Mathias W. Hornef

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50–75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota–host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

Secretory IgA in the Coordination of Establishment and Maintenance of the Microbiota.

Starting at birth, the intestinal microbiota changes dramatically from a highly individual collection of microorganisms, dominated by comparably few species, to a mature, competitive, and diverse microbial community. Microbial colonization triggers and accompanies the maturation of the mucosal immune system and ultimately results in a mutually beneficial host-microbe interrelation in the healthy host. Here, we discuss the role of secretory immunoglobulin A (SIgA) during the establishment of the infant microbiota and life-long host-microbial homeostasis. We critically review the published literature on how SIgA affects the enteric microbiota and highlight the accessibility of the infant microbiota to therapeutic intervention.

On the origin of species: Factors shaping the establishment of infant's gut microbiota

The human gut microbiota is a complex and dynamic ecosystem, which naturally lives in a symbiotic relationship with the host. Perturbations of the microbial composition (dysbiosis) and reduced diversity may promote disease susceptibility and recurrence. In contrast to the mature intestinal microbiota of healthy adults, which appears relatively stable over time, the infants microbiome only establishes and matures during the first years of life. In this respect, early childhood seems to represent a crucial age-window in disease prevention, since microbial diversification and maturation of the microbiome primarily occurs during this period of life. A better understanding of ecological processes and pioneer consortia in microbial development is crucial, in order to support the development of a beneficial microbiota. Various deterministic and stochastic aspects seem to shape the microbiome in early life, including maternal, environmental, and host factors. Here, we review the current understanding of the origin of pioneer bacteria and the evolutionary factors that influence the development of the gut microbiota in infants. In addition, future perspectives, including manipulating and promoting the succession of initial bacteria during infancy, will be highlighted.

The Neonatal Window of Opportunity: Setting the Stage for Life-Long Host-Microbial Interaction and Immune Homeostasis

The existence of a neonatal window was first highlighted by epidemiological studies that revealed the particular importance of this early time in life for the susceptibility to immune-mediated diseases in humans. Recently, the first animal studies emerged that present examples of early-life exposure–triggered persisting immune events, allowing a detailed analysis of the factors that define this particular time period. The enteric microbiota and the innate and adaptive immune system represent prime candidates that impact on the pathogenesis of immune-mediated diseases and are known to reach a lasting homeostatic equilibrium following a dynamic priming period after birth. In this review, we outline the postnatal establishment of the microbiota and maturation of the innate and adaptive immune system and discuss examples of early-life exposure–triggered immune-mediated diseases that start to shed light on the critical importance of the early postnatal period for life-long immune homeostasis.

The intestinal epithelium as guardian of gut barrier integrity

A single layer of epithelial cells separates the intestinal lumen from the underlying sterile tissue. It is exposed to a multitude of nutrients and a large number of commensal bacteria. Although the presence of commensal bacteria significantly contributes to nutrient digestion, vitamin synthesis and tissue maturation, their high number represents a permanent challenge to the integrity of the epithelial surface keeping the local immune system constantly on alert. In addition, the intestinal mucosa is challenged by a variety of enteropathogenic microorganisms. In both circumstances, the epithelium actively contributes to maintaining host–microbial homeostasis and antimicrobial host defence. It deploys a variety of mechanisms to restrict the presence of commensal bacteria to the intestinal lumen and to prevent translocation of commensal and pathogenic microorganisms to the underlying tissue. Enteropathogenic microorganisms in turn have learnt to evade the hosts immune system and circumvent the antimicrobial host response. In the present article, we review recent advances that illustrate the intense and intimate host‐microbial interaction at the epithelial level and improve our understanding of the mechanisms that maintain the integrity of the intestinal epithelial barrier.

Neonatal mucosal immunology.

Although largely deprived from exogenous stimuli in utero, the mucosal barriers of the neonate after birth are bombarded by environmental, nutritional, and microbial exposures. The microbiome is established concurrently with the developing immune system. The nature and timing of discrete interactions between these two factors underpins the long-term immune characteristics of these organs, and can set an individual on a trajectory towards or away from disease. Microbial exposures in the gastrointestinal and respiratory tracts are some of the key determinants of the overall immune tone at these mucosal barriers and represent a leading target for future intervention strategies. In this review, we discuss immune maturation in the gut and lung and how microbes have a central role in this process.

Age-Dependent Susceptibility to Enteropathogenic Escherichia coli (EPEC) Infection in Mice

Enteropathogenic Escherichia coli (EPEC) represents a major causative agent of infant diarrhea associated with significant morbidity and mortality in developing countries. Although studied extensively in vitro, the investigation of the host-pathogen interaction in vivo has been hampered by the lack of a suitable small animal model. Using RT-PCR and global transcriptome analysis, high throughput 16S rDNA sequencing as well as immunofluorescence and electron microscopy, we characterize the EPEC-host interaction following oral challenge of newborn mice. Spontaneous colonization of the small intestine and colon of neonate mice that lasted until weaning was observed. Intimate attachment to the epithelial plasma membrane and microcolony formation were visualized only in the presence of a functional bundle forming pili (BFP) and type III secretion system (T3SS). Similarly, a T3SS-dependent EPEC-induced innate immune response, mediated via MyD88, TLR5 and TLR9 led to the induction of a distinct set of genes in infected intestinal epithelial cells. Infection-induced alterations of the microbiota composition remained restricted to the postnatal period. Although EPEC colonized the adult intestine in the absence of a competing microbiota, no microcolonies were observed at the small intestinal epithelium. Here, we introduce the first suitable mouse infection model and describe an age-dependent, virulence factor-dependent attachment of EPEC to enterocytes in vivo.

Pathogens, Commensal Symbionts, and Pathobionts: Discovery and Functional Effects on the Host

During the last decade, we have witnessed a stunning increase in information on the composition of the microbiota; its influence on a variety of host functions; and associations with the susceptibility to inflammatory, metabolic, and autoimmune diseases. We have thus obtained insight into the potentially harmful consequences of an altered microbiota and also learned about the many beneficial functions of commensal bacteria. The present review aims at summarizing for the reader the general concept of pathogenic and commensal bacteria and their particular features. It also discusses the more recently defined pathobionts, members of the microbiota that exert specific effects on the hosts mucosal immune system associated with the development of clinical disease.

Ontogeny of intestinal epithelial innate immune responses.

Emerging evidence indicates that processes during postnatal development might significantly influence the establishment of mucosal host-microbial homeostasis. Developmental and adaptive immunological processes but also environmental and microbial exposure early after birth might thus affect disease susceptibility and health during adult life. The present review aims at summarizing the current understanding of the intestinal epithelial innate immune system and its developmental and adaptive changes after birth.

Does a prenatal bacterial microbiota exist

MICROBIOME The recent technical progress and enormous efforts to unravel the manifold interactions of the microbiota with the host’s organism have provided striking and unforeseen insights. This work assigns the microbiota a central role in human health and has identified novel strategies to prevent and fight diseases in the future. One particular aspect of this work has been the early colonization of the newborn and a strong influence of maternal sources on the developing microbiota of the neonate. Birth, or more accurately rupture of the amniotic membranes that surround the embryo and separate it physically from the lumen of the uterus first exposes the neonate to the environment and is generally considered the start of the microbiota establishment. More recently, the existence of a placental microbiome, and thus maternal-fetal transmission of microorganisms and microbial colonization of the fetal organism before birth has been suggested. This commentary critically discusses the available data. It is generally believed that the fetus in utero develops in the absence of viable microorganisms. This is consistent with the observation that cesarean sectionborn rodents can serve to generate germfree animals. Only with rupture of membranes and passage through the birth canal, the newborn becomes exposed to colonized maternal body surfaces and the environment initiating the establishment of the neonate’s own microbiota. Recently, maternal-fetal transmission of commensal bacteria and the existence of a placental microbiome have been suggested. Colonization of the healthy placental and/or fetal tissue with a diverse group of metabolically active bacteria would; however, fundamentally challenge our current thinking of the development of the fetus within a sterile, protected environment. It would require new concepts to explain how bacteria can persist within host tissue but remain anatomically restricted to prevent systemic spread within the fetal organism and how preterm birth, a condition causally linked to bacterial infection of the amniotic tissue, is prevented. It would also raise important questions on the origin, composition and stability of the placental microbiome and its influence on the developing host and postnatal microbiome. In support of the concept of a prenatal microbiome, Jiménez et al. reported on the cultural detection of low numbers of Enterococcus faecium, Staphylococcus epidermidis and Propionibacterium acnes from human cord blood samples after elective cesarean section. This analysis was complemented by a mouse study in which they administered a genetically labeled human E. faecium isolate orally to pregnant mice and reported detection of this strain from cultures of amniotic fluid. A subsequent study from the same group analyzed meconium samples of 21 healthy human neonates born by either vaginal delivery or caesarean section and cultured bacteria of the genera Staphylococcus, Enterococcus, Streptococcus, Leuconostoc, Bifidobacterium, Rothia, Bacteroides but also of the Proteobacteria Klebsiella, Enterobacter and Escherichia coli. Again, oral administration of the labeled E. faecium strain to pregnant mice led to the detection in meconium samples. They concluded the presence of ‘‘mother-to-child transmission’’ before birth. Three other groups described the PCR-based detection of bacteria in placental tissue. Rautava et al. detected bacterial DNA mainly from the genus Lactobacillus as well as the mostly obligate anaerobic growing genera Bifidobacterium, Bacteroides and Clostridium in 29 of 29 placental samples after elective cesarean section. The group of Versalovic performed a metagenomic approach on placental specimen collected under sterile conditions from 320 individuals after vaginal delivery or cesarean section and described a low-abundance microbiome including the phyla Firmicutes, Tenericutes, Proteobacteria, Bacteroides and Fusobacteria. A recent study by Bassols et al., examined placental tissue of 22 vaginally delivered neonates from mothers with or without gestational diabetes aseptically collected and prepared after childbirth in the delivery or operating room. PCR and 16S rDNA sequencing revealed the presence of