Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR

Breastfeeding premature infants affects the microbiota composition of breast milk

AIM

To determine whether and how breast feeding of premature infants influences the human milk (HM) bacterial communities.

METHODS

HM samples before and after breastfeeding were collected from 40 preterm infant mothers at 24-366/7 weeks of gestational age in the neonatal intensive care unit of our hospital. Of these 40 babies, 11 at 24-276/7 weeks of gestational age and 12 at 28-316/7 weeks were grouped into an extremely premature (EPM) group and a very premature (VPM) group, respectively. In addition, 11 with a birth weight (BWT) of 1000 g ≤ BWT < 1500 g were classified as a very low birth weight (VLBW) group and 12 with BWT < 1000 g an extremely low birth weight (ELBW) group. Breast feeding and kangaroo mother care were given once a day for 7 days, from 14 to 21 days of age. The bacterial composition of HM was analyzed using high-throughput sequencing before and after feeding.

RESULTS

Linear discriminant analysis effect size of HM samples before and after feeding showed that Bacillus, Prevotella and Fusobacterium were significantly enriched in HM before breastfeeding (P < 0.05). Post-feeding HM for the EPM group showed significant enrichment in Lactobacillales, Streptococcus, Desulfuromonadales, Ruminococcus, Geobacteraceae, Geobacter and Elizabethkingia_meningoseptica (P < 0.05). Bacillus was significantly enriched in the HM for EPM group before feeding (P < 0.05). For mothers with VLBW infants, Bacillus was enriched before feeding, while Lactobacillales was predominant after feeding (P < 0.05). There was a moderate correlation between the diversity of HM bacteria and infant development and immune outcomes.

CONCLUSION

Breastfeeding of preterm infants can significantly affect the bacterial diversity in HM.

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.

Exploring Anti-Breast Cancer Effects of Live Pediococcus acidilactici and Its Cell-Free Supernatant Isolated from Human Breast Milk

Current breast cancer treatment options are limited by drug resistance and adverse side effects, which calls for the need for alternatives or complementary remedies. Probiotic bacteria isolated from human breast milk have been shown to possess proapoptotic and anti-inflammatory properties against breast mastitis in breastfeeding mothers and are being studied as possible anticancer regimens. Thus, this study aimed at exploring the effect of lactic acid bacteria isolated from human breast milk on MDA-MB 231 breast cancer cells. A total of twenty-two bacteria were isolated from four human breast milk samples. The isolates were characterized and identified using biochemical tests and Sanger sequencing, respectively. For in vitro experiments, we used isolated P. acidilactici to treat MDA-MB-231 cells, and an MTT assay was used to detect proliferation. RT-qPCR and wound healing assays were performed to determine the effect of the isolated P. acidilactici on breast cancer cytokine expression and migration. Exposure of MDA-MB 231 breast cancer cells to live P. acidilactici and its cell-free supernatant (CFS) for 24 h resulted in a reduction in cancer cell viability. Also, the expression of the cytokines IL-6, IL-8, and IL-10 in the breast cancer cells increased following exposure to P. acidilactici and its CFS for 24 and 72 h. Additionally, the levels of the SLUG gene remained unchanged while the TWIST1 gene was upregulated following exposure of the cancer cells to bacteria, indicating that P. acidilactici may promote epithelial-mesenchymal transition in breast cancer. Finally, the CFS significantly inhibited cancer cell mobility. These findings serve as a foundation to further investigate the usefulness of P. acidilactici as a potential therapeutic agent in breast cancer therapy.

Human milk oligosaccharides and the association with microbiota in colostrum: a pilot study

HMOs (Human milk oligosaccharide) has an impact on maternal and infant health. Colostrum samples of 70 breastfeeding women in China were collected and recorded clinical characteristics. The major oligosaccharides and microbiota were quantitated in colostrum. The concentration of fucosylated HMOs in primipara was higher than that of multipara (p = 0.030). The concentration of N-acetylated HMOs in vaginal delivery milk was less than that of cesarean (p = 0.038). Non-fucosylated HMOs of breastfeeding women were less than that of breast pump (p = 0.038). Meanwhile, the concentration of LNT was positively correlated with Lactobacillus (r = 0.250, p = 0.037). DS-LNT was negatively correlated with Staphylococcus (r = - 0.240, p = 0.045). There was a positive correlation of Streptococcus with LNFP II (r = 0.314, p = 0.011) and 3-SL (r = 0.322, p = 0.009). In addition, there was a negative correlation between 2'-FL and 3-FL (r = - 0.465, p = 0.001). There was a positive correlation between LNT and LNnT (r = 0.778, p = 0.001). Therefore, the concentration of HMOs is related to number of deliveries, delivery mode, lactation mode and perinatal antibiotic. The concentration of HMOs is related to Lactobacillus, Streptococcus and Streptococcus in colostrum. In addition, there are connections between different oligosaccharides in content. The study protocol was also registered in the ClinicalTrails.gov (ChiCTR2200064454) (Oct. 2022).

Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a multifactorial disease, which is thought to be an interplay between genetic, environment, microbiota, and immune-mediated factors. Dysbiosis in the gut microbial composition, caused by antibiotics and diet, is closely related to the initiation and progression of IBD. Differences in gut microbiota composition between IBD patients and healthy individuals have been found, with reduced biodiversity of commensal microbes and colonization of opportunistic microbes in IBD patients. Gut microbiota can, therefore, potentially be used for diagnosing and prognosticating IBD, and predicting its treatment response. Currently, there are no curative therapies for IBD. Microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have been recognized as promising therapeutic strategies. Clinical studies and studies done in animal models have provided sufficient evidence that microbiota-based interventions may improve inflammation, the remission rate, and microscopic aspects of IBD. Further studies are required to better understand the mechanisms of action of such interventions. This will help in enhancing their effectiveness and developing personalized therapies. The present review summarizes the relationship between gut microbiota and IBD immunopathogenesis. It also discusses the use of gut microbiota as a noninvasive biomarker and potential therapeutic option.

Spectrum of bacterial pathogens in inflammatory and noninflammatory cutaneous ulcers of American tegumentary leishmaniasis

Background

Cutaneous leishmaniasis (CL) ulcers exhibiting an inflammatory phenotype, characterized by purulent exudate, erythema, pain, and/or lymphatic involvement, are empirically treated with antibiotics.

Objective

The spectrum of bacteria present in localized versus inflammatory phenotypes of CL is elucidated herein.

Methods

Filter paper lesion impressions (FPLIs) from 39 patients with CL (19 inflammatory and 20 noninflammatory ulcers) were evaluated via real-time polymerase chain reaction (qPCR) and end-point PCR targeting: Staphylococcus aureus, Enterobacter cloacae, Streptococcus pyogenes, Enterococcus spp., Citrobacter freundii, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and 16S rDNA. Whole genome sequencing (WGS) was performed on six specimens.

Results

In total, 30/39 (77%) patients' ulcers had ⩾1 bacterium detected, which included the following species: S. aureus (n = 16, 41%), C. freundii (n = 13, 33%), P. aeruginosa (n = 12, 31%), E. cloacae (n = 12, 31%), K. pneumoniae (n = 11, 28%), Enterococcus spp. (n = 7, 18%), E. coli (n = 6, 15%), and S. pyogenes (n = 4, 10). Prevalence of bacterial species did not differ by CL phenotype (p = 0.63). However, patients with inflammatory phenotypes were, on average, over a decade older than patients with noninflammatory phenotypes (42 years vs 27 years) (p = 0.01). The inflammatory phenotype was more prevalent among ulcers of Leishmania Viannia braziliensis (58%) and L. V. panamensis (83%) compared to those of L. V. guyanensis (20%) (p = 0.0369).

Conclusion

The distribution of flora did not differ between inflammatory and noninflammatory CL phenotypes. Further prospective analysis, including additional WGS studies of all CL ulcers for nonbacterial organisms, is necessary to determine the role of empiric antibiotic therapy in inflammatory and purulent CL.

Preventing and Treating Colic: An Update

Infantile colic (IC) is c is a self-limiting functional gastrointestinal disorder (FGID) with a favorable natural history. Worldwide, IC has a significant impact on many newborns and their families. Although not an indication of an illness, its symptoms are wide and generic and may indicate a potentially serious underlying issue in a tiny percentage of newborns who may require a medical evaluation. The pathogenesis appears to be multifactorial implying a complex relationship between the infant and the environment. One of the most studied theories attributes a key role to the gut microbiota in the pathogenesis of IC. A variety of approaches have been suggested for the clinical management of IC, and several randomized controlled trials have been reported in the literature. Probiotics can change the host's microbiota and positively impact health. They may be able to restore balance and create a better intestinal microbiota landscape since there is mounting evidence that the gut microbial environment of colicky newborns differs from that of healthy infants. In this review, we revise the most commonly studied probiotics and mixtures to treat and prevent IC and the most recent recommendations.

Unveiling the dynamics of the breast milk microbiome: impact of lactation stage and gestational age

BACKGROUND

Breast milk (BM) provides complete nutrition for infants for the first six months of life and is essential for the development of the newborn's immature immune and digestive systems. While BM was conventionally believed to be sterile, recent advanced high throughput technologies have unveiled the presence of diverse microbial communities in BM. These insights into the BM microbiota have mainly originated from uncomplicated pregnancies, possibly not reflecting the circumstances of mothers with pregnancy complications like preterm birth (PTB).

METHODS

In this article, we investigated the BM microbial communities in mothers with preterm deliveries (before 37 weeks of gestation). We compared these samples with BM samples from healthy term pregnancies across different lactation stages (colostrum, transitional and mature milk) using 16S rRNA gene sequencing.

RESULTS

Our analysis revealed that the microbial communities became increasingly diverse and compositionally distinct as the BM matured. Specifically, mature BM samples were significantly enriched in Veillonella and lactobacillus (Kruskal Wallis; p < 0.001) compared to colostrum. The comparison of term and preterm BM samples showed that the community structure was significantly different between the two groups (Bray Curtis and unweighted unifrac dissimilarity; p < 0.001). Preterm BM samples exhibited increased species richness with significantly higher abundance of Staphylococcus haemolyticus, Propionibacterium acnes, unclassified Corynebacterium species. Whereas term samples were enriched in Staphylococcus epidermidis, unclassified OD1, and unclassified Veillonella among others.

CONCLUSION

Our study underscores the significant influence of pregnancy-related complications, such as preterm birth (before 37 weeks of gestation), on the composition and diversity of BM microbiota. Given the established significance of the maternal microbiome in shaping child health outcomes, this investigation paves the way for identifying modifiable factors that could optimize the composition of BM microbiota, thereby promoting maternal and infant health.

Factors Influencing Neonatal Gut Microbiome and Health with a Focus on Necrotizing Enterocolitis

Maturational changes in the gut start in utero and rapidly progress after birth, with some functions becoming fully developed several months or years post birth including the acquisition of a full gut microbiome, which is made up of trillions of bacteria of thousands of species. Many factors influence the normal development of the neonatal and infantile microbiome, resulting in dysbiosis, which is associated with various interventions used for neonatal morbidities and survival. Extremely low gestational age neonates (<28 weeks' gestation) frequently experience recurring arterial oxygen desaturations, or apneas, during the first few weeks of life. Apnea, or the cessation of breathing lasting 15-20 s or more, occurs due to immature respiratory control and is commonly associated with intermittent hypoxia (IH). Chronic IH induces oxygen radical diseases of the neonate, including necrotizing enterocolitis (NEC), the most common and devastating gastrointestinal disease in preterm infants. NEC is associated with an immature intestinal structure and function and involves dysbiosis of the gut microbiome, inflammation, and necrosis of the intestinal mucosal layer. This review describes the factors that influence the neonatal gut microbiome and dysbiosis, which predispose preterm infants to NEC. Current and future management and therapies, including the avoidance of dysbiosis, the use of a human milk diet, probiotics, prebiotics, synbiotics, restricted antibiotics, and fecal transplantation, for the prevention of NEC and the promotion of a healthy gut microbiome are also reviewed. Interventions directed at boosting endogenous and/or exogenous antioxidant supplementation may not only help with prevention, but may also lessen the severity or shorten the course of the disease.

Potential Epigenetic Effects of Human Milk on Infants' Neurodevelopment

The advantages of human milk feeding, especially in preterm babies, are well recognized. Infants' feeding with breast milk lowers the likelihood of developing a diverse range of non-communicable diseases later in life and it is also associated with improved neurodevelopmental outcomes. Although the precise mechanisms through which human milk feeding is linked with infants' neurodevelopment are still unknown, potential epigenetic effects of breast milk through its bioactive components, including non-coding RNAs, stem cells and microbiome, could at least partly explain this association. Micro- and long-non-coding RNAs, enclosed in milk exosomes, as well as breast milk stem cells, survive digestion, reach the circulation and can cross the blood-brain barrier. Certain non-coding RNAs potentially regulate genes implicated in brain development and function, whereas nestin-positive stem cells can possibly differentiate into neural cells or/and act as epigenetic regulators in the brain. Furthermore, breast milk microbiota contributes to the establishment of infant's gut microbiome, which is implicated in brain development via epigenetic modifications and key molecules' regulation. This narrative review provides an updated analysis of the relationship between breast milk feeding and infants' neurodevelopment via epigenetics, pointing out how breast milk's bioactive components could have an impact on the neurodevelopment of both full-term and preterm babies.

Mechanisms and regulation of defensins in host defense

As a family of cationic host defense peptides, defensins are mainly synthesized by Paneth cells, neutrophils, and epithelial cells, contributing to host defense. Their biological functions in innate immunity, as well as their structure and activity relationships, along with their mechanisms of action and therapeutic potential, have been of great interest in recent years. To highlight the key research into the role of defensins in human and animal health, we first describe their research history, structural features, evolution, and antimicrobial mechanisms. Next, we cover the role of defensins in immune homeostasis, chemotaxis, mucosal barrier function, gut microbiota regulation, intestinal development and regulation of cell death. Further, we discuss their clinical relevance and therapeutic potential in various diseases, including infectious disease, inflammatory bowel disease, diabetes and obesity, chronic inflammatory lung disease, periodontitis and cancer. Finally, we summarize the current knowledge regarding the nutrient-dependent regulation of defensins, including fatty acids, amino acids, microelements, plant extracts, and probiotics, while considering the clinical application of such regulation. Together, the review summarizes the various biological functions, mechanism of actions and potential clinical significance of defensins, along with the challenges in developing defensins-based therapy, thus providing crucial insights into their biology and potential clinical utility.

The Impact of the Human Milk Microbiota in the Prevention of Disease and Infant Health

Background: Human milk is recognized as an ideal food for newborns and infants owing to the presence of various nutritive factors, including healthy bacteria. Aim/Objective: This review aimed to understand the effects of human milk microbiota in both the prevention of disease and the health of infants. Methods: Data were obtained from PubMed, Scopus, Web of Science, clinical trial registries, Dergipark, and Türk Atıf Dizini up to February 2023 without language restrictions. Results: It is considered that the first human milk microbiota ingested by the newborn creates the initial microbiome of the gut system, which in turn influences the development and maturation of immunity. Bacteria present in human milk modulate the anti-inflammatory response by releasing certain cytokines, protecting the newborn against certain infections. Therefore, certain bacterial strains isolated from human milk could serve as potential probiotics for various therapeutic applications. Conclusions: In this review, the origin and significance of human milk bacteria have been highlighted along with certain factors influencing the composition of human milk microbiota. In addition, it also summarizes the health benefits of human milk as a protective agent against certain diseases and ailments.

Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy

Environmental enteric dysfunction (EED) is a subclinical syndrome of intestinal inflammation, malabsorption and barrier disruption that is highly prevalent in low- and middle-income countries in which poverty, food insecurity and frequent exposure to enteric pathogens impair growth, immunity and neurodevelopment in children. In this Review, we discuss advances in our understanding of EED, intestinal adaptation and the gut microbiome over the 'first 1,000 days' of life, spanning pregnancy and early childhood. Data on maternal EED are emerging, and they mirror earlier findings of increased risks for preterm birth and fetal growth restriction in mothers with either active inflammatory bowel disease or coeliac disease. The intense metabolic demands of pregnancy and lactation drive gut adaptation, including dramatic changes in the composition, function and mother-to-child transmission of the gut microbiota. We urgently need to elucidate the mechanisms by which EED undermines these critical processes so that we can improve global strategies to prevent and reverse intergenerational cycles of undernutrition.

Interrogating the role of the milk microbiome in mastitis in the multi-omics era

There is growing interest in a functional understanding of milk-associated microbiota as there is ample evidence that host-associated microbial communities play an active role in host health and phenotype. Mastitis, characterized by painful inflammation of the mammary gland, is prevalent among lactating humans and agricultural animals and is associated with significant clinical and economic consequences. The etiology of mastitis is complex and polymicrobial and correlative studies have indicated alterations in milk microbial community composition. Recent evidence is beginning to suggest that a causal relationship may exist between the milk microbiota and host phenotype in mastitis. Multi-omic approaches can be leveraged to gain a mechanistic, molecular level understanding of how the milk microbiome might modulate host physiology, thereby informing strategies to prevent and ameliorate mastitis. In this paper, we review existing studies that have utilized omics approaches to investigate the role of the milk microbiome in mastitis. We also summarize the strengths and challenges associated with the different omics techniques including metagenomics, metatranscriptomics, metaproteomics, metabolomics and lipidomics and provide perspective on the integration of multiple omics technologies for a better functional understanding of the milk microbiome.

Effects of breast milk on Behçet's disease clinical features

BACKGROUND

The etiology of Behçet's disease (BD) is not clearly known, however, abnormal activity in T helper (Th) 1, Th 17, and regulatory T cells (Treg) has critical importance in pathogenesis. It has been shown that the intestinal microbiome can be effective in the modulation of these immune abnormalities in BD patients. Breastfeeding increases the maturation of the infant's intestinal permeability by affecting the newborn's immature intestinal microbiome and metagenome. We aimed to examine the effects of breastfeeding on disease related symptoms, organ involvements and course of the disease in BD patients.

METHODS

This study was designed as a cross-sectional study in Ankara City Hospital rheumatology clinic between December 2021 and March 2022. Patients who were diagnosed with BD by meeting the criteria of the 'International Study Group' and whose information we could access by agreeing to participate in the study were enrolled. The mothers of the patients were also contacted and asked whether these patients were breastfed, the duration of breastfeeding, and the mode of birth. Demographic and clinical data of the patients, comorbid diseases, and drugs used for BD were collected from the records in the hospital database. The presence of sacroiliitis in patients was evaluated with sacroiliac X-ray and/or magnetic resonance imaging (MRI), which was requested because of low back pain symptoms and only patients with previous sacroiliac imaging for low back pain were included in the study. BD-related organ damage was measured by the Vasculitis Damage Index (VDI) and Behçet's syndrome Overall Damage Index (BODI) scores.

RESULTS

: A total of 304 patients were included in the study. The percentage of patients who were reported to have ever breastfed (median duration (IQR): 12(12) months, 33.5% < 6 months, 66.4% ≥ 6 months, and 59.6% ≥ 12 months) is 92%. When the breastfed and nonbreastfed patients were compared, 6.8% of the breastfed patients needed TNF-i against 18.2% of the nonbreastfed patients (p = 0.052). While the rate of having at least one comorbidity was 26.4% for those who were breastfed, this rate was 50% for those who had never been breastfed. When the organ and system involvements of the patients were compared, the incidence of sacroiliitis was statistically significantly higher in the nonbreastfed group (p = 0.025). Patients who were breastfed for less than 6 months were diagnosed with BD at an earlier age than those who were breastfed for more than 6 months, and those who were breastfed for less than 12 months compared to those who were breastfed for more than 12 months (respectively, p = 0.039, p = 0.035).

DISCUSSION

Our results imply that history of breastfeeding may have some positive effects on the course of the disease in BD patients.

Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities

Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.

Adaptation of a clinical reasoning model for use in inflammatory conditions of the lactating breast: a retrospective mixed-methods study

Background

Many potential factors associated with Inflammatory Conditions of the Lactating Breast (ICLB) have been reported in the literature, by lactating mothers and clinicians. Clinicians, including general practitioners, lactation consultants and physiotherapists, require a clinical reasoning model that summarises associated or linked factors, to aid in the assessment, treatment, and prevention of ICLB. Thus, we aimed to adapt the existing Breastfeeding Pain Reasoning Model (BPRM), for use in the management of ICLB, using prior research and clinical audit data to guide adaptation. The existing BPRM categorises contributing factors for breastfeeding nipple pain, rather than ICLB.

Methods

Factors linked with ICLB were identified from prior research and considered for inclusion into the existing model. Clinical data from a retrospective audit of ICLB patient notes at a private physiotherapy practice were also examined. Any factors identified from prior research that could not be identified in the clinical notes were not considered for inclusion into the existing model. Additional factors from the clinical notes that appeared repeatedly were considered for inclusion into the adaptation of the BPRM. A draft adapted model was created comprising all eligible factors, considering their counts and percentages as calculated from the clinical data. The research team iteratively examined all factors for appropriate categorisation and modification within the adapted model.

Results

Prior research and data from 160 clinical notes were used to identify factors for inclusion in the adapted model. A total of 57 factors, 13 pre-existing in the BPRM and 44 extra identified from the prior research or clinical audit, comprised the draft adapted model. Factor consolidation and terminology modification resulted in a total of 34 factors in the final proposed adapted ICLB model. The three main categories, CNS modulation, External influences and Local stimulation, from the existing model were maintained, with one minor terminology change to the former Local stimulation category, resulting in 'Local influences' category. Terminology for five subcategories were modified to better reflect the types of factors for ICLB. The most common factors in the adapted model, calculated from the clinical audit population of mothers with ICLB, were employment (85%), high socioeconomic status (81%), antibiotic use during breastfeeding (61%), history of an ICLB (56%), any breast pump use (45%), multiparity (43%), birth interventions (35%), decreased milk transfer (33%), breastfeeding behaviour and practices (33%), nipple pain (30%) and fit and hold (attachment and positioning) difficulty (28%).

Conclusion

An ICLB-specific linked factors model is proposed in this paper. Clinicians treating mothers with ICLB can use this model to identify influencing and determining factors of ICLB clinical presentations and provide targeted education and effective treatment plans.

OUP accepted manuscript

The intestinal microbiota plays a crucial role in health and changes in its composition are linked with major global human diseases. Fully understanding what shapes the human intestinal microbiota composition and knowing ways of modulating the composition are critical for promotion of life-course health, combating diseases, and reducing global health disparities. We aim to provide a foundation for understanding what shapes the human intestinal microbiota on an individual and global scale, and how interventions could utilize this information to promote life-course health and reduce global health disparities. We briefly review experiences within the first 1,000 days of life and how long-term exposures to environmental elements or geographic specific cultures have lasting impacts on the intestinal microbiota. We also discuss major public health threats linked to the intestinal microbiota, including antimicrobial resistance and disappearing microbial diversity due to globalization. In order to promote global health, we argue that the interplay of the larger ecosystem with intestinal microbiota research should be utilized for future research and urge for global efforts to conserve microbial diversity.

Construct validity and internal consistency of the Breast Inflammatory Symptom Severity Index in lactating mothers with inflammatory breast conditions

Background

Inflammatory Conditions of the Lactating Breast (ICLB) affect more than one in five lactating mothers, yet no fully validated outcome measures exist to aid clinicians in their patient-centred care of women with ICLB. The Breast Inflammatory Symptom Severity Index (BISSI) is an ICLB-specific clinician administered patient-reported outcome measure, currently used by Australian clinicians, who treat mothers with ICLB. To date the BISSI has undergone partial psychometric development. This study, therefore, aimed to undertake the next stage of psychometric development by determining the construct validity and internal consistency of the BISSI.

Methods

A retrospective audit was conducted on patient records of 160 mothers who were treated for ICLB, at a private physiotherapy practice in Melbourne, Australia. An electronic data capture tool was used to collate BISSI scores and associated ICLB assessment variables. Construct validity was determined through factor analysis and discriminant performance. Reliability was determined by assessing measures of internal consistency.

Results

Factor analysis established that BISSI items (n = 10) loaded on to four factors, Wellness, Pain, Physical Characteristics of Affected Area (PCAA), and Inflammation, which together, explained 71.2% of variance. The remaining item (‘Wellness/sickness unspecified’) did not load. Wellness, Pain, PCAA and Inflammation factors individually and collectively displayed the ability to discriminate symptom severity, as scores were significantly higher in mothers with high symptom severity (assessed via AUC close to or >0.7 and P value <0.005 for each factor). The BISSI demonstrated internal consistency with an overall Cronbach alpha of 0.742.

Conclusions

The BISSI has adequate construct validity, demonstrating behaviour consistent with theoretical constructs of inflammation severity, via its dimensionality and ability to discriminate symptom severity. The BISSI also has adequate internal consistency demonstrating reliability. Therefore, clinicians can have confidence that the BISSI is valid, the individual item scores are correlated, and the concepts are consistently measured.

Role of Bifidobacteria on Infant Health

Bifidobacteria are among the predominant microorganisms during infancy, being a dominant microbial group in the healthy breastfed infant and playing a crucial role in newborns and infant development. Not only the levels of the Bifidobacterium genus but also the profile and quantity of the different bifidobacterial species have been demonstrated to be of relevance to infant health. Although no definitive proof is available on the causal association, reduced levels of bifidobacteria are perhaps the most frequently observed alteration of the intestinal microbiota in infant diseases. Moreover, Bifidobacterium strains have been extensively studied by their probiotic attributes. This review compiles the available information about bifidobacterial composition and function since the beginning of life, describing different perinatal factors affecting them, and their implications on different health alterations in infancy. In addition, this review gathers exhaustive information about pre-clinical and clinical studies with Bifidobacterium strains as probiotics in neonates.

Short- and Long-Term Implications of Human Milk Microbiota on Maternal and Child Health

Human milk (HM) is considered the most complete food for infants as its nutritional composition is specifically designed to meet infant nutritional requirements during early life. HM also provides numerous biologically active components, such as polyunsaturated fatty acids, milk fat globules, IgA, gangliosides or polyamines, among others; in addition, HM has a “bifidogenic effect”, a prebiotic effect, as a result of the low concentration of proteins and phosphates, as well as the presence of lactoferrin, lactose, nucleotides and oligosaccharides. Recently, has been a growing interest in HM as a potential source of probiotics and commensal bacteria to the infant gut, which might, in turn, influence both the gut colonization and maturation of infant immune system. Our review aims to address practical approaches to the detection of microbial communities in human breast milk samples, delving into their origin, composition and functions. Furthermore, we will summarize the current knowledge of how HM microbiota dysbiosis acts as a short- and long-term predictor of maternal and infant health. Finally, we also provide a critical view of the role of breast milk-related bacteria as a novel probiotic strategy in the prevention and treatment of maternal and offspring diseases.

Human Breast Milk Composition and Function in Human Health: From Nutritional Components to Microbiome and MicroRNAs

Human breast milk (HBM) is not only an indispensable source of nutrients for early human growth and development, supplying components that support infant growth and development, but also contains various essential immunologic components with anti-infectious activities and critical roles in the formation of immunity. It is also known that HBM contains its own unique microbiome, including beneficial, commensal, and potentially probiotic bacteria, that can contribute to infant gut colonization. In addition, HBM-derived extracellular vesicles, exosomes, and microRNA are attracting increasing interest for their potential to transfer to the infant and their role in infant development. In this article, we examine some of the various constituents in HBM and review the evidence supporting their associated health effects and their potential applications in human health.

Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

Microbiota and Metabolomic Patterns in the Breast Milk of Subjects with Celiac Disease on a Gluten-Free Diet

The intestinal microbiome may trigger celiac disease (CD) in individuals with a genetic disposition when exposed to dietary gluten. Research demonstrates that nutrition during infancy is crucial to the intestinal microbiome engraftment. Very few studies to date have focused on the breast milk composition of subjects with a history of CD on a gluten-free diet. Here, we utilize a multi-omics approach with shotgun metagenomics to analyze the breast milk microbiome integrated with metabolome profiling of 36 subjects, 20 with CD on a gluten-free diet and 16 healthy controls. These analyses identified significant differences in bacterial and viral species/strains and functional pathways but no difference in metabolite abundance. Specifically, three bacterial strains with increased abundance were identified in subjects with CD on a gluten-free diet of which one (Rothia mucilaginosa) has been previously linked to autoimmune conditions. We also identified five pathways with increased abundance in subjects with CD on a gluten-free diet. We additionally found four bacterial and two viral species/strains with increased abundance in healthy controls. Overall, the differences observed in bacterial and viral species/strains and in functional pathways observed in our analysis may influence microbiome engraftment in neonates, which may impact their future clinical outcomes.

Association and Occurrence of Bifidobacterial Phylotypes Between Breast Milk and Fecal Microbiomes in Mother-Infant Dyads During the First 2 Years of Life

Breast milk acts as an intermediary for the transfer of functionally important commensal bacteria from mother to infant, especially for Bifidobacterium that can colonize the infant gut. However, the vast majority of rRNA amplicon-based studies reported the conspicuous intercohort and interindividual variation for the prevalence of Bifidobacterium in breast milk. In order to elucidate whether Bifidobacterium phylotypes persistently co-occured at the species or strain level in mother–breast milk–infant triads, we analyzed collectively the next-generation sequencing (NGS) datasets of bacterial 16S rRNA gene and the Bifidobacterium-specific groEL gene from maternal feces, breast milk, and infant feces in a small yet very homogeneous cohort of 25 healthy Uyghur mother–infant pairs (lactation for 7–720 days) in Kashgar, Xinjiang, China. Overall, 16S rRNA gene analysis showed that microbiome in the newborn gut was closer to that of breast milk in the first 4 months of lactation, and subsequently showed an obvious trend of adulthood at 6–12 months. Based on the BLAST accurate taxonomic result of the representative sequences of all ASVs (amplicon sequencing variants), only three sets of ASVs could be clearly assigned into Bifidobacterium species, whereas the remaining eight sets of ASVs corresponded to four indefinite Bifidobacterium species group. By contrast, the groEL gene dataset was partitioned into 376 ASVs, at least belonging to 13 well-known Bifidobacterium species or subspecies, of which 15 ASVs, annotated to seven well-known Bifidobacterium species or subspecies, showed triadic synchronism in most 23 mother–infant pairs tested. However, several other rare bifidobacterial phylotypes, which were frequently encountered in animals, were found to display no correspondence of the presence between the three ecosystems of mother–infant pairs. Our test results were obviously to support the hypothesis that breast milk acts as an intermediary for the transfer of probiotic commensal bacteria from mother to infant, especially for endosymbiotic Bifidobacterium that can colonize the infant gut. Some oxygen-insensitive exogenous Bifidobacterium phylotypes with a cosmopolitan lifestyle may be indirectly transferred to breast milk and the infant’s intestinal tract through environmental contamination. Thus, the groEL gene proved to be a very effective target for the depth resolution of Bifidobacterium community by high-throughput sequencing technologies.

Variation in Human Milk Composition Is Related to Differences in Milk and Infant Fecal Microbial Communities

Previously published data from our group and others demonstrate that human milk oligosaccharide (HMOs), as well as milk and infant fecal microbial profiles, vary by geography. However, little is known about the geographical variation of other milk-borne factors, such as lactose and protein, as well as the associations among these factors and microbial community structures in milk and infant feces. Here, we characterized and contrasted concentrations of milk-borne lactose, protein, and HMOs, and examined their associations with milk and infant fecal microbiomes in samples collected in 11 geographically diverse sites. Although geographical site was strongly associated with milk and infant fecal microbiomes, both sample types assorted into a smaller number of community state types based on shared microbial profiles. Similar to HMOs, concentrations of lactose and protein also varied by geography. Concentrations of HMOs, lactose, and protein were associated with differences in the microbial community structures of milk and infant feces and in the abundance of specific taxa. Taken together, these data suggest that the composition of human milk, even when produced by relatively healthy women, differs based on geographical boundaries and that concentrations of HMOs, lactose, and protein in milk are related to variation in milk and infant fecal microbial communities.

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.

Acceptive Immunity: The Role of Fucosylated Glycans in Human Host-Microbiome Interactions

The growth in the number of chronic non-communicable diseases in the second half of the past century and in the first two decades of the new century is largely due to the disruption of the relationship between the human body and its symbiotic microbiota, and not pathogens. The interaction of the human immune system with symbionts is not accompanied by inflammation, but is a physiological norm. This is achieved via microbiota control by the immune system through a complex balance of pro-inflammatory and suppressive responses, and only a disturbance of this balance can trigger pathophysiological mechanisms. This review discusses the establishment of homeostatic relationships during immune system development and intestinal bacterial colonization through the interaction of milk glycans, mucins, and secretory immunoglobulins. In particular, the role of fucose and fucosylated glycans in the mechanism of interactions between host epithelial and immune cells is discussed.

Human Milk Microbiota in an Indigenous Population Is Associated with Maternal Factors, Stage of Lactation, and Breastfeeding Practices

BACKGROUND

Human milk contains a diverse community of bacteria that are modified by maternal factors, but whether these or other factors are similar in developing countries has not been explored. Our objective was to determine whether the milk microbiota was modified by maternal age, BMI, parity, lactation stage, subclinical mastitis (SCM), and breastfeeding practices in the first 6 mo of lactation in an indigenous population from Guatemala.

METHODS

For this cross-sectional study, Mam-Mayan indigenous mothers nursing infants aged <6 mo were recruited. Unilateral human milk samples were collected (n = 86) and processed for 16S rRNA sequencing at the genus level. Microbial diversity and relative abundance were compared with maternal factors [age, BMI, parity, stage of lactation, SCM, and 3 breastfeeding practices (exclusive, predominant, mixed)] obtained through questionnaires.

RESULTS

Streptococcus was the most abundant genus (33.8%), followed by Pseudomonas (18.7%) and Sphingobium (10.7%) but relative abundance was associated with maternal factors. First, Lactobacillus and Streptococcus were more abundant in early lactation whereas the common oral (Leptotrichia) and environmental (Comamonas) bacteria were more abundant in established lactation. Second, Streptococcus,Lactobacillus,Lactococcus,Leuconostoc, and Micrococcus had a higher abundance in multiparous mothers compared with primiparous mothers. Third, a more diverse microbiota characterized by a higher abundance of lactic acid bacteria (Lactobacillus,Leuconostoc, and Lactococcus), Leucobacter, and Micrococcus was found in mothers with a healthy BMI. Finally, distinct microbial communities differed by stage of lactation and by exclusive, predominant, or mixed breastfeeding practices.

CONCLUSION

Milk bacterial communities in an indigenous community were associated with maternal factors. Higher microbial diversity was supported by having a healthy BMI, the absence of SCM, and by breastfeeding. Interestingly, breastfeeding practices when assessed by lactation stage were associated with distinct microbiota profiles.

Impact of Maternal Nutritional Supplementation during Pregnancy and Lactation on the Infant Gut or Breastmilk Microbiota: A Systematic Review

Recent evidence indicates that maternal dietary intake, including dietary supplements, during pregnancy and lactation may alter the infant gut or breastmilk microbiota, with implications for health outcomes in both the mother and infant. To review the effects of maternal nutritional supplementation during pregnancy and lactation on the infant gut or breastmilk microbiota a systematic literature search was conducted. A total of 967 studies published until February 2020 were found, 31 were eligible and 29 randomized control trials were included in the qualitative synthesis. There were 23 studies that investigated the effects of probiotic supplementation, with the remaining studies investigating vitamin D, prebiotics or lipid-based nutrient supplements (LNS). The effects of maternal nutritional supplementation on the infant gut microbiota or breastmilk microbiota were examined in 21 and 12 studies, respectively. Maternal probiotic supplementation during pregnancy and lactation generally resulted in the probiotic colonization of the infant gut microbiota, and although most studies also reported alterations in the infant gut bacterial loads, there was limited evidence of effects on bacterial diversity. The data available show that maternal probiotic supplementation during pregnancy or lactation results in probiotic colonization of the breastmilk microbiota. There were no observed effects between probiotic supplementation and breastmilk bacterial counts of healthy women, however, administration of Lactobacillus probiotic to nursing women affected by mastitis was associated with significant reductions in breastmilk Staphylococcal loads. Maternal LNS supplementation during pregnancy and lactation increased bacterial diversity in the infant gut, whilst vitamin D and prebiotic supplementation did not alter either infant gut bacterial diversity or counts. Heterogeneity in study design precludes any firm conclusions on the effects of maternal nutritional supplementation during pregnancy and lactation on the infant gut or breastmilk microbiota, warranting further research.

Bacterial stability with freezer storage of human milk

OBJECTIVES

Human milk supports the development of a beneficial newborn intestinal microflora. We have shown previously that human milk had reduced bacteria but unchanged nutrient composition when stored at -20 °C for up to nine months. We suspected declining bacterial colony counts were manifestations of bacterial dormancy and not failure of survival. We investigated differences in selected bacterial colony counts (lactobacillus, bifidobacteria, staphylococcus, streptococcus and enterococcus) in human milk stored for 2 and 12 weeks at -20 °C in either manual or automatic defrost freezers and whether reduced bacterial counts at 12 weeks were the result of dormancy or failure of survival.

METHODS

Freshly expressed milk was obtained from mothers in the NICU, divided into aliquots and stored for 2 and 12 weeks at -20 °C in either automatic or manual defrost freezers. Subsequently, duplicate aliquots, one thawed and the other thawed and maintained at room temperature for 4 h, were plated to assess bacterial colony counts.

RESULTS

Significant declines in bacterial colony counts were seen from 2 to 12 weeks freezer storage for all bacteria. There were no differences in colony counts between freezer types. Once thawed, no further bacterial growth occurred.

CONCLUSIONS

Short-term freezer storage for 12 weeks resulted bacterial killing. Type of freezer used for storage did not have an impact on bacterial survival. It is unknown whether the paucity of important probiotic bacteria in stored human milk has adverse effects on infants.

Impact of synbiotics on gut microbiota during early life: a randomized, double-blind study

Human milk is considered the optimal nutrition for infants and found to contain significant numbers of viable bacteria. The aim of the study was to assess the effects of a specific synbiotic combination at doses closer to the bacterial cells present in human milk, on intestinal bifidobacteria proportions (relative abundance), reduction of potential pathogens and gut physiological conditions. A clinical study was conducted in 290 healthy infants aged from 6 to 19 weeks. Infants received either a control infant formula or one of the two investigational infant formulas (control formula with 0.8 g/100 ml scGOS/lcFOS and Bifidobacterium breve M-16V at either 1 × 10⁴ cfu/ml or 1 × 10⁶ cfu/ml). Exclusively breastfed infants were included as a reference. Analyses were performed on intention-to-treat groups and all-subjects-treated groups. After 6 weeks of intervention, the synbiotics at two different doses significantly increased the bifidobacteria proportions in healthy infants. The synbiotic supplementation also decreased the prevalence (infants with detectable levels) and the abundance of C. difficile. Closer to the levels in the breastfed reference group, fecal pH was significantly lower while l-lactate concentrations and acetate proportions were significantly higher in the synbiotic groups. All formulas were well tolerated and all groups showed a comparable safety profile based on the number and severity of adverse events and growth. In healthy infants, supplementation of infant-type bifidobacterial strain B. breve M-16V, at a dose close to bacterial numbers found in human milk, with scGOS/lcFOS (9:1) created a gut environment closer to the breastfed reference group. This specific synbiotic mixture may also support gut microbiota resilience during early life.

Clinical Trial Registration This clinical study named Color Synbiotics Study, was registered in ClinicalTrials.gov on 18 March 2013. Registration number is NCT01813175. https://clinicaltrials.gov/ct2/show/NCT01813175.

Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis

Human milk is the ideal food for infants due to its unique nutritional and immune properties, and more recently human milk has also been recognized as an important source of bacteria for infants. However, a substantial amount of fundamental human milk microbiome information remains unclear, such as the origin, composition and function of the community and its members. There is emerging evidence to suggest that the diversity and composition of the milk microbiome might differ between lactation stages, due to maternal factors and diet, agrarian and urban lifestyles, and geographical location. The evolution of the methods used for studying milk microbiota, transitioning from culture dependent-approaches to include culture-independent approaches, has had an impact on findings and, in particular, primer selection within 16S rRNA gene barcoding studies have led to discrepancies in observed microbiota communities. Here, the current state-of-the-art is reviewed and emerging frontiers essential to improving our understanding of the human milk microbiome are considered.

The Microbiota of the Human Mammary Ecosystem

Human milk contains a dynamic and complex site-specific microbiome, which is not assembled in an aleatory way, formed by organized microbial consortia and networks. Presence of some genera, such as Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium (formerly known as Propionibacterium), Lactobacillus, Lactococcus and Bifidobacterium, has been detected by both culture-dependent and culture-independent approaches. DNA from some gut-associated strict anaerobes has also been repeatedly found and some studies have revealed the presence of cells and/or nucleic acids from viruses, archaea, fungi and protozoa in human milk. Colostrum and milk microbes are transmitted to the infant and, therefore, they are among the first colonizers of the human gut. Still, the significance of human milk microbes in infant gut colonization remains an open question. Clinical studies trying to elucidate the question are confounded by the profound impact of non-microbial human milk components to intestinal microecology. Modifications in the microbiota of human milk may have biological consequences for infant colonization, metabolism, immune and neuroendocrine development, and for mammary health. However, the factors driving differences in the composition of the human milk microbiome remain poorly known. In addition to colostrum and milk, breast tissue in lactating and non-lactating women may also contain a microbiota, with implications in the pathogenesis of breast cancer and in some of the adverse outcomes associated with breast implants. This and other open issues, such as the origin of the human milk microbiome, and the current limitations and future prospects are addressed in this review.

Diet Influences the Oral Microbiota of Infants during the First Six Months of Life

Background: Oral microorganisms contribute to oral health and disease, but few have studied how infant feeding methods affect their establishment. Methods: Infant (n = 12) feeding records and tongue and cheek swabs were collected within 48 h of birth, and after 2, 4, and 6 mo. DNA was extracted from samples, bacterial and fungal amplicons were generated and sequenced using Illumina MiSeq, and sequences were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analysis System (SAS) to evaluate differences over time and among breast-fed, formula-fed, mixed-fed, and solid food-fed infants. Results: Considering all time points, breast milk- and mixed-fed infants had lower oral species richness than solid food-fed infants (p = 0.006). Regardless of feeding mode, species richness was lower at birth than at other time points (p = 0.006). Principal coordinates analysis (PCoA) of unique fraction metric (UniFrac) distances indicated that bacterial communities were impacted by feeding method (p < 0.005). Considering all time points, breast-fed infants had higher Streptococcus, while formula-fed infants had higher Actinomyces and Prevotella. Regardless of feeding mode, Propionibacterium, Porphyromonas, Prevotella, Gemella, Granulicatella, Veillonella, Fusobacterium, Leptotrichia, Neisseria, and Haemophilus increased with age, while Cloacibacterium and Dechloromonas decreased with age. Oral fungi were detected in infants but were not impacted by diet. Conclusions: These findings demonstrate that the establishment of oral bacteria depends on dietary composition and age. More research is necessary to determine whether this affects risk of oral caries and other health outcomes later in life.

The influence of the gastrointestinal microbiome on infant colic

INTRODUCTION

Although infantile colic is relatively frequent, its pathophysiology is not yet understood. The aim of this paper is to provide a better understanding of the link between infantile colic and the gastrointestinal microbiome.

AREAS COVERED

The gastro-intestinal microbiome may already start to develop in the womb and grows exponentially immediately after birth. Factors influencing the microbiome can cause dysbiosis and precipitate symptoms of colic through several mechanisms such as increased gas production and low grade gut inflammation. Other possible factors are immaturity of the enterohepatic bile acid cycle and administration of antibiotics and other medications during the perinatal period. An effective treatment for all colicky infants has yet to be discovered, but the probiotic Lactobacillus reuteri DSM17938 was shown to be effective in breastfed infants with colic. The scientific databases 'Pubmed' and 'Google scholar' were searched from inception until 02/2020. Relevant articles were selected based on the abstract.

EXPERT OPINION

Recent literature confirmed that the composition of the gastrointestinal microbiome is associated with the development of infantile colic. It can be speculated that full sequencing and bioinformatics analysis to identify the microbiome down to the species level may provide answers to the etiology and management of infantile colic.

Lactobacillus commensals autochthonous to human milk have the hallmarks of potent probiotics

Maternal milk is an important source of essential nutrients for the optimal growth of infants. Breastfeeding provides a continuous supply of beneficial bacteria to colonize the infant gastrointestinal tract (GIT) and offers health benefits for disease prevention and immunity. The purpose of this study was to isolate novel probiotic strains from the breast milk of native Pakistani mothers and to evaluate their probiotic potential. We isolated 21 strains of bacteria from the colostrum and mature milk of 20 healthy mothers, who had vaginal deliveries and were not taking antibiotics. After phenotypic and genotypic characterization, these isolates were tested for survival in the GIT using in vitro acid and bile tests. Nine strains showing good acid tolerance were assessed for their growth rate, bile resistance and ability to hydrolyze bile salts. Out of the four Lactobacillus isolates adjudged to be most promising as probiotics, three were Lactobacillus fermentum strains and one was a strain of Lactobacillus oris. This study demonstrates that human milk is a viable source of commensal bacteria beneficial to both adults and babies.

Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants

Colonization of the gastrointestinal tract with microorganisms during infancy represents a critical control point for shaping life-long immune-mediated disease susceptibility. Abnormal colonization or an imbalance of microbes, termed dysbiosis, is implicated in several diseases. Consequently, recent research has aimed at understanding ways to manipulate a dysbiotic microbiome during infancy to resemble a normal, healthy microbiome. However, one of the fundamental issues in microbiome research is characterizing what a "normal" infant microbiome is based on geography, ethnicity and cultural variations. This review provides a comprehensive account of what is currently known about the infant microbiome from a global context. In general, this review shows that the influence of cultural variations in feeding practices, delivery modes and hygiene are the biggest contributors to microbial variability. Despite geography or race, all humans have similar microbial succession during infancy.

Components of human breast milk: from macronutrient to microbiome and microRNA

Human breast milk (HBM) is essential for the infant's growth and development right after birth and is an irreplaceable source of nutrition for early human survival. Various infant formulas have many similarities to HBM in many components, but there is no perfect substitute for HBM. Recently, various breast milk components and their roles have been studied according to the development of various analysis techniques. As is already well known, HBM contains about 87%-88% water, and 124- g/L solid components as macronutrients, including about 7% (60-70 g/L) carbohydrates, 1% (8-10 g/L) protein, and 3.8% (35-40 g/L) fat. The composition may vary depending on the environmental factors, including maternal diet. Colostrum is low in fat but high in protein and relatively rich in immuneprotective components. Although HBM contains enough vitamins to ensure normal growth of the infant, vitamins D and K may be insufficient, and the infant may require their supplementation. Growth factors in HBM also serve as various bioactive proteins and peptides on the intestinal tract, vasculature, nervous system, and endocrine system. In the past, HBM of a healthy mother was thought to be sterile. However, several subsequent studies have confirmed the presence of rich and diverse microbial communities in HBM. Some studies suggested that the genera Staphylococcus and Streptococcus may be universally predominant in HBM, but the origin of microbiota still remains controversial. Lastly, milk is the one of most abundant body fluid of microRNAs, which are known to play a role in various functions, such as immunoprotection and developmental programming, through delivering from HBM and absorption by intestinal epithelial cells. In conclusion, HBM is the most important source of nutrition for infants and includes microbiomes and miRNAs for growth, development, and immunity.

Probiotic Supplementation During the Perinatal and Infant Period: Effects on Gut Dysbiosis and Disease

The perinatal period is crucial to the establishment of lifelong gut microbiota. The abundance and composition of microbiota can be altered by several factors such as preterm delivery, formula feeding, infections, antibiotic treatment, and lifestyle during pregnancy. Gut dysbiosis affects the development of innate and adaptive immune responses and resistance to pathogens, promoting atopic diseases, food sensitization, and infections such as necrotizing enterocolitis (NEC). Recent studies have indicated that the gut microbiota imbalance can be restored after a single or multi-strain probiotic supplementation, especially mixtures of Lactobacillus and Bifidobacterium strains. Following the systematic search methodology, the current review addresses the importance of probiotics as a preventive or therapeutic tool for dysbiosis produced during the perinatal and infant period. We also discuss the safety of the use of probiotics in pregnant women, preterm neonates, or infants for the treatment of atopic diseases and infections.

Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways

The early life human gut microbiota exerts life-long health effects on the host, but the mechanisms underpinning its assembly remain elusive. Particularly, the early colonization of Clostridiales from the Roseburia-Eubacterium group, associated with protection from colorectal cancer, immune- and metabolic disorders is enigmatic. Here, we describe catabolic pathways that support the growth of Roseburia and Eubacterium members on distinct human milk oligosaccharides (HMOs). The HMO pathways, which include enzymes with a previously unknown structural fold and specificity, were upregulated together with additional glycan-utilization loci during growth on selected HMOs and in co-cultures with Akkermansia muciniphila on mucin, suggesting an additional role in enabling cross-feeding and access to mucin O-glycans. Analyses of 4599 Roseburia genomes underscored the preponderance and diversity of the HMO utilization loci within the genus. The catabolism of HMOs by butyrate-producing Clostridiales may contribute to the competitiveness of this group during the weaning-triggered maturation of the microbiota.

Like mother, like microbe: human milk oligosaccharide mediated microbiome symbiosis

Starting shortly after parturition, and continuing throughout our lifetime, the gut microbiota coevolves with our metabolic and neurological programming. This symbiosis is regulated by a complex interplay between the host and environmental factors, including diet and lifestyle. Not surprisingly, the development of this microbial community is of critical importance to health and wellness. In this targeted review, we examine the gut microbiome from birth to 2 years of age to characterize the role human milk oligosaccharides play in early formation of microbial flora.

Diverse Bacteriocins Produced by Strains From the Human Milk Microbiota

Microbial colonization of the infant gut is a convoluted process dependent on numerous contributing factors, including age, mode of delivery and diet among others that has lifelong implication for human health. Breast milk also contains a microbiome which acts as a source of colonizing bacteria for the infant. Here, we demonstrate that human milk harbors a wide diversity of bacteriocin-producing strains with the potential to compete among the developing gut microbiota of the infant. We screened 37 human milk samples and found isolates with antimicrobial activity and distinct cross-immunity profiles. From these isolates, we detected 73 putative gene clusters for bacteriocins of all known sub-classes, including 16 novel prepeptides. More specifically, we detected two novel lantibiotics, four sactibiotics and three class IIa bacteriocins with an unusual modification of the pediocin box that is composed of YDNGI instead of the highly conserved motif YGNGV. Moreover, we identified a novel class IIb bacteriocin, four novel class IIc and two class IId bacteriocins. In conclusion, human milk contains a variety of bacteriocin-producing strains which may provide them a competitive advantage in the colonization of the infant gut and suggests that the milk microbiota is a source of antimicrobial potential.

Development and Functions of the Infant Gut Microflora: Western vs. Indian Infants

The human gut is colonized by trillions of bacteria as well as other microorganisms, collectively referred to as the “gut microflora.” This microflora plays an important role in metabolism as well as immunity, and alterations in its normal composition and pattern of colonization can disturb the development and functioning of the immune system, predisposing the individual to several diseases. Neonates acquire their gut microflora from the mother as well as the surroundings, and as the infant grows, the gut microflora undergoes several changes, ultimately acquiring an adult-like composition. Characterization of the gut microflora of healthy infants is important to protect infants from infectious diseases. Furthermore, formulation of prebiotics and probiotics for boosting infant immunity in a specific population also requires prior knowledge of the normal gut microflora in a healthy infant in that population. To this end, several studies have been performed on Western infants; however, the gut microflora of Indian infants is as yet insufficiently studied. Moreover, there has been no comparative analysis of the development and characteristics of the infant gut microflora between the two populations. In this review, we discuss the development and maturation of the infant gut microflora and its effect on immunity, as well as the factors affecting the patterns of colonization. In addition, we compare the patterns of colonization of gut microflora between Western and Indian infants based on the available literature in an attempt to identify the extent of similarity or difference between the two populations.

Isolation and Quantification of Uremic Toxin Precursor-Generating Gut Bacteria in Chronic Kidney Disease Patients

In chronic kidney disease (CKD), impaired kidney function results in accumulation of uremic toxins, which exert deleterious biological effects and contribute to inflammation and cardiovascular morbidity and mortality. Protein-bound uremic toxins (PBUTs), such as p-cresyl sulfate, indoxyl sulfate and indole-3-acetic acid, originate from phenolic and indolic compounds, which are end products of gut bacterial metabolization of aromatic amino acids (AAA). This study investigates gut microbial composition at different CKD stages by isolating, identifying and quantifying PBUT precursor-generating bacteria. Fecal DNA extracts from 14 controls and 138 CKD patients were used to quantify total bacterial number and 11 bacterial taxa with qPCR. Moreover, isolated bacteria from CKD 1 and CKD 5 fecal samples were cultured in broth medium supplemented with AAA under aerobic and anaerobic conditions, and classified as PBUT precursor-generators based on their generation capacity of phenolic and indolic compounds, measured with U(H)PLC. In total, 148 different fecal bacterial species were isolated, of which 92 were PBUT precursor-generators. These bacterial species can be a potential target for reducing PBUT plasma levels in CKD. qPCR indicated lower abundance of short chain fatty acid-generating bacteria, Bifidobacterium spp. and Streptococcus spp., and higher Enterobacteriaceae and E. coli with impaired kidney function, confirming an altered gut microbial composition in CKD.

Breast milk microbiota: A review of the factors that influence composition

Breastfeeding is associated with considerable health benefits for infants. Aside from essential nutrients, immune cells and bioactive components, breast milk also contains a diverse range of microbes, which are important for maintaining mammary and infant health. In this review, we summarise studies that have investigated the composition of the breast milk microbiota and factors that might influence it. We identified 44 studies investigating 3105 breast milk samples from 2655 women. Several studies reported that the bacterial diversity is higher in breast milk than infant or maternal faeces. The maximum number of each bacterial taxonomic level detected per study was 58 phyla, 133 classes, 263 orders, 596 families, 590 genera, 1300 species and 3563 operational taxonomic units. Furthermore, fungal, archaeal, eukaryotic and viral DNA was also detected. The most frequently found genera were Staphylococcus, Streptococcus Lactobacillus, Pseudomonas, Bifidobacterium, Corynebacterium, Enterococcus, Acinetobacter, Rothia, Cutibacterium, Veillonella and Bacteroides. There was some evidence that gestational age, delivery mode, biological sex, parity, intrapartum antibiotics, lactation stage, diet, BMI, composition of breast milk, HIV infection, geographic location and collection/feeding method influence the composition of the breast milk microbiota. However, many studies were small and findings sometimes contradictory. Manipulating the microbiota by adding probiotics to breast milk or artificial milk offers an exciting avenue for future interventions to improve infant health.

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve

Increasing evidence supports the importance of the breast milk microbiome in seeding the infant gut. However, the origin of bacteria in milk and the process of milk microbe-mediated seeding of infant intestine need further elucidation. Presumed sources of bacteria in milk include locations of mother-infant and mother-environment interactions. We investigate the role of mother-infant interaction on breast milk microbes. Shotgun metagenomics and 16S rRNA gene sequencing identified milk microbes of mother-infant pairs in breastfed infants and in infants that have never latched. Although breast milk has low overall biomass, milk microbes play an important role in seeding the infant gut. Breast milk bacteria were largely comprised of Staphylococcus, Streptococcus, Acinetobacter, and Enterobacter primarily derived from maternal areolar skin and infant oral sites in breastfeeding pairs. This suggests that the process of breastfeeding is a potentially important mechanism for propagation of breast milk microbes through retrograde flux via infant oral and areolar skin contact. In one infant delivered via Caesarian section, a distinct strain of Bifidobacteria breve was identified in maternal rectum, breast milk and the infant’s stool potentially suggesting direct transmission. This may support the existence of microbial translocation of this anaerobic bacteria via the enteromammary pathway in humans, where maternal bacteria translocate across the maternal gut and are transferred to the mammary glands. Modulating sources of human milk microbiome seeding potentially imply opportunities to ultimately influence the development of the infant microbiome and health.

DNA extraction approaches substantially influence the assessment of the human breast milk microbiome

In addition to providing nutritional and bioactive factors necessary for infant development, human breast milk contains bacteria that contribute to the establishment of commensal microbiota in the infant. However, the composition of this bacterial community differs considerably between studies. We hypothesised that bacterial DNA extraction methodology from breast milk samples are a substantial contributor to these inter-study differences. We tested this hypothesis by applying five widely employed methodologies to a mock breast milk sample and four individual human breast milk samples. Significant differences in DNA yield and purity were observed between methods (P < 0.05). Microbiota composition, assessed by 16S rRNA gene amplicon sequencing, also differed significantly with extraction methodology (P < 0.05), including in the contribution of contaminant signal. Concerningly, many of the bacterial taxa identified here as contaminants have been reported as components of the breast milk microbiome in other studies. These findings highlight the importance of using stringent, well-validated, DNA extraction methodologies for analysis of the breast milk microbiome, and exercising caution interpreting microbiota data from low-biomass contexts.