Mycobiome Profiles in Breast Milk from Healthy Women Depend on Mode of Delivery, Geographic Location, and Interaction with Bacteria

Intratumor fungi specific mechanisms to influence cell death pathways and trigger tumor cell apoptosis

Cancer, uncontrolled cell growth due to the loss of cell cycle regulation, is often found to be associated with viral infections and, as recent studies show, with bacterial infections as well. Emerging reports also suggest a strong link between fungi and cancer. The crucial virulence trait of fungi, the switch from yeast (Y) to hyphal (H) form, is found to be associated with carcinogenesis. The physicochemical properties and signal transduction pathways involved in the switch to the hyphal form overlap with those of tumor cell formation. Inhibiting differentiation causes apoptosis in fungi, whereas preventing apoptosis leads to cancer in multicellular organisms. Literature on the fungi-cancer linkage, though limited, is increasing rapidly. This review examines cancer-specific fungal communities, the impact of fungal microbiome on cancer cell progression, similarities between fungal differentiation and cells turning cancerous at biochemical and molecular levels, including the overlaps in signal transduction pathways between fungi and cancer. Based on the available evidence, we suggest that molecules inhibiting the yeast-hyphal transition in fungi can be combined with those targeting tumor cell apoptosis for effective cancer treatment. The review points out fertile research areas where mycologists and cancer researchers can collaborate to unravel common molecular mechanisms. Moreover, antibodies targeting fungal-specific chitin and glucan can be used for the selective neutralization of tumor cells. These new combinations of potential therapies are expected to facilitate the development of target-specific, less harmful and commercially feasible anticancer therapies. We bring together available evidence to argue that fungal infections could either trigger cancer or have a significant role in the development and progression of cancer. Hence, cancer-associated fungal populations could be utilized as a target for a combination therapy involving the integration of anticancer and antifungal drugs as well as inhibitors of fungal morphogenesis to develop more effective anticancer therapies.

Functional efficacy of Enterococcus faecium HN4 and Lactobacillus delbrueckii HN5 strains isolated from human milk

AIMS

The microbiota of human milk is described at length; however, variation in different bacterial genera in milk has been reported. Here, breast milk samples from Indian mothers were used to target bacterial species from the pool of microbial communities in human milk with probiotic potential.

MATERIALS AND METHODS

A culture-dependent technique was used to isolate bacterial cultures, and their physiological and functional properties were appraised.

RESULTS

Two bacterial cultures, E. faecium HN4 and L delbrueckii HN5, were identified as showing considerable tolerance to acid and bile conditions with 73.0-87.0% survival. The cultures showed other in vitro beneficial properties.

CONCLUSION

The study highlights the presence of potential probiotics in human milk that could be investigated for further use.

Impact of Maternal Exposure to SARS-CoV-2 on Immunological Components of Breast Milk

COVID-19, caused by SARS-CoV-2, has become a global public health threat. Although no replication-competent virus has been found in breast milk samples, breastfeeding practices during the pandemic were impacted. It is well known that breast milk is adapted to meet the needs of infants, providing the appropriate amounts of nutrients and various bioactive compounds that contribute to the maturation of the immune system and antioxidant protection, safeguarding infants against diseases. While its composition is variable, breast milk contains immune cells, antibodies, and cytokines, which have anti-inflammatory, pro-inflammatory, antiviral, and antibacterial properties that strengthen infant immunity. Since COVID-19 vaccines have not yet been approved for infants under six months of age, newborns rely on the passive transfer of antibodies via the placenta and breast milk to protect them against severe SARS-CoV-2 infection. Several studies that analyzed breast milk samples in the context of COVID-19 have demonstrated that a strong antibody response is induced following maternal infection with SARS-CoV-2. Therefore, this review aims to provide a comprehensive overview of the impact of maternal exposure to SARS-CoV-2 through natural infection and/or vaccination on the immunological composition of breast milk based on the studies conducted on this topic.

Early-life gut mycobiome core species modulate metabolic health in mice

The gut microbiome causally contributes to obesity; however, the role of fungi remains understudied. We previously identified three core species of the infant gut mycobiome (Rhodotorula mucilaginosa, Malassezia restricta and Candida albicans) that correlated with body mass index, however their causal contributions to obesity development are unknown. Here we show the effects of early-life colonization by these fungal species on metabolic health in gnotobiotic mice fed standard (SD) or high-fat-high-sucrose (HFHS) diets. Each species resulted in bacterial microbiome compositional and functional differences. R. mucilaginosa and M. restricta increased adiposity in mice fed SD, while only R. mucilaginosa exacerbated metabolic disease. In contrast, C. albicans resulted in leanness and resistance to diet-induced obesity. Intestinal nutrient transporter expression was unaffected by the presence of fungi in jejunal enteroids, yet the immune landscape in white adipose tissue was distinctly impacted by each fungal species, suggesting that these phenotypes may be a result of fungal immune regulation. This work revealed that three common fungal colonizers have distinct causal influences on obesity and metabolic inflammation and justifies the consideration of fungi in microbiome research on host metabolism.

Recurrent Nipple Duct Obstruction in Two Breastfeeding Patients: A Case Report and Discussion of the Underlying Pathophysiology

Nipple pain is a common reason for premature breastfeeding cessation. There exists anecdotal evidence that one cause of lactational nipple pain is a ductal obstruction, but there is no published literature describing this phenomenon. Herein we present two case reports for two patients who experienced breast and nipple pain concurrent with milk flow reduction. Both patients removed a small stone-like obstructing object from their nipple; this action was painful for one of the patients, resulting in immediate release of milk and relief from breast pain. Both patients experienced recurrence of stone formation in their nipple ducts. We analyzed the mineral composition of the obstructing objects and breast milk using inductively coupled mass spectroscopy. We use literature on teat obstructions in dairy cows and dacryolith and sialolith formation to propose hypotheses as to how the formation of obstructing objects in milk ducts might occur. Future research directions for determining the pathophysiology, clinical presentation, and management of human nipple duct obstructions are discussed.

Clinical implications of maternal multikingdom transmissions and early-life microbiota

Mother-to-infant transmission of the bacteriome, virome, mycobiome, archaeome, and their mobile genetic elements has been recognised in nature as an important step for the infant to acquire and maintain a healthy early-life (from birth till age 3 years) microbiota. A comprehensive overview of other maternal multikingdom transmissions remains unavailable, except for that of the bacteriome. Associations between microorganisms and diseases throughout the human life span have been gradually discovered; however, whether these microorganisms are maternally derived and how they concomitantly interact with other microbial counterparts remain poorly understood. This Review first discusses the current understanding of maternal multikingdom transmissions, their contributions to the development of early-life microbiota, and the primary factors that influence the transmission processes. The clinical implications of the inherited microbiota on human health in early life have been emphasised upon next, along with highlighting of knowledge gaps that should be addressed in future research. Finally, interventions to restore typical vertical transmission or disturbed early-life microbiota have been discussed as potential therapeutic approaches.

From Skin and Gut to the Brain: The Infectious Journey of the Human Commensal Fungus Malassezia and Its Neurological Consequences

The human mycobiome encompasses diverse communities of fungal organisms residing within the body and has emerged as a critical player in shaping health and disease. While extensive research has focused on the skin and gut mycobiome, recent investigations have pointed toward the potential role of fungal organisms in neurological disorders. Among those fungal organisms, the presence of the commensal fungus Malassezia in the brain has created curiosity because of its commensal nature and primary association with the human skin and gut. This budding yeast is responsible for several diseases, such as Seborrheic dermatitis, Atopic dermatitis, Pityriasis versicolor, Malassezia folliculitis, dandruff, and others. However recent findings surprisingly show the presence of Malassezia DNA in the brain and have been linked to diseases like Alzheimer's disease, Parkinson's disease, Multiple sclerosis, and Amyotrophic lateral sclerosis. The exact role of Malassezia in these disorders is unknown, but its ability to infect human cells, travel through the bloodstream, cross the blood-brain barrier, and reside along with the lipid-rich neuronal cells are potential mechanisms responsible for pathogenesis. This also includes the induction of pro-inflammatory cytokines, disruption of the blood-brain barrier, gut-microbe interaction, and accumulation of metabolic changes in the brain environment. In this review, we discuss these key findings from studies linking Malassezia to neurological disorders, emphasizing the complex and multifaceted nature of these cases. Furthermore, we discuss potential mechanisms through which Malassezia might contribute to the development of neurological conditions. Future investigations will open up new avenues for our understanding of the fungal gut-brain axis and how it influences human behavior. Collaborative research efforts among microbiologists, neuroscientists, immunologists, and clinicians hold promise for unraveling the enigmatic connections between human commensal Malassezia and neurological disorders.

Intestinal fungal-host interactions in promoting and maintaining health

The resident microbiota are a key component of a healthy organism. The vast majority of microbiome studies have focused on bacterial members, which constitute a significant portion of resident microbial biomass. Recent studies have demonstrated how the fungal component of the microbiota, or the mycobiome, influences mammalian biology despite its low abundance compared to other microbes. Fungi are known for their pathogenic potential, yet fungi are also prominent colonizers in healthy states, highlighting their duality. We summarize the characteristics that define the gut mycobiome across life, the factors that can impact its composition, and studies that identify mechanisms of how fungi confer health benefits. The goal of this review is to synthesize our knowledge regarding the composition and function of a healthy mycobiome with a view to inspiring future therapeutic advances.

Neonatal Gut Mycobiome: Immunity, Diversity of Fungal Strains, and Individual and Non-Individual Factors

The human gastrointestinal ecosystem, or microbiome (comprising the total bacterial genome in an environment), plays a crucial role in influencing host physiology, immune function, metabolism, and the gut-brain axis. While bacteria, fungi, viruses, and archaea are all present in the gastrointestinal ecosystem, research on the human microbiome has predominantly focused on the bacterial component. The colonization of the human intestine by microbes during the first two years of life significantly impacts subsequent composition and diversity, influencing immune system development and long-term health. Early-life exposure to pathogens is crucial for establishing immunological memory and acquired immunity. Factors such as maternal health habits, delivery mode, and breastfeeding duration contribute to gut dysbiosis. Despite fungi's critical role in health, particularly for vulnerable newborns, research on the gut mycobiome in infants and children remains limited. Understanding early-life factors shaping the gut mycobiome and its interactions with other microbial communities is a significant research challenge. This review explores potential factors influencing the gut mycobiome, microbial kingdom interactions, and their connections to health outcomes from childhood to adulthood. We identify gaps in current knowledge and propose future research directions in this complex field.

Difference in the Intestinal Microbiota between Breastfeed Infants and Infants Fed with Artificial Milk: A Systematic Review

The gut microbiota (GM) plays a crucial role in human health, particularly during the first years of life. Differences in GM between breastfed and formula (F)-fed infants may influence long-term health outcomes. This systematic review aims to compare the gut microbiota of breastfed infants with that of F-fed infants and to evaluate the clinical implications of these differences. We searched databases on Scopus, Web of Science, and Pubmed with the following keywords: "gut microbiota", "gut microbiome", and "neonatal milk". The inclusion criteria were articles relating to the analysis of the intestinal microbiome of newborns in relation to the type of nutrition, clinical studies or case series, excluding reviews, meta-analyses, animal models, and in vitro studies. The screening phase ended with the selection of 13 publications for this work. Breastfed infants showed higher levels of beneficial bacteria such as Bifidobacterium and Lactobacillus, while F-fed infants had a higher prevalence of potentially pathogenic bacteria, including Clostridium difficile and Enterobacteriaceae. Infant feeding type influences the composition of oral GM significantly. Breastfeeding promotes a healthier and more diverse microbial ecosystem, which may offer protective health benefits. Future research should explore strategies to improve the GM of F-fed infants and understand the long-term health implications.

The Association Between Lactational Infective Mastitis and the Microbiome: Development, Onset, and Treatments

Lactational infective mastitis (LIM) was previously thought to occur due to trapped milk causing inadequate milk drainage and consequent infection. However, advances in genome sequencing techniques have shown that the abundance of Staphylococcus aureus, Staphylococcus epidermidis, Lactobacilli species, and Bifidobacterium species in the breast milk of lactating women play a key role in the development of LIM. Recent discoveries have revealed that the breast milk microbiome is composed of bacteria and other microorganisms, which are seeded through multiple pathways and are influenced by maternal factors. An imbalance in the microbial abundance in breast milk can lead to LIM. Given that this infection can cause early termination of breastfeeding, it is imperative to discuss prevention and treatment options. The objective of this review is to highlight the pathogens involved in LIM affecting human mothers, routes of bacterial transfer, and contributing factors that may influence changes in the composition of the milk microbiota, as well as propose preventative and curative treatment options.

Role of the Gut Microbiota-Brain Axis in Brain Damage in Preterm Infants

The greatest repository of microbes in the human body, the intestinal microbiome, is involved in neurological development, aging, and brain illnesses such as white matter injury (WMI) in preterm newborns. Intestinal microorganisms constitute a microbial gut-brain axis that serves as a crucial conduit for communication between the gut and the nervous system. This axis controls inflammatory cytokines, which in turn influence the differentiation of premyelinating oligodendrocytes (pre-OLs) and influence the incidence of WMI in premature newborns through the metabolites generated by gut microbes. Here, we describe the effects of white matter injury (WMI) on intestinal dysbiosis and gut dysfunction and explain the most recent research findings on the gut-brain axis in both humans and animals. We also emphasize the delicate relationship that exists between the microbiota and the brain following acute brain injury. The role that the intestinal microflora plays in influencing host metabolism, the immune system, brain health, and the course of disease is becoming increasingly clear, but there are still gaps in the field of WMI treatment. Thus, this review demonstrates the function of the gut microflora-brain axis in WMI and elucidates the possible mechanisms underlying the communication between gut bacteria and the developing brain via the gut-brain axis, potentially opening up new avenues for microbial-based intervention and treatment for preterm WMI.

Human Milk Microbiome-A Review of Scientific Reports

One of the most important bioactive components of breast milk are free breast milk oligosaccharides, which are a source of energy for commensal intestinal microorganisms, stimulating the growth of Bifidobacterium, Lactobacillus, and Bacteroides in a child's digestive tract. There is some evidence that maternal, perinatal, and environmental-cultural factors influence the modulation of the breast milk microbiome. This review summarizes research that has examined the composition of the breast milk microbiome and the factors that may influence it. The manuscript highlights the potential importance of the breast milk microbiome for the future development and health of children. The origin of bacteria in breast milk is thought to include the mother's digestive tract (entero-mammary tract), bacterial exposure to the breast during breastfeeding, and the retrograde flow of breast milk from the infant's mouth to the woman's milk ducts. Unfortunately, despite increasingly more precise methods for assessing microorganisms in human milk, the topic of the human milk microbiome is still quite limited and requires scientific research that takes into account various conditions.

Malian Children's Core Gut Mycobiome

Because data on the fungal gut community structure of African children are scarce, we aimed to describe it by reanalysing rRNA ITS1 and ITS2 metabarcoding data from a study designed to assess the influence of microbiota in malaria susceptibility in Malian children from the Dogon country. More specifically, we aimed to establish the core gut mycobiome and compare the gut fungal community structure of breastfed children, aged 0-2 years, with other age groups. Briefly, DNA was extracted from 296 children's stool samples. Both rRNA ITS1 and ITS2 genomic barcodes were amplified and subjected to Illumina MiSeq sequencing. The ITS2 barcode generated 1,975,320 reads and 532 operational taxonomic units (OTUs), while the ITS1 barcode generated 647,816 reads and 532 OTUs. The alpha diversity was significantly higher by using the ITS1 compared to the ITS2 barcode (p < 0.05); but, regardless of the ITS barcode, we found no significant difference between breastfed children, aged 0-2 years, compared to the other age groups. The core gut mycobiome of the Malian children included Saccharomyces cerevisiae, Candida albicans, Pichia kudriavzevii, Malassezia restricta, Candida tropicalis and Aspergillus section Aspergillus, which were present in at least 50% of the 296 children. Further studies in other African countries are warranted to reach a global view of African children's core gut mycobiome.

Ascomycetes yeasts: The hidden part of human microbiome

The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.

Bovine milk microbiota: Key players, origins, and potential contributions to early-life gut development

BACKGROUND

Bovine milk is a significant substitute for human breast milk and holds great importance in infant nutrition and health. Apart from essential nutrients, bovine milk also contains bioactive compounds, including a microbiota derived from milk itself rather than external sources of contamination.

AIM OF REVIEW

Recognizing the profound impact of bovine milk microorganisms on future generations, our review focuses on exploring their composition, origins, functions, and applications.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Some of the primary microorganisms found in bovine milk are also present in human milk. These microorganisms are likely transferred to the mammary gland through two pathways: the entero-mammary pathway and the rumen-mammary pathway. We also elucidated potential mechanisms by which milk microbiota contribute to infant intestinal development. The mechanisms include the enhancing of the intestinal microecological niche, promoting the maturation of immune system, strengthening the intestinal epithelial barrier function, and interacting with milk components (e.g., oligosaccharides) via cross-feeding effect. However, given the limited understanding of bovine milk microbiota, further studies are necessary to validate hypotheses regarding their origins and to explore their functions and potential applications in early intestinal development.

Microbiological risk assessment and resistome analysis from shotgun metagenomics of bovine colostrum microbiome

Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in rural sites of a developing country. The focus was on microbiological safety assessments and antimicrobial resistance, taking into account the risks linked with the consumption of raw colostrum. Shotgun sequencing was employed to analyze microbiome in raw buffalo and cow colostrum. Alpha and beta diversity analyses revealed increased inter and intra-variability within colostrum samples' microbiome from both livestock species. The colostrum microbiome was mainly comprised of bacteria, with over 90% abundance, whereas fungi and viruses were found in minor abundance. Known probiotic species, such as Leuconostoc mesenteroides, Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus paracasei, were found in the colostrum samples. A relatively higher number of pathogenic and opportunistic pathogenic bacteria were identified in colostrum from both animals, including clinically significant bacteria like Clostridium botulinum, Pseudomonas aeruginosa, Escherichia coli, and Listeria monocytogenes. Binning retrieved 11 high-quality metagenome-assembled genomes (MAGs), with three MAGs potentially representing novel species from the genera Psychrobacter and Pantoea. Notably, 175 antimicrobial resistance genes (ARGs) and variants were detected, with 55 of them common to both buffalo and cow colostrum metagenomes. These ARGs confer resistance against aminoglycoside, fluoroquinolone, tetracycline, sulfonamide, and peptide antibiotics. In conclusion, this study describes a thorough overview of microbial communities in buffalo and cow colostrum samples. It emphasizes the importance of hygienic processing and pasteurization in minimizing the potential transmission of harmful microorganisms linked to the consumption of colostrum.

It's time to shed some light on the importance of fungi in neonatal intensive care units: what do we know about the neonatal mycobiome?

The 21st century, thanks to the development of molecular methods, including DNA barcoding, using Sanger sequencing, and DNA metabarcoding, based on next-generation sequencing (NGS), is characterized by flourishing research on the human microbiome. Microbial dysbiosis is perceived as a new pathogenetic factor for neonatal diseases. Fungi are crucial, but neglected, components of the neonatal microbiome, which, despite their low abundance, significantly impact morbidity and mortality rates of premature infants hospitalized in Neonatal Intensive Care Units (NICUs). The neonatal mycobiome's composition and effect on health remain poorly studied research areas. Our knowledge about neonatal mycobiome, composed of limited genera, is mainly based on research on the bacterial microbiome. We presume it is influenced by clinical factors, including prematurity, antibiotic therapy, and type of delivery. Understanding these risk factors may be useful in prevention strategies against dysbiosis and invasive fungal infections. Despite the methodological challenges resulting from the biology of the fungal cell, this topic is an attractive area of research that may contribute to more effective treatment, especially of newborns from risk groups. In this mini review, we discuss the current state of knowledge, research gaps, study difficulties, and future research directions on the neonatal mycobiome, concerning potential future clinical applications.

The Role of Early Life Gut Mycobiome on Child Health

The human gut microbiota is composed of bacteria (microbiota or microbiome), fungi (mycobiome), viruses, and archaea, but most of the research is primarily focused on the bacterial component of this ecosystem. Besides bacteria, fungi have been shown to play a role in host health and physiologic functions. However, studies on mycobiota composition during infancy, the factors that might shape infant gut mycobiota, and implications to child health and development are limited. In this review, we discuss the factors likely shaping gut mycobiota, interkingdom interactions, and associations with child health outcomes and highlight the gaps in our current knowledge of this ecosystem.

Metataxonomic analysis of milk microbiota in the bovine subclinical mastitis

Subclinical mastitis is one of the most widespread diseases affecting dairy herds with detrimental effects on animal health, milk productivity, and quality. Despite its multifactorial nature, the presence of pathogenic bacteria is regarded one of the main drivers of subclinical mastitis, causing a disruption of the homeostasis of the bovine milk microbial community. However, bovine milk microbiota alterations associated with subclinical mastitis still represents a largely unexplored research area. Therefore, the species-level milk microbiota of a total of 75 milk samples, collected from both healthy and subclinical mastitis-affected cows from two different stables, was deeply profiled through an ITS, rather than a traditional, and less informative, 16S rRNA gene microbial profiling. Surprisingly, the present pilot study not only revealed that subclinical mastitis is characterized by a reduced biodiversity of the bovine milk microbiota, but also that this disease does not induce standard alterations of the milk microbial community across stables. In addition, a flow cytometry-based total bacterial cell enumeration highlighted that subclinical mastitis is accompanied by a significant increment in the number of milk microbial cells. Furthermore, the combination of the metagenomic and flow cytometry approaches allowed to identify different potential microbial marker strictly correlated with subclinical mastitis across stables.

Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life

Milk production is an ancient adaptation that unites all mammals. Milk contains a microbiome that can contribute to offspring health and microbial-immunological development. We generated a comprehensive milk microbiome dataset (16S rRNA gene) for the class Mammalia, representing 47 species from all placental superorders, to determine processes structuring milk microbiomes. We show that across Mammalia, milk exposes offspring to maternal bacterial and archaeal symbionts throughout lactation. Deterministic processes of environmental selection accounted for 20% of milk microbiome assembly processes; milk microbiomes were similar from mammals with the same host superorder (Afrotheria, Laurasiathera, Euarchontoglires, and Xenarthra: 6%), environment (marine captive, marine wild, terrestrial captive, and terrestrial wild: 6%), diet (carnivore, omnivore, herbivore, and insectivore: 5%), and milk nutrient content (sugar, fat, and protein: 3%). We found that diet directly and indirectly impacted milk microbiomes, with indirect effects being mediated by milk sugar content. Stochastic processes, such as ecological drift, accounted for 80% of milk microbiome assembly processes, which was high compared to mammalian gut and mammalian skin microbiomes (69% and 45%, respectively). Even amid high stochasticity and indirect effects, our results of direct dietary effects on milk microbiomes provide support for enteromammary trafficking, representing a mechanism by which bacteria are transferred from the mother's gut to mammary gland and then to offspring postnatally. The microbial species present in milk reflect both selective pressures and stochastic processes at the host level, exemplifying various ecological and evolutionary factors acting on milk microbiomes, which, in turn, set the stage for offspring health and development.

Limosilactobacillus fermentum CECT5716: Clinical Potential of a Probiotic Strain Isolated from Human Milk

Breastfeeding provides the ideal nutrition for infants. Human milk contains a plethora of functional ingredients which foster the development of the immune system. The human milk microbiota predominantly contributes to this protective effect. This is mediated by various mechanisms, such as an antimicrobial effect, pathogen exclusion and barrier integrity, beneficial effects on the gastrointestinal microbiota, vitamin synthesis, immunity enhancement, secreted probiotic factors, and postbiotic mechanisms. Therefore, human milk is a good source for isolating probiotics for infants who cannot be exclusively breastfed. One such probiotic which was isolated from human milk is Limosilactobacillus fermentum CECT5716. In this review, we give an overview of available interventional studies using Limosilactobacillus fermentum CECT5716 and summarise preclinical trials in several animal models of different pathologies, which have given first insights into its mechanisms of action. We present several randomised clinical studies, which have been conducted to investigate the clinical efficacy of the Limosilactobacillus fermentum CECT5716 strain in supporting the host's health.

Improvement and Validation of a Genomic DNA Extraction Method for Human Breastmilk

The human milk microbiota (HMM) of healthy women can vary substantially, as demonstrated by recent advances in DNA sequencing technology. However, the method used to extract genomic DNA (gDNA) from these samples may impact the observed variations and potentially bias the microbiological reconstruction. Therefore, it is important to use a DNA extraction method that is able to effectively isolate gDNA from a diverse range of microorganisms. In this study, we improved and compared a DNA extraction method for gDNA isolation from human milk (HM) samples to commercial and standard protocols. We evaluated the extracted gDNA using spectrophotometric measurements, gel electrophoresis, and PCR amplifications to assess its quantity, quality, and amplifiability. Additionally, we tested the improved method’s ability to isolate amplifiable gDNA from fungi, Gram-positive and Gram-negative bacteria to validate its potential for reconstructing microbiological profiles. The improved DNA extraction method resulted in a higher quality and quantity of the extracted gDNA compared to the commercial and standard protocols and allowed for polymerase chain reaction (PCR) amplification of the V3–V4 regions of the 16S ribosomal gene in all the samples and the ITS-1 region of the fungal 18S ribosomal gene in 95% of the samples. These results suggest that the improved DNA extraction method demonstrates better performance for gDNA extraction from complex samples such as HM.

Uromycobiome in infants and toddlers with and without urinary tract infections

BACKGROUND

The bacterial components of the urobiome have been described in children, both with and without urinary tract infections (UTI). However, less is known about the pediatric uromycobiome: the community of fungi in the urine. The objectives of this study were to describe the uromycobiome in children and determine whether the uromycobiome differs between children with and without UTI.

METHODS

This was a cross-sectional study of febrile children less than 3 years of age who presented to the Emergency Department and had a catheterized urine sample sent as part of clinical care. We obtained residual urine for use in this study and identified components of the uromyobiome through amplification and sequencing of the fungal ITS2 region. We then compared the uromycobiome between those with and without UTI.

RESULTS

We included 374 children in this study (UTI = 50, no UTI = 324). Fungi were isolated from urine samples of 310 (83%) children. Fungi were identified in a higher proportion of children with UTI, compared to those without UTI (96% vs. 81%, p = 0.01). Shannon diversity index was higher in children with UTI, compared to those without (p = 0.04). Although there were differences in the most abundant taxa between children with and without UTI, there was no significant difference in beta diversity between groups.

CONCLUSIONS

Fungi were detected in the majority of catheterized urine samples from children. While a higher proportion of children with UTI had fungi in their urine, compared to children without UTI, there was no difference in the composition of these groups. A higher resolution version of the Graphical abstract is available as Supplementary information.

Maternal weight status and the composition of the human milk microbiome: A scoping review

The human milk microbiome is thought to partly contribute to the assembly of the infant gut microbiome, a microbial community with important implications for infant health and development. While obesity has well-established links with the adult gut microbiome, less is known about how it affects the human milk microbiome. In this scoping review, we synthesize the current literature on the microbial composition of human milk by maternal weight status, defined broadly as BMI (prepregnancy and postpartum) and gestational weight gain (GWG). This study followed the a priori protocol published in Prospero (registration #: CRD42020165633). We searched the following databases for studies reporting maternal weight status and a characterization of milk microbiota through culture-dependent and culture-independent methods: MEDLINE, Embase, Web of Science, CINAHL, and Scopus. After screening 6,365 studies, we found 20 longitudinal and cross-sectional studies investigating associations between maternal weight status and the composition of the milk microbiome. While some studies reported no associations, many others reported that women with a pre-pregnancy or postpartum BMI characterized as overweight or obese, or with excessive GWG, had higher abundances of the genus Staphylococcus, lower Bifidobacterium abundance, and lower alpha diversity (within-sample diversity). This review suggests that maternal weight status is minorly associated with the composition of the milk microbiome in various ways. We offer potential explanations for these findings, as well as suggestions for future research.

Characterization of the Urinary Metagenome and Virome in Healthy Children

Recent advances in next-generation sequencing and metagenomic studies have provided insights into the microbial profile of different body sites. However, research on the microbial composition of urine is limited, particularly in children. The goal of this study was to optimize and develop reproducible metagenome and virome protocols using a small volume of urine samples collected from healthy children. We collected midstream urine specimens from 40 healthy children. Using the metagenomics shotgun approach, we tested various protocols. Different microbial roots such as Archaea, Bacteria, Eukaryota, and Viruses were successfully identified using our optimized urine protocol. Our data reflected much variation in the microbial fingerprints of children. Girls had significantly higher levels of Firmicutes, whereas boys had significantly higher levels of Actinobacteria. The genus Anaerococcus dominated the urinary bacteriome of healthy girls, with a significant increase in Anaerococcus prevotii, Anaerococcus vaginalis, and Veillonella parvula (p-value < 0.001) when compared with that of boys. An increased relative abundance of Xylanimonas and Arthrobacter, with a significantly high abundance of Arthrobacter sp. FB24 (p-value 0.0028) and Arthrobacter aurescences (p-value 0.015), was observed in boys. The urinary mycobiome showed a significant rise in the genus Malassezia and Malassezia globose fungus (p-value 0.009) in girls, whereas genus Saccharomyces (p-value 0.009) was significantly high in boys. The beta diversity of the urinary mycobiome was found to differ between different age groups. Boys had significantly more Mastadenovirus and Human mastadenovirus-A in their urinary virome than girls. With increasing age, we noticed an increase in the relative abundance of the order Caudovirales. Our optimized protocols allowed us to identify the unique microbes for each sex by using an adequate volume of urine (3−10 mL) to screen for the bacteriome, mycobiome, and virome profiles in the urine of healthy children. To the best of our knowledge, this is the first study to characterize the metagenomics profiles of urine in a healthy pediatric population.

Methodological approaches for studying the human milk microbiome

Human milk contains a low-biomass, low-diversity microbiome, consisting largely of bacteria. This community is of great research interest in the context of infant health and maternal and mammary health. However, this sample type presents many unique methodological challenges. In particular, there are numerous technical considerations relating to sample collection and storage, DNA extraction and sequencing, viability, and contamination. Failure to properly address these challenges may lead to distortion of bacterial DNA profiles generated from human milk samples, ultimately leading to spurious conclusions. Here, these technical challenges are discussed, and various methodological approaches used to address them are analyzed. Data were collected from studies in which a breadth of methodological approaches were used, and recommendations for robust and reproducible analysis of the human milk microbiome are proposed. Such methods will ensure high-quality data are produced in this field, ultimately supporting better research outcomes for mothers and infants.

Lactation time influences the composition of Bifidobacterium and Lactobacillus at species level in human breast milk

Human breast milk is a source of microorganisms for infants that play an important role in building infant gut health and immunity. The bacterial composition in human breast milk is influenced by lactation time. This study aimed to investigate the influence of lactation time on bacteria in breast milk at the genus level and the species levels of Bifidobacterium and Lactobacillus on days 2-4, 8, 14, and 30. Eighteen individuals were recruited and 60 milk samples were collected. The 16S rRNA gene, and the bifidobacterial groEL and lactobacilli groEL genes were used for amplicon sequencing. The results revealed that the alpha diversities of colostrum and transition 1 (day 8) milk were lower than that of transition 2 (day 14) and mature milk. PCoA analysis showed that bacterial composition in colostrum and transition 1 milk differed from transition 2 and mature milk. A lower relative abundance of Blautia was found in colostrum and transition 1 milk compared with mature milk and lower abundances of Ruminococcus, Dorea, and Escherichia-Shigella were found in transition 1 compared with mature milk. Bifidobacterium ruminantium, Limosilactobacillus mucosae, and Ligilactobacillus ruminis were the predominant species across all four lactation stages, while Bifidobacterium bifidum was lower in transition 1, and Bifidobacterium pseudocatenulatum and Bifidobacterium pseudolongum were higher in transition 1 milk. This study indicated that the bacterial composition in colostrum was more similar to that of transition 1 milk, whereas the bacterial community in transition 2 milk was similar to that of mature milk which suggests that bacterial composition in human breast milk shows stage-specific signatures even within a short period at both genus level and Bifidobacterium and Lactobacillus species levels, providing insights into probiotic supplementation for the nursing mother.

Maternal Diet Is Associated with Human Milk Oligosaccharide Profile

SCOPE

Human milk oligosaccharides (HMOs) are complex glycans that are abundant in human milk. The potential impact of a maternal diet on individual HMOs and the association with secretor status is unknown. Thus, this study is aimed to examine the association between maternal diet and HMO profiles.

METHODS AND RESULTS

This is a cross-sectional study of the MAMI cohort with 101 human milk samples from healthy mothers. HMO profiling is assessed by quantitative HPLC. Maternal dietary information is recorded through an FFQ, and perinatal factors including the mode of delivery, antibiotic exposure, and breastfeeding practices, are collected. A more significant effect of diet on HMO profiles is observed in secretor mothers than in non-secretor mothers. (Poly)phenols and fibers, both soluble and insoluble, and several insoluble polysaccharides, pectin, and MUFA are associated with the secretor HMO profiles.

CONCLUSIONS

Maternal diet is associated with the composition and diversity of HMO in a secretor status-dependent manner. The relationship between maternal diet and bioactive compounds, including HMOs, which are present in human milk, needs further research due its potential impact on infant development and health outcomes.

Human milk microbiota: what did we learn in the last 20 years?

Human milk (HM) is the gold standard for infant nutrition during the first months of life. Beyond its nutritional components, its complex bioactive composition includes microorganisms, their metabolites, and oligosaccharides, which also contribute to gut colonization and immune system maturation. There is growing evidence of the beneficial effects of bacteria present in HM. However, current research presents limited data on the presence and functions of other organisms. The potential biological impacts on maternal and infant health outcomes, the factors contributing to milk microbes' variations, and the potential functions in the infant's gut remain unclear. This review provides a global overview of milk microbiota, what the actual knowledge is, and what the gaps and challenges are for the next years.

Composition of Human Breast Milk Microbiota and Its Role in Children's Health

Human milk contains a number of nutritional and bioactive molecules including microorganisms that constitute the so-called "Human Milk Microbiota (HMM)". Recent studies have shown that not only bacterial but also viral, fungal, and archaeal components are present in the HMM. Previous research has established, a "core" microbiome, consisting of Firmicutes (i.e., Streptococcus, Staphylococcus), Proteobacteria (i.e., Serratia, Pseudomonas, Ralstonia, Sphingomonas, Bradyrhizobium), and Actinobacteria (i.e., Propionibacterium, Corynebacterium). This review aims to summarize the main characteristics of HMM and the role it plays in shaping a child's health. We reviewed the most recent literature on the topic (2019-2021), using the PubMed database. The main sources of HMM origin were identified as the retrograde flow and the entero-mammary pathway. Several factors can influence its composition, such as maternal body mass index and diet, use of antibiotics, time and type of delivery, and mode of breastfeeding. The COVID-19 pandemic, by altering the mother-infant dyad and modifying many of our previous habits, has emerged as a new risk factor for the modification of HMM. HMM is an important contributor to gastrointestinal colonization in children and therefore, it is fundamental to avoid any form of perturbation in the HMM that can alter the microbial equilibrium, especially in the first 100 days of life. Microbial dysbiosis can be a trigger point for the development of necrotizing enterocolitis, especially in preterm infants, and for onset of chronic diseases, such as asthma and obesity, later in life.

"Molding" immunity-modulation of mucosal and systemic immunity by the intestinal mycobiome in health and disease

Fungi are important yet understudied contributors to the microbial communities of the gastrointestinal tract. Starting at birth, the intestinal mycobiome undergoes a period of dynamic maturation under the influence of microbial, host, and extrinsic influences, with profound functional implications for immune development in early life, and regulation of immune homeostasis throughout life. Candida albicans serves as a model organism for understanding the cross-talk between fungal colonization dynamics and immunity, and exemplifies unique mechanisms of fungal-immune interactions, including fungal dimorphism, though our understanding of other intestinal fungi is growing. Given the prominent role of the gut mycobiome in promoting immune homeostasis, emerging evidence points to fungal dysbiosis as an influential contributor to immune dysregulation in a variety of inflammatory and infectious diseases. Here we review current knowledge on the factors that govern host-fungi interactions in the intestinal tract and immunological outcomes in both mucosal and systemic compartments.

Human milk: From complex tailored nutrition to bioactive impact on child cognition and behavior

Human milk is a highly complex liquid food tailor-made to match an infant's needs. Beyond documented positive effects of breastfeeding on infant and maternal health, there is increasing evidence that milk constituents also impact child neurodevelopment. Non-nutrient milk bioactives would contribute to the (long-term) development of child cognition and behavior, a process termed 'Lactocrine Programming'. In this review we discuss the current state of the field on human milk composition and its links with child cognitive and behavioral development. To promote state-of-the-art methodologies and designs that facilitate data pooling and meta-analytic endeavors, we present detailed recommendations and best practices for future studies. Finally, we determine important scientific gaps that need to be filled to advance the field, and discuss innovative directions for future research. Unveiling the mechanisms underlying the links between human milk and child cognition and behavior will deepen our understanding of the broad functions of this complex liquid food, as well as provide necessary information for designing future interventions.

Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations

Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman’s large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas.

The first fungi: mode of delivery determines early life fungal colonization in the intestine of preterm infants

Aim: The role of intestinal fungi in human health and disease is becoming more evident. The mycobiota composition and diversity of preterm infants is affected by interactions with bacteria and clinical variables. In this study, we aimed to characterize the composition and the diversity of the preterm infant mycobiota and the effect of clinical variables on it in the first six postnatal weeks. Methods: Preterm infants (n = 50) and full-term infants (n = 6) admitted to Isala Women and Children's hospital (Zwolle, The Netherlands) who were born during 24-36 or 37-40 weeks of gestation, respectively, were included in this study. Feces were collected during the first six postnatal weeks (n = 109) and their mycobiota composition and diversity were characterized by ITS2 amplicon sequencing. Results: Composition analyses identified fungi and other eukaryotic kingdoms, of which Viridiplantae was most abundant. Of the fungal kingdom, Ascomycota and Basidiomycota were the first and second most prominent phyla in early life of all infants. Candida was the most abundant genus in the first six weeks of life and increased with gestational and postnatal age. Fungal phylogenetic diversity remained stable in the first six postnatal weeks. The individuality and the mode of delivery were identified as significant predictors for the variation in the mycobiota composition. Vaginally delivered infants were enriched in Candida spp., whereas infants delivered through emergency C-section were characterized by Malassezia spp. Conclusion: These results indicate that fungi and other eukaryotic kingdoms are detected in the intestine of preterm and full-term infants in the first six postnatal weeks. Similar to the microbiota, colonization of the preterm intestine with fungi is determined by clinical variables including individuality and mode of delivery.

Breast Milk: A Meal Worth Having

A mother is gifted with breast milk, the natural source of nutrition for her infant. In addition to the wealth of macro and micro-nutrients, human milk also contains many microorganisms, few of which originate from the mother, while others are acquired from the mouth of the infant and the surroundings. Among these microbes, the most commonly residing bacteria are Staphylococci, Streptococci, Lactobacilli and Bifidobacteria. These microorganisms initiate and help the development of the milk microbiota as well as the microbiota of the gastrointestinal tract in infants, and contribute to developing immune regulatory factors such as cytokines, growth factors, lactoferrin among others. These factors play an important role in reducing the risk of developing chronic diseases like type 2 diabetes, asthma and others later in life. In this review, we will summarize the known benefits of breastfeeding and highlight the role of the breast milk microbiota and its cross-talk with the immune system in breastfed babies during the early years of life.

The hidden universe of human milk microbiome: origin, composition, determinants, role, and future perspectives

Although traditionally considered sterile, human milk is currently recognized as an alive ecosystem that harbors not only bacteria, but also viruses, fungi and yeasts, and minor genera, collectively known as the human milk microbiome (HMM). The seeding of HMM is a complex phenomenon whose dynamics are still a matter of research. Many factors contribute to its determination, both maternal, neonatal, environmental, and related to human milk itself. The transmission of microorganisms to the infant through breastfeeding may impact its present and future health, mainly shaping the GI tract microbiome and immune system. The existence and persistence of HMM as a conserved feature among different species may also have an evolutionary meaning, which will become apparent only in evolutionary times.

CONCLUSION

The complexities of HMM warrant further research in order to deepen our knowledge on its origin, determinants, and impact on infants' health. The practical and translational implications of research on HMM (e.g., reconstitution of donor human milk through inoculation of infant's own mother milk, modulation of HMM through maternal dietary supplementation) should not be overlooked.

WHAT IS KNOWN

• Human milk harbors a wide variety of microorganisms, ranging from bacteria to viruses, fungi and yeasts, and minor genera. • Human milk microbiome is shaped over time by many factors: maternal, neonatal, environmental, and related to human milk itself. • The transmission of microorganisms through breastfeeding may impact the infant's present and future health.

WHAT IS NEW

• We provide an overview on human milk microbiome, hopefully encouraging physicians to consider it among the other better-known breastfeeding benefits. • Further studies, with standardized and rigorous study designs to enhance accuracy and reproducibility of the results, are needed to deepen our knowledge of the human milk microbiota and its role in newborn and infant's health.

Re-thinking benign inflammation of the lactating breast: A mechanobiological model

Despite the known benefits of breastfeeding for both infant and mother, clinical support for problems such as inflammation of the lactating breast remains a research frontier. Breast pain associated with inflammation is a common reason for premature weaning. Multiple diagnoses are used for inflammatory conditions of the lactating breast, such as engorgement, blocked ducts, phlegmon, mammary candidiasis, subacute mastitis, mastitis and white spots, which lack agreed or evidence-based aetiology, definitions and treatment. This is the first in a series of three articles which review the research literature concerning benign lactation-related breast inflammation. This article investigates aetiological models. A complex systems perspective is applied to analyse heterogeneous and interdisciplinary evidence elucidating the functional anatomy and physiology of the lactating breast; the mammary immune system, including the human milk microbiome and cellular composition; the effects of mechanical forces during lactation; and the interactions between these. This analysis gives rise to a mechanobiological model of breast inflammation, in which very high intra-alveolar and intra-ductal pressures are hypothesized to strain or rupture the tight junctions between lactocytes and ductal epithelial cells, triggering inflammatory cascades and capillary dilation. Resultant elevation of stromal tension exerts pressure on lactiferous ducts, worsening intraluminal backpressure. Rising leucocyte and epithelial cell counts in the milk and alterations in the milk microbiome are signs that the mammary immune system is recruiting mechanisms to downregulate inflammatory feedback loops. From a complex systems perspective, the key mechanism for the prevention or treatment of breast inflammation is avoidance of excessively high intra-alveolar and intra-ductal pressures, which prevents a critical mass of mechanical strain and rupture of the tight junctions between lactocytes and ductal epithelial cells.

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

BACKGROUND

The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies.

METHODOLOGY

We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction.

RESULTS

We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168).

CONCLUSIONS

There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.

Factors influencing the microbial composition of human milk

Aside from nutritional components, human milk is rich in microorganisms. Through breastfeeding these microorganisms are introduced to the infant gut where they may transiently or persistently colonize it. Therefore, the human milk microbiota may be an important factor which shapes the infant gut microbiota further influencing infant health and disease. In the current review we aim to give a brief updated insight into the putative origin of the human milk microbiota, its constituents and the possible factors that shape it. Understanding the factors that determine the human milk microbiota composition and function will aid developing optimal postnatal feeding and intervention strategies to reduce the risk of communicable and noncommunicable diseases.

The role of gut mycobiome in health and diseases

The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut "mycobiome") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.

Bacterial and Fungal Gut Community Dynamics Over the First 5 Years of Life in Predominantly Rural Communities in Ghana

Background

Bacterial and fungal microbiotas are increasingly recognized as important in health and disease starting early in life. However, microbiota composition has not yet been investigated in most rural, low-resource settings, and in such settings, bacterial and fungal microbiotas have not been compared. Thus, we applied 16S and ITS2 amplicon sequencing, respectively, to investigate bacterial and fungal fecal microbiotas in rural Ghanaian children cross-sectionally from birth to 5 years of age. Corresponding maternal fecal and breast milk microbiotas were additionally investigated.

Results

While bacterial communities differed systematically across the age spectrum in composition and diversity, the same was not observed for the fungal microbiota. We also identified a novel and dramatic change in the maternal postpartum microbiota. This change included much higher abundance of Escherichia coli and much lower abundance of Prevotella in the first vs. fourth week postpartum. While infants shared more bacterial taxa with their mother’s stool and breast milk than with those of unrelated mothers, there were far fewer shared fungal taxa.

Conclusion

Given the known ability of commensal fungi to influence host health, the distinct pattern of their acquisition likely has important health consequences. Similarly, the dynamics of mothers’ bacterial microbiotas around the time of birth may have important consequences for their children’s health. Both topics require further study.

New Insights Into Microbiota Modulation-Based Nutritional Interventions for Neurodevelopmental Outcomes in Preterm Infants

Gut microbiota and the central nervous system have parallel developmental windows during pre and post-natal life. Increasing evidences suggest that intestinal dysbiosis in preterm infants predisposes the neonate to adverse neurological outcomes later in life. Understanding the link between gut microbiota colonization and brain development to tailor therapies aimed at optimizing initial colonization and microbiota development are promising strategies to warrant adequate brain development and enhance neurological outcomes in preterm infants. Breast-feeding has been associated with both adequate cognitive development and healthy microbiota in preterms. Infant formula are industrially produced substitutes for infant nutrition that do not completely recapitulate breast-feeding benefices and could be largely improved by the understanding of the role of breast milk components upon gut microbiota. In this review, we will first discuss the nutritional and bioactive component information on breast milk composition and its contribution to the assembly of the neonatal gut microbiota in preterms. We will then discuss the emerging pathways connecting the gut microbiota and brain development. Finally, we will discuss the promising microbiota modulation-based nutritional interventions (including probiotic and prebiotic supplementation of infant formula and maternal nutrition) for improving neurodevelopmental outcomes.

A systematic review of microbiome changes and impact of probiotic supplementation in children and adolescents with neuropsychiatric disorders

OBJECTIVES

In recent decades, the diagnostic and therapeutic implications of the microbiome changes and the impact of probiotic supplementation have increased rapidly. However, the potential for clinical translation of microbiome research for children and adolescents with psychiatric disorders is unclear. This review examined available evidence related to gut microbiota as well as the impact of probiotic supplementation on psychiatric disorders in the pediatric population reported to date.

METHODS

We performed a literature search for the gut microbiota in child and adolescent population (0-18 years old) with mental health disorders from July 1999 through July 2019 in several databases: ClinicalTrials.gov, Ovid EBM Reviews, Ovid Embase, Ovid Medline, Ovid PsycINFO, Scopus, and Web of Science.

RESULTS

A total of 7 studies met inclusion criteria consisting of randomized controlled trials and cohort studies that examined various associations between psychiatric disorders and gut microbiota in youth. Six studies examined the effects of various treatment interventions such as probiotic supplementation on microbiota composition and behaviors. One study showed an increase in prosocial behavior in children with Autism Spectrum Disorder (ASD) and an increase in the Lachnospiraceae family following prebiotic supplementation. Another study suggested that prebiotic supplementation increased bifidobacterial populations for ASD and healthy controls. A study evaluating infant supplementation of prebiotics showed both a decreased likelihood of developing Attention Deficit Hyperactivity Disorder (ADHD) or ASD and decreased gut Bifidobacterium. One study did not find significant differences in microbiome composition after micronutrient treatment.

CONCLUSION

The main goal of this systematic review was to comprehensively examine and summarize the current evidence focused on the potential effect of the relationship between microbiota gut composition as well as the effects of probiotic supplementation on psychiatric disorders in children and adolescents. This is a relatively new area of research and the number of included studies is limited. More studies are needed to determine whether gut dysbiosis leads to the development and/or contributes to the severity of mental disorders or whether gut dysbiosis is a result of other processes that accompany mental disorders.

CLINICAL SIGNIFICANCE

A better understanding of the specific bacteria contributions, gut-brain pathways, and role in pathophysiological mechanisms in neuropsychiatric disorders in the child and adolescent populations can possibly provide alternative tools for a clinical psychiatrist. Moreover, it may ultimately aid the clinician with intervention strategies, or detect populations at risk for developing neuropsychiatric disorders.

Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes

Although often neglected in gut microbiota studies, recent evidence suggests that imbalanced, or dysbiotic, gut mycobiota (fungal microbiota) communities in infancy coassociate with states of bacterial dysbiosis linked to inflammatory diseases such as asthma. In the present study, we (i) characterized the infant gut mycobiota at 3 months and 1 year of age in 343 infants from the CHILD Cohort Study, (ii) defined associations among gut mycobiota community composition and environmental factors for the development of inhalant allergic sensitization (atopy) at age 5 years, and (iii) built a predictive model for inhalant atopy status at age 5 years using these data. We show that in Canadian infants, fungal communities shift dramatically in composition over the first year of life. Early-life environmental factors known to affect gut bacterial communities were also associated with differences in gut fungal community alpha diversity, beta diversity, and/or the relative abundance of specific fungal taxa. Moreover, these metrics differed among healthy infants and those who developed inhalant allergic sensitization (atopy) by age 5 years. Using a rationally selected set of early-life environmental factors in combination with fungal community composition at 1 year of age, we developed a machine learning logistic regression model that predicted inhalant atopy status at 5 years of age with 81% accuracy. Together, these data suggest an important role for the infant gut mycobiota in early-life immune development and indicate that early-life behavioral or therapeutic interventions have the potential to modify infant gut fungal communities, with implications for an infant's long-term health. IMPORTANCE Recent evidence suggests an immunomodulatory role for commensal fungi (mycobiota) in the gut, yet little is known about the composition and dynamics of early-life gut fungal communities. In this work, we show for the first time that the composition of the gut mycobiota of Canadian infants changes dramatically over the course of the first year of life, is associated with environmental factors such as geographical location, diet, and season of birth, and can be used in conjunction with knowledge of a small number of key early-life factors to predict inhalant atopy status at age 5 years. Our study highlights the importance of considering fungal communities as indicators or inciters of immune dysfunction preceding the onset of allergic disease and can serve as a benchmark for future studies aiming to examine infant gut fungal communities across birth cohorts.

The human milk microbiome: who, what, when, where, why, and how?

Human milk (HM) contains an incredible array of microorganisms. These likely contribute to the seeding of the infant gastrointestinal microbiome, thereby influencing infant immune and metabolic development and later-life health. Given the importance of the HM microbiota in this context, there has been an increase in research efforts to characterize this in different populations and in relation to different maternal and infant characteristics. However, despite a decade of intensive research, there remain several unanswered questions in this field. In this review, the "5 W+H" approach (who, what, when, where, why, and how) is used to comprehensively describe the composition, function, and origin of the HM microbiome. Here, existing evidence will be drawn together and critically appraised to highlight avenues for further research, both basic and applied. Perhaps the most interesting of these is the potential to modulate the HM microbiome using pre/probiotics or dietary interventions. Another exciting possibility is the personalization of donor milk for women with insufficient supply. By gaining a deeper understanding of the HM microbiome, opportunities to intervene to optimize infant and lifelong health may be identified.

The intestinal mycobiome as a determinant of host immune and metabolic health

The inclusion of fungi in recent human and animal microbiome studies has revealed that microbiome features associated with health or disease are not exclusively bacterial. Factors known to impact bacterial microbiome development, such as gestational age at birth, breast feeding status and antibiotics also impact the mycobiome. Strong inter-kingdom interactions take place in the luminal gut, and while the mycobiome exhibits increased inter-individual variability, certain fungi are stable colonizers. Here, we review recent studies showing that the gut mycobiome also plays an important role in disease states related to host immunity and energy metabolism. Some persistent species, such as Candida sp., as well as other less stable colonizers have been shown to play an important role in host-mycobiome immune cross talk. Mechanisms by which gut fungi interact with immune development have begun to be elucidated yet the majority remain elusive. Further investigation into these immune and metabolic mechanisms hold great potential for novel discoveries and will provided a much needed multi-kingdom understanding of the microbiome's influence on host health.