Maternal influences on fetal microbial colonization and immune development

Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach

Fungi have a complex role in the intestinal tract, influencing health and disease, with dysbiosis contributing to obesity. Our objectives were to investigate fungal diversity in human gut microbiota among eutrophic, overweight, and obese. Epidemiological and nutritional information were collected from adult individuals, as well as stool samples processed for selective fungi isolation and identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (yeasts) or microculture (filamentous fungi). Further 18S rDNA sequencing was performed to confirm identification. The mean count of fungi was 241 CFU/g of feces. Differences in the population level of the filamentous fungi were observed within eutrophic and obese groups. Overall, 34 genera were identified. The predominant phylum was Ascomycota with 20 different genera, followed by Basidiomycota and Zygomycota. As for Ascomycota, the most prevalent species were Paecilomyces sp., Penicillium sp., Candida sp., Aspergillus sp., Fonsecaea sp., and Geotrichum sp. (76.39, 65.28, 59.72, 58.33, 12.50, and 9.72%, respectively). As for Basidiomycota, Trichosporon sp. and Rhodotorula sp. were the most prevalent (30.56 and 15.28%, respectively), and for Zygomycota, Rhizopus sp. and Mucor sp. were the most numerous (15.28 and 9.72%, respectively). As expected there is a mycobiota shift towards obesity, with slightly higher diversity associated to eutrophic individuals. This mycobiota shift seems also to be related to the nutritional behavior of the individuals, as observed that the macronutrients intake may be positively related to the different fungi occurrences. Other studies are needed to better understand relationships between mycobiota and obesity, which could be used in future obesity treatments.

Re-evaluation of celluloses E 460(i), E 460(ii), E 461, E 462, E 463, E 464, E 465, E 466, E 468 and E 469 as food additives

Following a request from the European Commission, the EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS) was asked to deliver a scientific opinion re-evaluating the safety of microcrystalline cellulose (E 460(i)), powdered cellulose (E 460(ii)), methyl cellulose (E 461), ethyl cellulose (E 462), hydroxypropyl cellulose (E 463), hydroxypropyl methyl cellulose (E 464), ethyl methyl cellulose (E 465), sodium carboxy methyl cellulose (E 466), enzymatically hydrolysed carboxy methyl cellulose (E 469) and cross-linked carboxy methyl cellulose (E 468) as food additives. The Joint FAO/WHO Expert Committee on Food Additives (JECFA) and the Scientific Committee on Food (SCF) established an acceptable daily intake (ADI) 'not specified' for unmodified and modified celluloses. Celluloses are not absorbed and are excreted intact in the faeces; in addition, microcrystalline cellulose, powdered and modified celluloses could be fermented by the intestinal flora in animals and humans. Specific toxicity data were not always available for all the celluloses evaluated in the present opinion and for all endpoints. Given their structural, physicochemical and biological similarities, the Panel considered it possible to read-across between all the celluloses. The acute toxicity of celluloses was low and there was no genotoxic concern. Short-term and subchronic dietary toxicity studies performed with E 460(i), E 461, E 462, E 463, E 464, E 466 and E 469 at levels up to 10% did not indicate specific treatment related adverse effects. In chronic toxicity studies performed with E 460(i), E 461, E 463, E 464, E 465 and E 466, the no observed adverse effect level (NOAEL) values reported ranged up to 9,000 mg/kg body weight (bw) per day. No carcinogenic properties were detected for microcrystalline cellulose and modified celluloses. Adverse effects on reproductive performance or developmental effects were not observed with celluloses at doses greater than 1,000 mg/kg bw by gavage (often the highest dose tested). The combined exposure to celluloses (E 460-466, E 468 and E 469) at 95th percentile of the refined (brand-loyal) exposure assessment for the general population was up to 506 mg/kg bw per day. The Panel concluded that there was no need for a numerical ADI and that there would be no safety concern at the reported uses and use levels for the unmodified and modified celluloses (E 460(i); E 460(ii); E 461-466; E 468 and E 469). The Panel considered an indicative total exposure of around 660-900 mg/kg bw per day for microcrystalline, powdered and modified celluloses.

The microbiota influences cell death and microglial colonization in the perinatal mouse brain

The mammalian fetus develops in a largely sterile environment, and direct exposure to a complex microbiota does not occur until birth. We took advantage of this to examine the effect of the microbiota on brain development during the first few days of life. The expression of anti- and pro-inflammatory cytokines, developmental cell death, and microglial colonization in the brain were compared between newborn conventionally colonized mice and mice born in sterile, germ-free (GF) conditions. Expression of the pro-inflammatory cytokines interleukin 1β and tumor necrosis factor α was markedly suppressed in GF newborns. GF mice also had altered cell death, with some regions exhibiting higher rates (paraventricular nucleus of the hypothalamus and the CA1 oriens layer of the hippocampus) and other regions exhibiting no change or lower rates (arcuate nucleus of the hypothalamus) of cell death. Microglial labeling was elevated in GF mice, due to an increase in both microglial cell size and number. The changes in cytokine expression, cell death and microglial labeling were evident on the day of birth, but were absent on embryonic day 18.5, approximately one-half day prior to expected delivery. Taken together, our results suggest that direct exposure to the microbiota at birth influences key neurodevelopmental events and does so within hours. These findings may help to explain some of the behavioral and neurochemical alterations previously seen in adult GF mice.

Re-evaluation of polyglycerol esters of fatty acids (E 475) as a food additive

The EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS) provides a scientific opinion re-evaluating the safety of polyglycerol esters of fatty acids (PEFA) (E 475) when used as a food additive. In 1978, the Scientific Committee on Food (SCF) endorsed an acceptable daily intake (ADI) of 25 mg/kg body weight (bw) per day previously established by the Joint FAO/WHO Expert Committee on Food Additives (JECFA). Absorption of intact PEFA in the gastrointestinal tract was extremely low. PEFA was rapidly and almost fully hydrolysed to polyglycerols and fatty acids in the gastrointestinal tract. The safety of polyglycerols and specific fatty acids has recently been assessed and no adverse effects were identified in the available studies. No adverse effects of PEFA at any dose have been observed in short-term, subchronic or chronic toxicity studies. A no observed adverse effect level (NOAEL) of 9,000 mg/kg bw per day was identified from subchronic studies and of 2,500 mg/kg bw per day from chronic studies, the highest doses tested. No genotoxic potential of PEFA was identified from the limited information available. The reproductive toxicity studies showed no adverse effects of PEFA but had major limitations. Clinical chemistry and urinalysis, from a clinical study with limited information, did not reveal any adverse effects in volunteers receiving up to 300 mg/kg bw per day for 3 weeks. The highest exposure to PEFA used as a food additive was 2.6 and 6.4 mg/kg bw per day in children at the mean and the 95th percentile, respectively, for the non-brand loyal scenario. Considering all the above, the Panel concluded that the food additive PEFA (E 475) was not of safety concern at the reported uses and use levels and that there was no need for a numerical ADI. The Panel recommended some modifications of the EU specifications for E 475.

Safety of nisin (E 234) as a food additive in the light of new toxicological data and the proposed extension of use

The present scientific opinion deals with the evaluation of the safety of nisin (E 234) in the light of new toxicological data and with the proposed extension of use in unripened cheese and heat-treated meat products. Nisin (E 234) is currently an authorised food additive in the EU under Annex II of Regulation (EC) 1333/2008 for use in several food categories. The safety of nisin (E 234) as a food additive has been evaluated in 2006 by the EFSA Panel on Food Additives, Flavourings, Processing Aids and Materials in Contact with Food, where an acceptable daily intake (ADI) of 0.13 mg/kg body weight (bw) was confirmed as previously established by Scientific Committee on Food (SCF). In addition to the studies previously evaluated by EFSA in 2006, the Panel considered in the present opinion, data from a new subchronic toxicity study. No adverse effects were observed in a repeated dose oral toxicity study in which rats were administered nisin A for 90 days. A no observed adverse effect level (NOAEL) of 225 mg nisin A/kg bw per day, the highest dose tested, was identified for this study. Using this NOAEL, an ADI of 1 mg nisin A/kg bw per day for nisin (E 234) was calculated applying a default uncertainty factor of 200 for extrapolation of subchronic to chronic exposure and inter- and intra-species variability. The Panel calculated exposure estimates for both the current and the proposed uses based on the data available in the EFSA Comprehensive Database. The Panel considered that the overall exposure estimate was below the new ADI for nisin A for all population groups. The Panel concluded that the proposed extension of use of nisin (E 234) as a food additive in unripened cheese (at maximum level of 12 mg/kg) and in heat-treated meat products (at maximum level of 25 mg/kg) would not be of safety concern.

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.

Re-evaluation of mono- and di-glycerides of fatty acids (E 471) as food additives

The EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS) provides a scientific opinion re-evaluating the safety of mono- and di-glycerides of fatty acids (E 471) when used as a food additive. The Panel considered that it is very likely that hydrolysis of mono- and di-glycerides of fatty acids by lipases in the gastrointestinal tract would occur, resulting in the release of glycerol and fatty acids. Glycerol (E 422) and fatty acids (E 570) have been re-evaluated and the Panel concluded that there was no safety concern regarding their use as food additives. Toxicological studies with mono- and di-glycerides rich in unsaturated fatty acids were considered for the re-evaluation of E 471. No evidence for adverse effects was reported in short-term, subchronic studies, chronic, reproductive and developmental toxicity studies. Neither carcinogenic potential nor a promotion effect in initiation/promotion was reported. The available studies did not raise any concern with regard to genotoxicity. The refined estimates were based on 31 out of 84 food categories in which E 471 is authorised. The Panel noted that the contribution of E 471 represented at the mean only 0.8-3.5% of the recommended daily fat intake. Based on the approach described in the conceptual framework for the risk assessment of certain food additives re-evaluated under Commission Regulation (EU) No 257/2010 and taking into account the considerations mentioned above, the Panel concluded that there was no need for a numerical acceptable daily intake (ADI) and that the food additive mono- and di-glycerides of fatty acids (E 471) was of no safety concern at the reported uses and use levels. The Panel recommended some modifications of the EU specifications for E 471.

Association of Maternal Gestational Weight Gain With the Infant Fecal Microbiota

OBJECTIVES

Pregnancy characteristics may influence the infant fecal microbiota during early life. We aimed to examine associations of maternal gestational weight gain with infant fecal microbiota composition, bacterial community richness, and Shannon diversity index.

METHODS

We analyzed data from a prospective cohort study of healthy infants. We collected prenatal data, including report of mother's gestational weight gain, and infant fecal samples from 84 infant-mother dyads. By applying 16S rRNA gene sequencing and an unbiased clustering by partitioning around medoids using Bray-Curtis distances, we identified 4 fecal microbiota profiles, and examined the associations of maternal gestational weight gain with the 4 fecal microbiota profiles, bacterial community richness, and Shannon diversity index.

RESULTS

Overall, the median age of infants was 4.0 months and 43% were girls. The mothers of the 84 infants gained a mean of 14.2 kg (standard deviation, 5.4 kg) during pregnancy. We identified 4 distinct microbiota profiles: Bifidobacterium-dominant (42%), Enterobacter/Veillonella-dominant (23%), Bacteroides-dominant (19%), and Escherichia-dominant (17%). Infants whose mothers had higher gestational weight gain were less likely to have a Bacteroides-dominant profile, corresponding to a relative risk ratio of 0.83 (95% confidence interval, 0.71-0.96; P = 0.01) per 1 kg increase in weight. In addition, higher gestational weight gain was also associated with lower bacterial community richness and Shannon diversity index (P < 0.05).

CONCLUSIONS

In this prospective cohort study of healthy infants, maternal gestational weight gain was associated with the infant fecal microbiota profiles, bacterial community richness, and Shannon diversity index.

Antibiotic stewardship in perinatal and neonatal care

The spread of antibiotic resistance due to the use and misuse of antibiotics around the world is now a major health crisis. Neonates are exposed to antibiotics both before and after birth, often empirically because of risk factors for infection, or for non-specific signs which may or may not indicate sepsis. There is increasing evidence that, apart from antibiotic resistance, the use of antibiotics in pregnancy and in the neonatal period alters the microbiome in the fetus and neonate with an increased risk of immediate and long-term adverse effects. Antibiotic stewardship is a co-ordinated program that promotes the appropriate use of antibiotics, improves patient outcomes, reduces microbial resistance, and decreases the spread of infections caused by multidrug-resistant organisms. This review addresses some of the controversies in antibiotic use in the perinatal period, examines opportunities for reduction of unnecessary antibiotic exposure in neonates, and provides a framework for antibiotic stewardship in neonatal care.

A cross-sectional comparative study of gut bacterial community of Indian and Finnish children

The human gut microbiome plays a crucial role in the compositional development of gut microbiota. Though well documented in western pediatrics population, little is known about how various host conditions affect populations in different geographic locations such as the Indian subcontinent. Given the impact of distinct environmental conditions, our study assess the gut bacterial diversity of a small cohort of Indian and Finnish children and investigated the influence of FUT2 secretor status and birth mode on the gut microbiome of these populations. Using multiple profiling techniques, we show that the gut bacterial community structure in 13-14-year-old Indian (n = 47) and Finnish (n = 52) children differs significantly. Specifically, Finnish children possessed higher Blautia and Bifidobacterium, while genera Prevotella and Megasphaera were predominant in Indian children. Our study also demonstrates a strong influence of FUT2 and birth mode variants on specific gut bacterial taxa, influence of which was noticed to differ between the two populations under study.

The skin microbiome: impact of modern environments on skin ecology, barrier integrity, and systemic immune programming

Skin barrier structure and function is essential to human health. Hitherto unrecognized functions of epidermal keratinocytes show that the skin plays an important role in adapting whole-body physiology to changing environments, including the capacity to produce a wide variety of hormones, neurotransmitters and cytokine that can potentially influence whole-body states, and quite possibly, even emotions. Skin microbiota play an integral role in the maturation and homeostatic regulation of keratinocytes and host immune networks with systemic implications. As our primary interface with the external environment, the biodiversity of skin habitats is heavily influenced by the biodiversity of the ecosystems in which we reside. Thus, factors which alter the establishment and health of the skin microbiome have the potential to predispose to not only cutaneous disease, but also other inflammatory non-communicable diseases (NCDs). Indeed, disturbances of the stratum corneum have been noted in allergic diseases (eczema and food allergy), psoriasis, rosacea, acne vulgaris and with the skin aging process. The built environment, global biodiversity losses and declining nature relatedness are contributing to erosion of diversity at a micro-ecological level, including our own microbial habitats. This emphasises the importance of ecological perspectives in overcoming the factors that drive dysbiosis and the risk of inflammatory diseases across the life course.

Early-Life Host-Microbiome Interphase: The Key Frontier for Immune Development

Human existence can be viewed as an "animal in a microbial world." A healthy interaction of the human host with the microbes in and around us heavily relies on a well-functioning immune system. As development of both the microbiota and the host immune system undergo rapid changes in early life, it is not surprising that even minor alterations during this co-development can have profound consequences. Scrutiny of existing data regarding pre-, peri-, as well as early postnatal modulators of newborn microbiota indeed suggest strong associations with several immune-mediated diseases with onset far beyond the newborn period. We here summarize these data and extract overarching themes. This same effort in turn sets the stage to guide effective countermeasures, such as probiotic administration. The objective of our review is to highlight the interaction of host immune ontogeny with the developing microbiome in early life as a critical window of susceptibility for lifelong disease, as well as to identify the enormous potential to protect and promote lifelong health by specifically targeting this window of opportunity.

Re-evaluation of sorbitan monostearate (E 491), sorbitan tristearate (E 492), sorbitan monolaurate (E 493), sorbitan monooleate (E 494) and sorbitan monopalmitate (E 495) when used as food additives

The Panel on Food Additives and Nutrient Sources added to Food (ANS) provides a scientific opinion re-evaluating the safety of sorbitan monostearate (E 491), sorbitan tristearate (E 492), sorbitan monolaurate (E 493), sorbitan monooleate (E 494) and sorbitan monopalmitate (E 495) when used as food additives. The Scientific Committee on Food (SCF) allocated an acceptable daily intake (ADI) of 25 mg/kg body weight (bw) per day for E 491, E 492 and E 495 singly or in combination; and a separate group ADI for E 493 and E 494 singly or in combination of 5 mg/kg bw per day calculated as sorbitan monolaurate in 1974. The Panel noted that after oral administration sorbitan monostearate can be either hydrolysed to its fatty acid moiety and the corresponding anhydrides of sorbitol and excreted via urine or exhaled as CO 2 or excreted intact in the faeces. The Panel considered that sorbitan esters did not raise concern for genotoxicity. Based on the no observed adverse effect level (NOAEL) of 2,600 mg sorbitan monostearate/kg bw per day, taking into account the ratio between the molecular weight of sorbitan monostearate (430.62 g/mol) and sorbitan (164.16 g/mol), and applying an uncertainty factor of 100, the Panel derived a group ADI of 10 mg/kg bw per day expressed as sorbitan for sorbitan esters (E 491-495) singly or in combination. This group ADI of 10 mg sorbitan/kg bw per day is equivalent to 26 mg sorbitan monostearate/kg bw per day. The Panel concluded that the exposure at the mean and the 95th percentile level, using non-brand-loyal scenario, did not exceed the ADI in any of the population groups. The Panel on the request for an amendment of specifications regarding the removal of 'congealing range' concluded that it could be eventually replaced by another identification parameter such as melting point.

Evolutionary and ecological forces that shape the bacterial communities of the human gut

Since microbes were first described in the mid-1600s, we have come to appreciate that they live all around and within us with both beneficial and detrimental effects on nearly every aspect of our lives. The human gastrointestinal tract is inhabited by a dynamic community of trillions of bacteria that constantly interact with each other and their human host. The acquisition of these bacteria is not stochastic but determined by circumstance (environment), host rules (genetics, immune state, mucus, etc), and dynamic self-selection among microbes to form stable, resilient communities that are in balance with the host. In this review, we will discuss how these factors lead to formation of the gut bacterial community and influence its interactions with the host. We will also address how gut bacteria contribute to disease and how they could potentially be targeted to prevent and treat a variety of human ailments.

Guidance on the risk assessment of substances present in food intended for infants below 16 weeks of age

Following a request from the European Commission to EFSA, the EFSA Scientific Committee (SC) prepared a guidance for the risk assessment of substances present in food intended for infants below 16 weeks of age. In its approach to develop this guidance, the EFSA SC took into account, among others, (i) an exposure assessment based on infant formula as the only source of nutrition; (ii) knowledge of organ development in human infants, including the development of the gut, metabolic and excretory capacities, the brain and brain barriers, the immune system, the endocrine and reproductive systems; (iii) the overall toxicological profile of the substance identified through the standard toxicological tests, including critical effects; (iv) the relevance for the human infant of the neonatal experimental animal models used. The EFSA SC notes that during the period from birth up to 16 weeks, infants are expected to be exclusively fed on breast milk and/or infant formula. The EFSA SC views this period as the time where health-based guidance values for the general population do not apply without further considerations. High infant formula consumption per body weight is derived from 95th percentile consumption. The first weeks of life is the time of the highest relative consumption on a body weight basis. Therefore, when performing an exposure assessment, the EFSA SC proposes to use the high consumption value of 260 mL/kg bw per day. A decision tree approach is proposed that enables a risk assessment of substances present in food intended for infants below 16 weeks of age. The additional information needed when testing substances present in food for infants below 16 weeks of age and the approach to be taken for the risk assessment are on a case-by-case basis, depending on whether the substance is added intentionally to food and is systemically available.

Re-evaluation of polyglycerol polyricinoleate (E 476) as a food additive

The Panel on Food Additives and Nutrient Sources added to Food (ANS) provides a scientific opinion re-evaluating the safety of polyglycerol polyricinoleate (PGPR, E 476) used as a food additive. In 1978, the Scientific Committee for Food (SCF) established an acceptable daily intake (ADI) of 7.5 mg/kg body weight (bw) per day for PGPR. PGPR is hydrolysed in the gut resulting in the liberation of free polyglycerols, polyricinoleic acid and ricinoleic acid. Di- and triglycerol are absorbed and excreted unchanged in the urine; long-chain polyglycerols show lower absorption and are mainly excreted unchanged in faeces. Acute oral toxicity of PGPR is low, and short-term and subchronic studies indicate PGPR is tolerated at high doses without adverse effects. PGPR (E 476) is not of concern with regard to genotoxicity or carcinogenicity. The single reproductive toxicity study with PGPR was limited and was not an appropriate study for deriving a health-based guidance value. Human studies with PGPR demonstrated that there is no indication of significant adverse effect. The Panel considered a 2-year combined chronic toxicity/carcinogenicity study for determining a reference point and derived a no observed adverse effect level (NOAEL) for PGPR (E 476) of 2,500 mg/kg bw per day, the only dose tested. Therefore, the Panel concluded that the present data set give reason to revise the ADI of 7.5 mg/kg bw per day allocated by SCF to 25 mg/kg bw per day. Exposure estimates did not exceed the ADI of 25 mg/kg bw per day and a proposed extension of use would not result in an exposure exceeding this ADI. The Panel recommended modification of the EU specifications for PGPR (E 476).

Biology of the Microbiome 1: Interactions with the Host Immune Response

The intestinal immune system is intimately connected with the vast diversity of microbes present within the gut and the diversity of food components that are consumed daily. The discovery of novel molecular mechanisms, which mediate host-microbe-nutrient communication, have highlighted the important roles played by microbes and dietary factors in influencing mucosal immune responses. Dendritic cells, epithelial cells, innate lymphoid cells, T regulatory cells, effector lymphocytes, natural killer T cells, and B cells can all be influenced by the microbiome. Many of the mechanisms being described are bacterial strain or metabolite specific.

Antibiotic treatment at delivery shapes the initial oral microbiome in neonates

Oral microorganisms are important determinants of health and disease. The source of the initial neonatal microbiome and the factors dictating initial human oral microbiota development are unknown. This study aimed to investigate this in placental, oral and gut microbiome profiles from 36 overweight or obese mother-baby dyads as determined by 16S rRNA sequencing. Expression of five antibiotic resistance genes of the β-lactamase class was analysed in the infant oral microbiota samples by QPCR. The neonatal oral microbiota was 65.35% of maternal oral, 3.09% of placental, 31.56% of unknown and 0% of maternal gut origin. Two distinct neonatal oral microbiota profiles were observed: one strongly resembling the maternal oral microbiota and one with less similarity. Maternal exposure to intrapartum antibiotics explained the segregation of the profiles. Families belonging to Proteobacteria were abundant after antibiotics exposure while the families Streptococcaceae, Gemellaceae and Lactobacillales dominated in unexposed neonates. 26% of exposed neonates expressed the Vim-1 antibiotic resistance gene. These findings indicate that maternal intrapartum antibiotic treatment is a key regulator of the initial neonatal oral microbiome.

Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period

Pregnancy is a special physical period in reproductive age women, which has a beneficial influence on the course of certain autoimmune diseases. It has been recently suggested that the microbiome undergoes profound changes during pregnancy that are associated with host physiological and immunological adaptations. The maternal microbiome remodeling during pregnancy is an active response of the mother, possibly to alter immune system status and to facilitate metabolic and immunological adaptations, which are needed for a successful pregnancy. In this review, we attempt to discuss (i) the role of maternal microbiome in pregnancy outcomes known to adversely influence neonatal and infant health, including preterm birth, cardiometabolic complications of pregnancy, and gestational weight gain; (ii) the association of microbiome with autoimmunity, allergy diseases, and asthma during pregnancy; and (iii) the impact of helminth infection during pregnancy.

Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid

Background

Microcephaly has become a major public health problem in Brazil. The total number of newborns with microcephaly was reported to be >4000 in June 2016. Studies suggest that Zika Virus is a major cause of new microcephaly cases in Brazil. Inside the uterus, the foetus is surrounded by the Amniotic Fluid, a proximal fluid that contains foetal and maternal cells as well as microorganisms and where Zika Virus was already found.

Case presentation

A previous study reported the presence of the Zika Virus in the amniotic fluid (collected in the 28th gestational week) of two pregnant women carrying microcephaly foetuses in Brazil. The virus was detected by means of real-time PCR and metatranscriptomic analysis. We compared the microbiome of these two cases with metatranscriptomic sequences from 16 pregnant women collected at various times in their pregnancies

Conclusion

Several strains of bacteria (e.g., Streptococcus and Propionibacterium) found in Amniotic Fluid may be involved in neurological diseases. When the foetus is infected by the Zika Virus, due to neurological damage, they do not move inside the uterus, thus changing the Amniotic Fluid environment, potentially leading to secondary problems. Zika infection could also lead to an immunodeficient state, making bacterial colonization of the foetuses easier. An altered microbial composition during pregnancy may also result in harmful secondary metabolite production from certain microbes that further impair foetal brain development. However, these observations of potentially harmful microbial species are correlations and thus cannot be assumed to be causative agents of (microcephaly) disease. In our study, microbial and parasitic diversity of the Amniotic Fluid was lower in patients infected by ZIKV, compared to that of Prenatal and Preterm controls. The present study was a first attempt to shed light on the microbial and parasitic diversity associated with ZIKV-infected pregnant women bearing microcephaly foetuses, and the presence of diverse microbial and parasite communities in the Amniotic Fluid suggests a poor health status of both the pregnant women and the foetuses they carry.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-016-0242-1) contains supplementary material, which is available to authorized users.

[Association between risk factors during maternal pregnancy and the neonatal period and childhood bronchial asthma]

OBJECTIVE

To study the association of the risk factors during maternal pregnancy and the neonatal period with childhood bronchial asthma.

METHODS

A total of 306 children with asthma (asthma group) and 250 healthy children (control group) were enrolled. Their clinical data during the neonatal period and the maternal data during pregnancy were retrospectively studied.

RESULTS

The univariate analysis showed that there were significant differences in the rates of maternal use of antibiotics during pregnancy, use of antibiotics and probiotics during the neonatal period, preterm birth, cesarean section, low birth weight, and breast feeding (>6 months) between the asthma and control groups (P<0.05). The multivariate logistic regression analysis showed that use of antibiotics during pregnancy (OR=3.908, 95%CI: 1.277-11.962), use of antibiotics during neonatal period (OR=24.154, 95%CI: 7.864-74.183), preterm birth (OR=8.535, 95%CI: 2.733-26.652), and cesarean section (OR=4.588, 95%CI: 2.887-7.291) were independent risk factors for childhood asthma. The use of probiotics during the neonatal period (OR=0.014, 95%CI: 0.004-0.046) and breast feeding (>6 months) (OR=0.161, 95%CI: 0.103-0.253) were protective factors for childhood asthma.

CONCLUSIONS

The early prevention of childhood asthma can be improved by reducing the use of antibiotics during pregnancy, reducing cesarean section, avoiding abuse of antibiotics during the neonatal period, trying breast feeding and taking probiotics in early stage.

Planting the seed: Origins, composition, and postnatal health significance of the fetal gastrointestinal microbiota

It has long been assumed that establishment of the fetal microbiome commences with the birthing process. However, recent studies have found bacterial DNA in umbilical cord blood, placenta, amniotic fluid, meconium, and fetal membranes in healthy normal pregnancies, leading to suggestions that the seeding of the fetal microbiome may commence in utero long before delivery. The origins of the microbiota of the fetal gastrointestinal (GI) tract have not yet been conclusively determined, although bacterial translocation from the maternal circulation, or ascension from the vagina, are both likely to be contributing pathways. Mother-to-child efflux of bacteria during pregnancy has the potential to markedly influence postnatal health, as the composition of gut microbiota determines production of important metabolites which are absorbed systemically and which modify immune function and development. Hence, the importance of understanding the colonization of the fetal GI microbiome is becoming clear, although few studies have investigated the origins, dynamics, and timing of the fetal microbiome. This is the topic of this review. By gaining a deeper understanding of the mechanisms underpinning fetal microbiome seeding, strategies may be developed to optimize fetal immune development and reduce the risk of adverse health and developmental outcomes.

Perinatal Microbiomes' Influence on Preterm Birth and Preterms' Health: Influencing Factors and Modulation Strategies

Microbial communities inhabiting the human host play important roles in maintaining health status, including reproduction and early life programming, which is particularly important in the context of preterm neonates' health. Preterm birth (PTB) is often the result of a microbial dysbiosis or infection. In addition, preterm neonates experience different levels of organ immaturity and an abnormal gut microbiota establishment, as compared to full-term neonates. This exacerbates their developmental problems and can have negative consequences at systemic level. In addition, preterm babies are commonly exposed to delayed enteral feeding and hospital environments, which increases the risk of short- and long-term health problems. Some of these clinical conditions, such as necrotizing enterocolitis or sepsis, may be life threatening, whereas others may translate into life-long conditions, including cognitive problems. Increasing scientific interest has focused on understanding developmental problems in preterm neonates related to abnormalities in the settlement of their microbial communities, with the final goal of selecting appropriate microbiome-targeted strategies (eg, probiotics), to reduce preterm health risks and improve overall quality of life.This review aims to summarize current knowledge on microbiological factors influencing PTB initiation and gastrointestinal development, and on the health consequences to the preterm neonate. Scientific evidences on dietary strategies reducing PTB incidence and minimizing sequelae in this particularly sensitive human group subpopulation are also discussed.

Influence of microbiome and diet on immune responses in food allergy models

The intestinal immune system is intimately connected with the vast array of microbes present within the gut and the diversity of food components that are consumed daily. The discovery of novel molecular mechanisms, which mediate host-microbe-nutrient communication, have highlighted the important roles played by microbes and dietary factors in influencing mucosal inflammatory and allergic responses. In this review, we summarize the recent important findings in this field, which are important for food allergy and particularly relevant to animal models of food allergy.

The Gut-Brain Axis, BDNF, NMDA and CNS Disorders

Gastro-intestinal (GI) microbiota and the 'gut-brain axis' are proving to be increasingly relevant to early brain development and the emergence of psychiatric disorders. This review focuses on the influence of the GI tract on Brain-Derived Neurotrophic Factor (BDNF) and its relationship with receptors for N-methyl-D-aspartate (NMDAR), as these are believed to be involved in synaptic plasticity and cognitive function. NMDAR may be associated with the development of schizophrenia and a range of other psychopathologies including neurodegenerative disorders, depression and dementias. An analysis of the routes and mechanisms by which the GI microbiota contribute to the pathophysiology of BDNF-induced NMDAR dysfunction could yield new insights relevant to developing novel therapeutics for schizophrenia and related disorders. In the absence of GI microbes, central BDNF levels are reduced and this inhibits the maintenance of NMDAR production. A reduction of NMDAR input onto GABA inhibitory interneurons causes disinhibition of glutamatergic output which disrupts the central signal-to-noise ratio and leads to aberrant synaptic behaviour and cognitive deficits. Gut microbiota can modulate BDNF function in the CNS, via changes in neurotransmitter function by affecting modulatory mechanisms such as the kynurenine pathway, or by changes in the availability and actions of short chain fatty acids (SCFAs) in the brain. Interrupting these cycles by inducing changes in the gut microbiota using probiotics, prebiotics or antimicrobial drugs has been found promising as a preventative or therapeutic measure to counteract behavioural deficits and these may be useful to supplement the actions of drugs in the treatment of CNS disorders.

Predictive value of maternal serum NF-κB p65 and sTREM-1 for subclinical chorioamnionitis in premature rupture of membranes

PROBLEM

The aim of this study was to investigate the levels of nuclear factor kappa B-p65 (NF-κB p65) and soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) in maternal blood with premature rupture of membranes (PROM) and to assess their values for prediction of subclinical chorioamnionitis.

METHOD

NF-κB p65 and sTREM-1 levels were measured in maternal blood and cord blood by fluorescence quantitative RT-PCR assay. According to the placental membranes pathological examination, pregnant women with PROM were divided into chorioamnionitis group (n=28) and non-chorioamnionitis group (n=22).

RESULTS

In the PROM group,the NF-κB p65 and sTREM-1 levels in maternal blood were significantly higher in women with chorioamnionitis than women without chorioamnionitis (P<.05). The cutoff value of maternal NF-κB p65, sTREM-1, C-reactive protein (CRP), and WBC level were 6.73, 2.93, 6.75 mg/L, and 10.8×10(9) /L, respectively, through analysis of the area under the ROC curve (AUC). The optimal combination test was detection of maternal blood NF-κB p65 and CRP levels, which resulted in a sensitivity of 89.3% and a specificity of 72.7% for the prediction of subclinical chorioamnionitis.

CONCLUSION

Combined measurements of maternal NF-κB p65 and CRP levels may be used as early biological indicators that predict subclinical chorioamnionitis in premature rupture of membranes.

Microbiota at the crossroads of autoimmunity

Autoimmune diseases have a multifactorial etiology including genetic and environmental factors. Recently, there has been increased appreciation of the critical involvement of the microbiota in the pathogenesis of autoimmunity, although in many cases, the cause and the consequence are not easy to distinguish. Here, we suggest that many of the known cues affecting the function of the immune system, such as genetics, gender, pregnancy and diet, which are consequently involved in autoimmunity, exert their effects by influencing, at least in part, the microbiota composition and activity. This, in turn, modulates the immune response in a way that increases the risk for autoimmunity in predisposed individuals. We further discuss current microbiota-based therapies.

Peptidylarginine Deiminases as Drug Targets in Neonatal Hypoxic-Ischemic Encephalopathy

Oxygen deprivation and infection are major causes of perinatal brain injury leading to cerebral palsy and other neurological disabilities. The identification of novel key factors mediating white and gray matter damage are crucial to allow better understanding of the specific contribution of different cell types to the injury processes and pathways for clinical intervention. Recent studies in the Rice-Vannucci mouse model of neonatal hypoxic ischemia (HI) have highlighted novel roles for calcium-regulated peptidylarginine deiminases (PADs) and demonstrated neuroprotective effects of pharmacological PAD inhibition following HI and synergistic infection mimicked by lipopolysaccharide stimulation.

Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats

Maternal obesity and overnutrition during pregnancy and lactation can program an increased risk of obesity in offspring. In this context, improving maternal metabolism may help reduce the intergenerational transmission of obesity. Here we show that, in Sprague-Dawley rats, selectively altering obese maternal gut microbial composition with prebiotic treatment reduces maternal energy intake, decreases gestational weight gain, and prevents increased adiposity in dams and their offspring. Maternal serum metabolomics analysis, along with satiety hormone and gut microbiota analysis, identified maternal metabolic signatures that could be implicated in programming offspring obesity risk and highlighted the potential influence of maternal gut microbiota on maternal and offspring metabolism. In particular, the metabolomic signature of insulin resistance in obese rats normalized when dams consumed the prebiotic. In summary, prebiotic intake during pregnancy and lactation improves maternal metabolism in diet-induced obese rats in a manner that attenuates the detrimental nutritional programming of offspring associated with maternal obesity. Overall, these findings contribute to our understanding of the maternal mechanisms influencing the developmental programming of offspring obesity and provide compelling pre-clinical evidence for a potential strategy to improve maternal and offspring metabolic outcomes in human pregnancy.

16S rRNA gene-based metagenomic analysis reveals differences in bacteria-derived extracellular vesicles in the urine of pregnant and non-pregnant women

Recent evidence has indicated that bacteria-derived extracellular vesicles (EVs) are important for host–microbe communication. The aims of the present study were to evaluate whether bacteria-derived EVs are excreted via the urinary tract and to compare the composition of bacteria-derived EVs in the urine of pregnant and non-pregnant women. Seventy-three non-pregnant and seventy-four pregnant women were enrolled from Dankook University and Ewha Womans University hospitals. DNA was extracted from urine EVs after EV isolation using the differential centrifugation method. 16S ribosomal RNA (16S rRNA) gene sequencing was performed using high-throughput 454 pyrosequencing after amplification of the V1–V3 region of the 16S rDNA. The composition of 13 taxa differed significantly between the pregnant and non-pregnant women. At the genus level, Bacillus spp. EVs were more significantly enriched in the urine of the pregnant women than in that of the non-pregnant women (45.61% vs 0.12%, respectively). However, Pseudomonas spp. EVs were more dominant in non-pregnant women than in pregnant women (13.2% vs 4.09%, respectively). Regarding the compositional difference between pregnant women with normal and preterm delivery, EVs derived from Ureaplasma spp. and the family Veillonellaceae (including Megasphaera spp.) were more abundant in the urine of preterm-delivered women than in that of women with normal deliveries. Taken together, these data showed that Bacillus spp. EVs predominate in the urine of pregnant women, whereas Pseudomonas spp. EVs predominate in the urine of non-pregnant women; this suggests that Bacillus spp. EVs might have an important role in the maintenance of pregnancy.

Development of the Neonatal Intestinal Microbiome and Its Association With Necrotizing Enterocolitis

PURPOSE

Neonatal necrotizing enterocolitis (NEC) remains the most devastating gastrointestinal disease for premature infants. In the United States alone, NEC affects >4000 premature infants yearly, has a mortality rate of nearly 33%, and costs the health care system >$1 billion annually. Although NEC has been actively researched for several decades, its pathophysiology remains elusive. One potential mechanism suggests that disruption of the normal neonatal intestinal bacterial flora induces a proinflammatory state, allowing translocation of pathogens across the intestinal epithelia. Disruption of the normal intestinal flora (dysbiosis) is associated with many human diseases. Thus, it is a reasonable hypothesis that dysbiosis may play an important role in the development of NEC. This hypothesis is supported by evidence that probiotic use in premature infants can prevent the development of NEC. Although the role of probiotics and NEC is covered in other reviews, this review instead focuses on normal bacterial colonization in both term and preterm infants and on the association of dysbiosis and the development of NEC.

METHODS

PubMed was queried with the use of the following key search terms: NEC, neonatal microbiome, fetal microbiome, maternal microbiome, neonatal dysbiosis, and microbiome ontogeny. Relevant literature was reviewed and selected for inclusion in accordance with the objectives of the article according to the authors' discretion. Articles that made key salient points in review articles were further pulled from PubMed.

FINDINGS

Although the onset of NEC is thought to involve bacteria, the mechanisms behind their involvement remain unclear. Research to date has failed to identify a single causative organism, and current theories and data now indicate that a disruption of the host intestinal flora is associated with the onset of disease. Recent reports have found that a bloom of Proteobacteria, specifically Enterobacteriacae species, occurs just before the diagnosis of NEC. Whether this is a causative event or merely a marker of intestinal disease is still unclear.

IMPLICATIONS

Because of the complexity of these interactions, it is vital that we continue to investigate the host-bacterial axis in the developing intestine in both humans and in animal models.

Sex differences in the gut microbiome-brain axis across the lifespan

In recent years, the bidirectional communication between the gut microbiome and the brain has emerged as a factor that influences immunity, metabolism, neurodevelopment and behaviour. Cross-talk between the gut and brain begins early in life immediately following the transition from a sterile in utero environment to one that is exposed to a changing and complex microbial milieu over a lifetime. Once established, communication between the gut and brain integrates information from the autonomic and enteric nervous systems, neuroendocrine and neuroimmune signals, and peripheral immune and metabolic signals. Importantly, the composition and functional potential of the gut microbiome undergoes many transitions that parallel dynamic periods of brain development and maturation for which distinct sex differences have been identified. Here, we discuss the sexually dimorphic development, maturation and maintenance of the gut microbiome-brain axis, and the sex differences therein important in disease risk and resilience throughout the lifespan.

Microbial programming of health and disease starts during fetal life

The pioneer microbiota of the neonatal gut are essential for gut maturation, and metabolic and immunologic programming. Recent research has shown that early bacterial colonization may impact the occurrence of disease later in life (microbial programming). Despite early conflicting evidence, it has long been considered that the womb is a sterile environment and human microbial colonization begins at birth. In the last few years, several findings have reiterated the presence of microbes in infant first stool (meconium) and pointed to the existence of in utero microbial colonization of the infant gut. The dominant bacterial taxa detected in meconium specimens belong to the Enterobacteriaceae family (Escherichia genus) and lactic acid bacteria (notably members of the genera Leuconostoc, Enterococcus, and Lactococcus). Maternal atopy promotes dominance of Enterobacteriaceae in newborn meconium, which in turn may lead to respiratory problems in the infant. This microbial interaction with the host immune system may in fact, originate during fetal life. Our review evaluates the evidence for an intrauterine origin of meconium microbiota, their composition and influences, and potential clinical implications on infant health.

What can ecosystems learn? Expanding evolutionary ecology with learning theory

Background

The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole?

Results

Here we answer this question by incorporating principles from connectionist learning, a previously unrelated discipline already using well-developed theories on how emergent behaviours arise in simple networks. Specifically, we show conditions where natural selection on ecological interactions is functionally equivalent to a simple type of connectionist learning, ‘unsupervised learning’, well-known in neural-network models of cognitive systems to produce many non-trivial collective behaviours. Accordingly, we find that a community can self-organise in a well-defined and non-trivial sense without selection at the community level; its organisation can be conditioned by past experience in the same sense as connectionist learning models habituate to stimuli. This conditioning drives the community to form a distributed ecological memory of multiple past states, causing the community to: a) converge to these states from any random initial composition; b) accurately restore historical compositions from small fragments; c) recover a state composition following disturbance; and d) to correctly classify ambiguous initial compositions according to their similarity to learned compositions. We examine how the formation of alternative stable states alters the community’s response to changing environmental forcing, and we identify conditions under which the ecosystem exhibits hysteresis with potential for catastrophic regime shifts.

Conclusions

This work highlights the potential of connectionist theory to expand our understanding of evo-eco dynamics and collective ecological behaviours. Within this framework we find that, despite not being a Darwinian unit, ecological communities can behave like connectionist learning systems, creating internal conditions that habituate to past environmental conditions and actively recalling those conditions.

Reviewers

This article was reviewed by Prof. Ricard V Solé, Universitat Pompeu Fabra, Barcelona and Prof. Rob Knight, University of Colorado, Boulder.

Congenital Chagas disease as an ecological model of interactions between Trypanosoma cruzi parasites, pregnant women, placenta and fetuses

The aim of this paper is to discuss the main ecological interactions between the parasite Trypanosoma cruzi and its hosts, the mother and the fetus, leading to the transmission and development of congenital Chagas disease. One or several infecting strains of T. cruzi (with specific features) interact with: (i) the immune system of a pregnant woman whom responses depend on genetic and environmental factors, (ii) the placenta harboring its own defenses, and, finally, (iii) the fetal immune system displaying responses also susceptible to be modulated by maternal and environmental factors, as well as his own genetic background which is different from her mother. The severity of congenital Chagas disease depends on the magnitude of such final responses. The paper is mainly based on human data, but integrates also complementary observations obtained in experimental infections. It also focuses on important gaps in our knowledge of this congenital infection, such as the role of parasite diversity vs host genetic factors, as well as that of the maternal and placental microbiomes and the microbiome acquisition by infant in the control of infection. Investigations on these topics are needed in order to improve the programs aiming to diagnose, manage and control congenital Chagas disease.

Periconceptional and Gestational Exposure to Antibiotics and Childhood Asthma

Background

Previous studies suggest that maternal antibiotics exposure during pregnancy may increase the risk of childhood asthma, but the results were inconsistent. Furthermore, most studies did not examine periconception period as an exposure window. We aim to assess the associations between maternal exposure to specific antibiotics before and during pregnancy and the risk of asthma in early childhood.

Methods

Data from the Collaborative Perinatal Project were used. Maternal exposure to antibiotics before and during pregnancy was recorded at each prenatal visit. A total of 39,907 singleton children were followed up to 7 years of age. Multilevel multiple logistic regression models were used to control for potential confounders and account for multiple pregnancies per woman.

Results

Maternal use of penicillin or chloramphenicol was associated with an increased risk of asthma in the offspring (adjusted odds ratio = 1.21, 95% confidence interval 1.08–1.36 for penicillin; 1.72 [1.14–2.59] for chloramphenicol). The risk was significantly increased if penicillin or chloramphenicol was used in the 1st trimester (1.09 [1.04–1.13] for penicillin and 1.23 [1.01–1.51] for chloramphenicol).

Conclusion

Maternal exposure to certain antibiotics is associated with childhood asthma by 7 years of age. Early pregnancy may be a sensitive window.

What is the placenta?

Discarded at birth, the placenta is a highly complex and fascinating organ. During the course of a pregnancy, it acts as the lungs, gut, kidneys, and liver of the fetus. The placenta also has major endocrine actions that modulate maternal physiology and metabolism and provides a safe and protective milieu in which the fetus can develop. The human placenta undergoes dramatic transformations in form and function between the first trimester, when organogenesis occurs, and the remainder of pregnancy that reflect evolutionary responses to changing oxygen concentrations in the earth's atmosphere. Recent research indicates a more interactive dialogue between the placenta and the maternal tissues than previously recognized. The endometrial glands provide histotrophic support during the first weeks of pregnancy, and the placenta appears able to stimulate its own development by up-regulating gland activity in response to endocrine signals. Extravillous trophoblast cells migrate from the placenta into the uterine wall, in which they interact with cells of the maternal innate immune system. These interactions have a physiological, rather than a classical immunological, outcome and most probably mediate remodeling of the uterine spiral arteries that supply the placenta. Furthermore, deportation of aggregates of transcriptionally active trophoblast nuclei, and the release of exosomes carrying microribonucleic acids challenge our perceptions of fetal-maternal signaling and where the placental interface actually lies. Here we reconsider definitions of the placenta in the light of these recent advances.

Metabolome of human gut microbiome is predictive of host dysbiosis

Background

Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome.

Results

Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles.

Conclusions

Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.

Electronic supplementary material

The online version of this article (doi:10.1186/s13742-015-0084-3) contains supplementary material, which is available to authorized users.