-accessible carbohydrates (MACs), which the GM breaks down through specific enzymes, referred to as carbohydrate-active enzymes (CAZymes). This degradation constitutes the first step in the production of short-chain fatty acids (SCFAs), key microbial small molecules having multiple health-promoting effects for the host organism. The decline in MAC dietary intake in urban Western populations forced the shrinkage of CAZyme repertoire in the GM, as shown by the literature comparing the microbiome layout between Western urban citizens and traditional rural populations. Even if this reduction in GM functional complexity has been associated with the onset of the so-called “diseases of civilization,” only few information regarding the CAZyme variation within Western populations has been provided to date, and its connections with diet and health are still unexplored. In this scenario, here we explore the GM-encoded CAZyme repertoire across two Italian adult cohorts, including healthy lean subjects consuming a Mediterranean diet and obese patients affected by type 2 diabetes, consuming a high-fat diet. In order to impute the CAZyme panel, a pipeline consisting of publicly available software – QIIME, FragGeneScan and HMMER – was specifically implemented. Our study highlighted the existence of robust clusters of bacterial species sharing a common MAC degradation profile in the Italian GM, allowing the stratification of the individual GM into different steady states according to the carbohydrate degradation profile, with possible connections with diet and health

ViromeScan: a new tool for metagenomic viral community profiling

Bioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype

Changes in the Fecal Microbiota Associated with a Broad-Spectrum Antimicrobial Administration in Hospitalized Neonatal Foals with Probiotics Supplementation

There is a wide array of evidence across species that exposure to antibiotics is associated with dysbiosis, and due to their widespread use, this also raises concerns also in medicine. The study aimed to determine the changes on the fecal microbiota in hospitalized neonatal foals administered with broad-spectrum antimicrobials and supplemented probiotics. Fecal samples were collected at hospital admission (Ta), at the end of the antimicrobial treatment (Te) and at discharge (Td). Feces were analysed by next-generation sequencing of the 16S rRNA gene on Illumina MiSeq. Seven foals treated with IV ampicillin and amikacin/gentamicin were included. The mean age at Ta was 19 h, the mean treatment length was 7 days and the mean time between Te and Td was 4.3 days. Seven phyla were identified: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, TM7 and Verrucomicrobia. At Ta, Firmicutes (48.19%) and Proteobacteria (31.56%) were dominant. The alpha diversity decreased from Ta to Te, but it was the highest at Td. The beta diversity was higher at Ta than at Te and higher at Td than at Te. An increase in Akkermansia over time was detected. The results suggest that the intestinal microbiota of neonatal foals rapidly returns to a high diversity after treatment. It is possible that in foals, the effect of antimicrobials is strongly influenced or overshadowed by the time-dependent changes in the developing gut microbiota

Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500

Background: The intestinal microbial communities and their temporal dynamics are gaining increasing interest due to the significant implications for human health. Recent studies have shown the dynamic behavior of the gut microbiota in free-living, healthy persons. To date, it is not known whether these dynamics are applicable during prolonged life sharing in a confined and controlled environment. Results: The MARS500 project, the longest ground-based space simulation ever, provided us with a unique opportunity to trace the crew microbiota over 520 days of isolated confinement, such as that faced by astronauts in real long-term interplanetary space flights, and after returning to regular life, for a total of 2 years. According to our data, even under the strictly controlled conditions of an enclosed environment, the human gut microbiota is inherently dynamic, capable of shifting between different steady states, typically with rearrangements of autochthonous members. Notwithstanding a strong individuality in the overall gut microbiota trajectory, some key microbial components showed conserved temporal dynamics, with potential implications for the maintenance of a health-promoting, mutualistic microbiota configuration. Conclusions: Sharing life in a confined habitat does not affect the resilience of the individual gut microbial ecosystem, even in the long term. However, the temporal dynamics of certain microbiota components should be monitored when programming future mission simulations and real space flights, to prevent breakdowns in the metabolic and immunological homeostasis of the crewmembers