Human milk microbiota and its relationship with milk components in health and during lactational mastitis

Tesis por compendio[ES] Antecedentes: La leche humana es el alimento natural ideal para el desarrollo y la protección del recién nacido y el niño en crecimiento. Estudios recientes han demostrado la presencia de bacterias en la leche humana en condiciones de salud, y se cree que podrían conferir propiedades beneficiosas para el bebé. Sin embargo, poco se sabe sobre la relación entre las bacterias y los macronutrientes de la leche y las células humanas, y no existe un protocolo óptimo para estimar el número de bacterias en las muestras. Además, hasta la fecha no se ha explorado la posible presencia de hongos en la leche humana, a pesar de que previamente éstos se han encontrado en la leche de otros animales y en el intestino neonatal. Por otro lado, la etiología de la mastitis sub-aguda no está bien descrita, y esfuerzos para describir la composición de la microbiota de la leche durante este proceso por medio de tecnologías de secuenciación próxima, y su potencial implicación en la enfermedad son escasos. Esta tesis está dirigida a mejorar nuestra comprensión de la microbiota de la leche humana, su composición y diversidad, e interacciones con otros componentes de la leche en condiciones de salud y durante la mastitis sub-aguda. También exploramos el efecto potencial de factores ambientales, como el tipo de parto y el origen geográfico, y el periodo de la lactancia en la composición de la microbiota de la leche. Métodos: Se utilizaron tecnologías de secuenciación de próxima generación dirigidas al gen bacteriano 16S rRNA y a los genes fúngicos 28S rRNA y la región ITS1, en combinación con análisis microbiológicos clásicos, para evaluar la composición bacteriana y fúngica en la leche de madres sanas, y de madres con mastitis sub-aguda. Las cargas bacterianas y fúngicas en la leche humana se obtuvieron mediante la metodología qPCR calibrada con citometría de flujo. Resultados: La composición bacteriana en la leche humana tiene una alta variabilidad interindividual, y también a lo largo del tiempo, y está compuesta predominantemente por bacterias de la familia Staphylococacceae. Se encontró un "núcleo" de bacterias y hongos en la leche humana de donantes españolas. Se observaron algunas correlaciones entre bacterias con los macronutrientes de la leche y células somáticas humanas, lo que indica una relación activa entre microbiota y ambiente. La carga bacteriana resultó ser más alta que lo estimado previamente, a una media de 106 células/ml, presentes en estado libre y asociadas a células humanas. No se observaron correlaciones entre carga bacteriana, número de células somáticas, y la riqueza y diversidad bacteriana, lo que podría indicar que un aumento en la densidad bacteriana en condiciones de salud no activa una respuesta inmune en la glándula mamaria, ni altera la comunidad microbiana. Además, nuestros resultados revelaron la existencia de hongos en la leche humana que se confirmó mediante métodos de cultivo y microscopía. El 89% de las muestras españolas analizadas tenían niveles detectables de ADN fúngico, con una carga aproximada de 105 células/ml. Malassezia, Candida y Saccharomyces eran prevalentes en las muestras, y se observaron diferentes interacciones fúngicas con los componentes de la leche. La presencia de hongos en la leche se confirmó posteriormente en muestras de orígenes geográficos distantes, y se observó que factores maternos y tipo de parto pueden afectar a las comunidades microbianas de la leche. Tras describir la microbiota de la leche en condiciones de salud, realizamos un estudio observacional prospectivo de casos/controles, donde se estudió el ADN y el ARN de la microbiota de la leche de madres sanas y madres con mastitis sub-aguda, antes y después del tratamiento. La carga bacteriana aumentó durante la enfermedad, la diversidad disminuyó y las alteraciones en la composición bacteriana probablemente reflejen un proceso disbiótico en la glándula mamari[CA] Antecedents: La llet humana és l'aliment natural ideal per al desenvolupament i la protecció del nadó i el nen en creixement. Estudis recents han demostrat la presència de bacteris a la llet humana en condicions normals de salut, i es creu que podrien conferir propietats beneficioses per al nadó. No obstant això, poc se sap sobre la relació entre els bacteris i els macronutrients de la llet i les cèl·lules humanes, i no hi ha un protocol òptim per estimar el nombre de bacteris en les aquestes mostres. A més, fins a la data no s'ha explorat la possible presència de fongs en la llet humana, tot i que prèviament s'havien trobat en la llet d'animals i en l'intestí neonatal. D'altra banda, l'etiologia de la mastitis sub-aguda no està ben descrita, i esforços per descriure la composició de la microbiota de la llet durant aquest procés per mitjà de tecnologies de seqüenciació propera, i la seua potencial implicació en la malaltia són escassos. Aquesta tesi està dirigida a millorar la nostra comprensió de la microbiota de la llet humana, la seva composició i diversitat, i les interaccions amb altres components de la llet, en condicions de salut i durant la mastitis sub-aguda. També explorem l'efecte potencial de factors ambientals, com el tipus de part i l'origen geogràfic, i el període de la lactància en la composició de la microbiota de la llet humana. Mètodes: Es van utilitzar tecnologies de seqüenciació de pròxima generació dirigides al gen bacterià 16S rRNA i als gens fúngics 28S rRNA i la regió ITS1, en combinació amb anàlisis microbiològiques clàssics, per avaluar la composició bacteriana i fúngica en la llet de mares sanes i de mares amb mastitis sub-aguda. Les quantitats bacterianes i fúngiques en la llet humana es van obtenir mitjançant la metodologia qPCR calibrada amb citometria de flux. Resultats: La composició bacteriana en la llet humana té una alta variabilitat interindividual, i també al llarg del temps, i està composta predominantment per bacteris de la família Staphylococacceae. Es va trobar un "nucli" de bacteris i fongs a la llet humana de donants espanyoles. Es van observar algunes correlacions entre bacteris amb els macronutrients de la llet i cèl·lules somàtiques humanes, el que indica una relació activa entre la microbiota de la llet i el medi. La densitat bacteriana va resultar ser més alta que l'estimat prèviament, a una mitjana de 106 cèl·lules/ml, presents en estat lliure i associades a cèl·lules humanes. No es van observar correlacions entre càrrega bacteriana, el nombre de cèl·lules somàtiques, i la riquesa i diversitat bacteriana, la qual cosa podria indicar que un augment en la densitat bacteriana en condicions de salut no activa una resposta immune en la glàndula mamària, ni alteren la comunitat microbiana. A més, els nostres resultats de seqüenciació van revelar l'existència de certa diversitat de fongs a la llet humana que es va confirmar mitjançant mètodes de cultiu i microscòpia. El 89% de les mostres espanyoles analitzades tenien nivells detectables d'ADN fúngic, amb una càrrega mitjana de 105 cèl·lules/ml. Malassezia, Candida i Saccharomyces eren prevalents en les mostres, i es van observar interaccions fúngiques amb els components de la llet de diferents maneres. La presència de fongs a la llet es va confirmar posteriorment en mostres d'orígens geogràfics distants, i es va observar que els factors materns i de part poden afectar les comunitats microbianes de la llet. Després de descriure la microbiota de la llet en condicions de salut, vam realitzar un estudi observacional prospectiu de casos/controls, on es va estudiar l'ADN i l'ARN de la microbiota de la llet humana de mares sanes i mares amb mastitis sub-aguda, abans i després del tractament. La càrrega bacteriana va augmentar durant la malaltia, la diversitat va disminuir i les alteracions en la composició bacteriana probablement reflecteixin un procés d[EN] Background: Human milk is nature's ideal food for the nurture and protection of the new-born and growing infant. Recent evidence reported the presence of bacteria in human milk under normal, healthy conditions, which are thought to confer beneficial properties to the infant. However, little is known about the relationship between bacteria and milk macronutrients and human cells, and there is no optimal protocol to estimate bacterial numbers in the samples. Also, the potential presence of fungi in human milk has not been explored to date, despite the fact that fungi has been previously detected in dairy animal's milk and in the neonatal gut. In addition, the aetiology of sub-acute mastitis is not well understood, and information about the composition of the milk microbiota during this process by means of next-generation sequencing and its potential implications in the disease is scarce. This thesis is aimed to improve our understanding of human milk microbiota, its composition and diversity as well as the interactions with other milk components, in health and during sub-acute mastitis. We also explore the potential effect of environmental factors, such as mode of delivery and geographic location, and the lactation stage on milk's microbiota composition. Methods: Next-generation sequencing technologies targeting the bacterial 16S rRNA gene, and the fungal 28S rRNA gene and ITS1 genetic region, in combination with classic microbiological analyses, were used in order to assess the bacterial and fungal composition in milk of healthy mothers, and in mothers suffering sub-acute mastitis. Bacterial and fungal loads in human milk were obtained by qPCR methodology calibrated with flow cytometry. Results: Bacterial composition in human milk has a high inter-individual variability, and also over time, and is predominantly comprised of bacteria from the Staphylococacceae family. A bacterial and fungal "core" were found in the human milk of Spanish donors. Some correlations were observed between bacteria with milk macronutrients and somatic cells, indicating an active relationship between milk microbiota and the environment. Bacterial density appeared to be higher than previously estimated, at a mean of 106 cells/ml, and bacteria were found both in a free-living state and associated to human cells. No correlations were observed between bacterial load with number of somatic cells nor bacterial richness and diversity, indicating that higher bacterial densities under healthy conditions do not trigger an immune response in the mammary gland, nor alter the microbial community. In addition, our results revealed the existence of certain diversity of fungi in human milk that was further confirmed by culture-dependent methods and microscopy. 89% of the Spanish samples analysed had detectable levels of fungal DNA, at a median load of approximately 105 cells/ml. Malassezia, Candida and Saccharomyces prevailed in the samples, and fungi interacted with milk components in different ways. The presence of fungi in milk was further confirmed in samples from distant geographic origins, and it was observed that maternal and delivery factors can impact milk microbial communities. After describing milk microbiota in healthy conditions, we performed an observational, prospective case-control study, where DNA and RNA from human milk microbiota from healthy and sub-acute mastitis-suffering mothers were studied before and after the treatment. Bacterial loads increased during the disease, diversity decreased and alterations in bacterial composition likely reflected a dysbiotic process in the mammary gland. This supports that sub-acute mastitis is a microbial-driven disease.Boix Amorós, A. (2019). Human milk microbiota and its relationship with milk components in health and during lactational mastitis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/129870TESISCompendi

Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation

Human breast milk is considered the optimal nutrition for infants, providing essential nutrients and a broad range of bioactive compounds, as well as its own microbiota. However, the interaction among those components and the biological role of milk microorganisms is still uncovered. Thus, our aim was to identify the relationships between milk microbiota composition, bacterial load, macronutrients, and human cells during lactation. Bacterial load was estimated in milk samples from a total of 21 healthy mothers through lactation time by bacteria-specific qPCR targeted to the single-copy gene fusA. Milk microbiome composition and diversity was estimated by 16S-pyrosequencing and the structure of these bacteria in the fluid was studied by flow cytometry, qPCR, and microscopy. Fat, protein, lactose, and dry extract of milk as well as the number of somatic cells were also analyzed. We observed that milk bacterial communities were generally complex, and showed individual-specific profiles. Milk microbiota was dominated by Staphylococcus, Pseudomonas, Streptococcus, and Acinetobacter. Staphylococcus aureus was not detected in any of these samples from healthy mothers. There was high variability in composition and number of bacteria per milliliter among mothers and in some cases even within mothers at different time points. The median bacterial load was 106 bacterial cells/ml through time, higher than those numbers reported by 16S gene PCR and culture methods. Furthermore, milk bacteria were present in a free-living, “planktonic” state, but also in equal proportion associated to human immune cells. There was no correlation between bacterial load and the amount of immune cells in milk, strengthening the idea that milk bacteria are not sensed as an infection by the immune system.MC would like to greatefully acknowledge ERC Starting Grant 639226-MAMI. MC is involved in the “ISCH COST Action-IS1405” entitled “Building Intrapartum Research Through Health—an interdisciplinary whole system approach to understanding and contextualizing physiological labor and birth (BIRTH).”Peer reviewedPeer Reviewe

Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease

We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, myco - biome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression

Microbiota of human precolostrum and its potential role as a source of bacteria to the infant mouth

[EN] Human milk represents a source of bacteria for the initial establishment of the oral (and gut) microbiomes in the breastfed infant, however, the origin of bacteria in human milk remains largely unknown. While some evidence points towards a possible endogenous enteromammary route, other authors have suggested that bacteria in human milk are contaminants from the skin or the breastfed infant mouth. In this work 16S rRNA sequencing and bacterial culturing and isolation was performed to analyze the microbiota on maternal precolostrum samples, collected from pregnant women before delivery, and on oral samples collected from the corresponding infants. The structure of both ecosystems demonstrated a high proportion of taxa consistently shared among ecosystems, Streptococcus spp. and Staphylococcus spp. being the most abundant. Whole genome sequencing on those isolates that, belonging to the same species, were isolated from both the maternal and infant samples in the same mother-infant pair, evidenced that in 8 out of 10 pairs both isolates were >99.9% identical at nucleotide level. The presence of typical oral bacteria in precolostrum before contact with the newborn indicates that they are not a contamination from the infant, and suggests that at least some oral bacteria reach the infant’s mouth through breastfeedingSIThis research was supported by grant AGL2016-75476-R. LR was funded by grant 624773 (FP-7-PEOPLE-2013- IEF, European Commission) and is currently supported by the Juan de la Cierva Postdoctoral Trainee Program of the Spanish Ministry of Economy and Competitiveness (MINECO; IJCI-2015-23196

Human milk microbiota in sub-acute lactational mastitis induces inflammation and undergoes changes in composition, diversity and load

Sub-acute mastitis (SAM) is a prevalent disease among lactating women, being one of the main reasons for early weaning. Although the etiology and diagnosis of acute mastitis (AM) is well established, little is known about the underlying mechanisms causing SAM. We collected human milk samples from healthy and SAM-suffering mothers, during the course of mastitis and after symptoms disappeared. Total (DNA-based) and active (RNA-based) microbiota were analysed by 16S rRNA gene sequencing and qPCR. Furthermore, mammary epithelial cell lines were exposed to milk pellets, and levels of the pro-inflammatory interleukin IL8 were measured. Bacterial load was significantly higher in the mastitis samples and decreased after clinical symptoms disappeared. Bacterial diversity was lower in SAM milk samples, and differences in bacterial composition and activity were also found. Contrary to AM, the same bacterial species were found in samples from healthy and SAM mothers, although at different proportions, indicating a dysbiotic ecological shift. Finally, mammary epithelial cell exposure to SAM milk pellets showed an over-production of IL8. Our work therefore supports that SAM has a bacterial origin, with increased bacterial loads, reduced diversity and altered composition, which partly recovered after treatment, suggesting a polymicrobial and variable etiology.This work was funded by the ERC Starting Grant 639226-MAMI, and the RTI2018-102032-B-I00 Grant from the Spanish Ministry of Science, Technology and UniversitiesPeer reviewe

Heteromers of amyloid precursor protein in cerebrospinal fluid

Background: Soluble fragments of the amyloid precursor protein (APP) generated by α- and β-secretases, sAPPα and sAPPβ, have been postulated as promising new cerebrospinal fluid (CSF) biomarkers for the clinical diagnosis of Alzheimer’s disease (AD). However, the capacity of these soluble proteins to assemble has not been explored and could be relevant. Our aim is to characterize possible sAPP oligomers that could contribute to the quantification of sAPPα and sAPPβ in CSF by ELISA, as well as to characterize the possible presence of soluble full-length APP (sAPPf).Results: We employed co-immunoprecipitation, native polyacrylamide gel electrophoresis and ultracentrifugation in sucrose density gradients to characterize sAPP oligomers in CSF. We have characterized the presence of sAPPf in CSF from NDC and AD subjects and demonstrated that all forms, including sAPPα and sAPPβ, are capable of assembling into heteromers, which differ from brain APP membrane-dimers. We measured sAPPf, sAPPα and sAPPβ by ELISA in CSF samples from AD (n = 13) and non-disease subjects (NDC, n = 13) before and after immunoprecipitation with antibodies against the C-terminal APP or against sAPPβ. We demonstrated that these sAPP heteromers participate in the quantification of sAPPα and sAPPβ by ELISA. Immunoprecipitation with a C-terminal antibody to remove sAPPf reduced by ~30% the determinations of sAPPα and sAPPβ by ELISA, whereas immunoprecipitation with an APPβ antibody reduced by ~80% the determination of sAPPf and sAPPα.Conclusions: The presence of sAPPf and sAPP heteromers should be taken into consideration when exploring the levels of sAPPα and sAPPβ as potential CSF biomarkers.This study was funded in part by the EU BIOMARKAPD-Joint Programming on Neurodegenerative Diseases (JPND) project. This project is supported through the Instituto de Salud Carlos III (ISCIII; grants PI11/03026 to JSV and PI11/03023 to JLM) under the aegis of JPND, and through CIBERNED, ISC-III. We also acknowledge the support for the publication fee to the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Peer reviewe

Multiple Approaches Detect the Presence of Fungi in Human Breastmilk Samples from Healthy Mothers

A correction to this article has been published in https://doi.org/10.1038/s41598-017-13270-xHuman breastmilk contains a variety of bacteria that are transmitted to the infant and have been suggested to contribute to gut microbiota development and immune maturation. However, the characterization of fungal organisms in milk from healthy mothers is currently unknown although their presence has been reported in the infant gut and also in milk from other mammals. Breastmilk samples from healthy lactating mothers (n = 65) within 1 month after birth were analyzed. Fungal presence was assessed by different techniques, including microscopy, growth and identification of cultured isolates, fungal load estimation by qPCR, and fungal composition using 28S rRNA gene high-throughput sequencing. In addition, milk macronutrients and human somatic cells were quantified by spectrophotometry and cytometry. qPCR data showed that 89% of samples had detectable levels of fungal DNA, at an estimated median load of 3,5 × 105 cells/ml, potentially including both viable and non-viable fungi. Using different culture media, 33 strains were isolated and identified, confirming the presence of viable fungal species. Pyrosequencing results showed that the most common genera were Malassezia (44%), followed by Candida (19%) and Saccharomyces (12%). Yeast cells were observed by fluorescence microscopy. Future work should study the origin of these fungi and their potential contribution to infant health.This work was funded by ERC Starting Grant 639226-MAMIPeer reviewe

Gut Microbiota and Mucosal Immunity in the Neonate

Gut microbiota colonization is a complex, dynamic, and step-wise process that is in constant development during the first years of life. This microbial settlement occurs in parallel with the maturation of the immune system, and alterations during this period, due to environmental and host factors, are considered to be potential determinants of health-outcomes later in life. Given that host–microbe interactions are mediated by the immune system response, it is important to understand the close relationship between immunity and the microbiota during birth, lactation, and early infancy. This work summarizes the evidence to date on early gut microbiota colonization, and how it influences the maturation of the infant immune system and health during the first 1000 days of life. This review will also address the influence of perinatal antibiotic intake and the importance of delivery mode and breastfeeding for an appropriate development of gut immunity.The authors would like to acknowledge the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (ERC Starting Grant, project no. 639226) and the grants AGL2015-707487-P and BIO2015-68711-R from the Spanish Ministerio de Economía, Industria y Competitividad (MINECO). MSR would like to acknowledge the support from the Ayudas para la Contratación de Personal Investigador en Formación (ACIF) program of Generalitat Valenciana with the European Social Fund (ESF).Peer reviewe