Vertical and horizontal transmission of intestinal commensal bacteria in the rat model

The role of animal hosts in shaping gut microbiome variation

Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Faecal Microbiota Characterisation of Potamochoerus porcus Living in a Controlled Environment

Intestinal bacteria establish a specific relationship with the host animal, which causes the acquisition of gut microbiota with a unique composition classified as the enterotype. As the name suggests, the Red River Hog is a wild member of the pig family living in Africa, in particular through the West and Central African rainforest. To date, very few studies have analysed the gut microbiota of Red River Hogs (RRHs) both housed under controlled conditions and in wild habitats. This study analysed the intestinal microbiota and the distribution of Bifidobacterium species in five Red River Hog (RRH) individuals (four adults and one juvenile), hosted in two different modern zoological gardens (Parco Natura Viva, Verona, and Bioparco, Rome) with the aim of disentangling the possible effects of captive different lifestyle and host genetics. Faecal samples were collected and studied both for bifidobacterial counts and isolation by means of culture-dependent method and for total microbiota analysis through the high-quality sequences of the V3-V4 region of bacterial 16S rRNA. Results showed a host-specific bifidobacterial species distribution. Indeed, B. boum and B. thermoacidophilum were found only in Verona RRHs, whereas B. porcinum species were isolated only in Rome RRHs. These bifidobacterial species are also typical of pigs. Bifidobacterial counts were about 10⁶ CFU/g in faecal samples of all the individuals, with the only exception for the juvenile subject, showing 10⁷ CFU/g. As in human beings, in RRHs a higher count of bifidobacteria was also found in the young subject compared with adults. Furthermore, the microbiota of RRHs showed qualitative differences. Indeed, Firmicutes was found to be the dominant phylum in Verona RRHs whereas Bacteroidetes was the most represented in Roma RRHs. At order level, Oscillospirales and Spirochaetales were the most represented in Verona RRHs compared with Rome RRHs, where Bacteroidales dominated over the other taxa. Finally, at the family level, RRHs from the two sites showed the presence of the same families, but with different levels of abundance. Our results highlight that the intestinal microbiota seems to reflect the lifestyle (i.e., the diet), whereas age and host genetics are the driving factors for the bifidobacterial population.

Maternal effects on early-life gut microbiota maturation in a wild nonhuman primate

Early-life microbial colonization is an important process shaping host physiology,^1-3 immunity,^4-6 and long-term health outcomes^7-10 in humans. However, our understanding of this dynamic process remains poorly investigated in wild animals,^11-13 where developmental mechanisms can be better understood within ecological and evolutionarily relevant contexts.^11,12 Using one of the largest developmental datasets on a wild primate-the gelada (Theropithecus gelada)-we used 16S rRNA amplicon sequencing to characterize gut microbiota maturation during the first 3 years of life and assessed the role of maternal effects in shaping offspring microbiota assembly. In contrast to recent data on chimpanzees, postnatal microbial colonization in geladas was highly similar to humans:¹⁴ microbial alpha diversity increased rapidly following birth, followed by gradual changes in composition until weaning. Dietary changes associated with weaning (from milk- to plant-based diet) were the main drivers of shifts in taxonomic composition and microbial predicted functional pathways. Maternal effects were also an important factor influencing the offspring gut microbiota. During nursing (<12 months), offspring of experienced (multi-time) mothers exhibited faster functional microbial maturation, likely reflecting the general faster developmental pace of infants born to these mothers. Following weaning (>18 months), the composition of the juvenile microbiota tended to be more similar to the maternal microbiota than to the microbiota of other adult females, highlighting that maternal effects may persist even after nursing cessation.^15,16 Together, our findings highlight the dynamic nature of early-life gut colonization and the role of maternal effects in shaping this trajectory in a wild primate.

Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota

BACKGROUND

Inter-population variation in host-associated microbiota reflects differences in the hosts' environments, but this characterization is typically based on studies comparing few populations. The diversity of natural habitats and captivity conditions occupied by any given host species has not been captured in these comparisons. Moreover, intraspecific variation in gut microbiota, generally attributed to diet, may also stem from differential acquisition of environmental microbes-an understudied mechanism by which host microbiomes are directly shaped by environmental microbes. To more comprehensively characterize gut microbiota in an ecologically flexible host, the ring-tailed lemur (Lemur catta; n = 209), while also investigating the role of environmental acquisition, we used 16S rRNA sequencing of lemur gut and soil microbiota sampled from up to 13 settings, eight in the wilderness of Madagascar and five in captivity in Madagascar or the U.S. Based on matched fecal and soil samples, we used microbial source tracking to examine covariation between the two types of consortia.

RESULTS

The diversity of lemur gut microbes varied markedly within and between settings. Microbial diversity was not consistently greater in wild than in captive lemurs, indicating that this metric is not necessarily an indicator of host habitat or environmental condition. Variation in microbial composition was inconsistent both with a single, representative gut community for wild conspecifics and with a universal 'signal of captivity' that homogenizes the gut consortia of captive animals. Despite the similar, commercial diets of captive lemurs on both continents, lemur gut microbiomes within Madagascar were compositionally most similar, suggesting that non-dietary factors govern some of the variability. In particular, soil microbial communities varied across geographic locations, with the few samples from different continents being the most distinct, and there was significant and context-specific covariation between gut and soil microbiota.

CONCLUSIONS

As one of the broadest, single-species investigations of primate microbiota, our study highlights that gut consortia are sensitive to multiple scales of environmental differences. This finding begs a reevaluation of the simple 'captive vs. wild' dichotomy. Beyond the important implications for animal care, health, and conservation, our finding that environmental acquisition may mediate aspects of host-associated consortia further expands the framework for how host-associated and environmental microbes interact across different microbial landscapes.

The microbiome impacts host hybridization and speciation

Microbial symbiosis and speciation profoundly shape the composition of life's biodiversity. Despite the enormous contributions of these two fields to the foundations of modern biology, there is a vast and exciting frontier ahead for research, literature, and conferences to address the neglected prospects of merging their study. Here, we survey and synthesize exemplar cases of how endosymbionts and microbial communities affect animal hybridization and vice versa. We conclude that though the number of case studies remain nascent, the wide-ranging types of animals, microbes, and isolation barriers impacted by hybridization will likely prove general and a major new phase of study that includes the microbiome as part of the functional whole contributing to reproductive isolation. Though microorganisms were proposed to impact animal speciation a century ago, the weight of the evidence supporting this view has now reached a tipping point.

Evaluation of the impact of in ovo administered bacteria on microbiome of chicks through 10 days of age

Initial inoculation and colonization of the chicken gastrointestinal tract (GIT) by microbiota have been suggested to have a major influence on the growth performance and health of birds. Commercial practices in chicken production may alter or delay microbial colonization by pioneer colonizing bacteria that can have an impact on the development and maturation of the GIT and intestinal microflora. The objective of this study was to compare the impact of apathogenic Gram-negative isolates or lactic acid bacteria (LAB) as pioneer colonizers on the microbiome at the day of hatch (DOH) and evaluate the influence through 10 D of age on ceca. At 18 embryonic days (E), the amnion of embryos was inoculated with either saline (S), approximately 102 CFU of LAB (L), Citrobacter freundii (C), or Citrobacter species (C2). Once DNA was isolated from mucosal and digesta contents, samples underwent 2 × 300 paired-end Illumina MiSeq library preparation for microbiome analysis. An increased abundance of Lactobacillaceae family and Lactobacillus genus was observed in the L group at DOH (P < 0.05), whereas the abundance of Enterococcaceae and Enterococcus was numerically decreased. While Lactobacillus salivarius was one of the pioneer colonizers in the L group at 18E, the population decreased by 10 D (39.59 to 0.09%) and replaced with a population of undefined Lactobacillus (10.36%) and Lactobacillus reuteri (3.63%). Results suggest that L treatment may have accelerated a mature microbiota. Enterobacteriaceae was the dominant family (57.44%) in C group at DOH (P < 0.05). The C2 group only showed some abundance of the C2 species (7.92%) at DOH but had the highest overall abundance of undefined Lactobacillus in the ceca by 10 D (25.28%). Taken together, different isolates provided in ovo can have an impact on the initial microbiome of the GIT, and some of these differences in ceca remain notable at 10 D.

Thinking bigger: How early-life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease

Imbalance, or dysbiosis, of the gut microbiome of infants has been linked to an increased risk of asthma and allergic diseases. Most studies to date have provided a wealth of data showing correlations between early-life risk factors for disease and changes in the structure of the gut microbiome that disrupt normal immunoregulation. These studies have typically focused on one specific risk factor, such as mode of delivery or early-life antibiotic use. Such "micro-level" exposures have a considerable impact on affected individuals but not necessarily the whole population. In this review, we place these mechanisms under a larger lens that takes into account the influence of upstream "macro-level" environmental factors such as air pollution and the built environment. While these exposures likely have a smaller impact on the microbiome at an individual level, their ubiquitous nature confers them with a large influence at the population level. We focus on features of the indoor and outdoor human-made environment, their microbiomes and the research challenges inherent in integrating the built environment microbiomes with the early-life gut microbiome. We argue that an exposome perspective integrating internal and external microbiomes with macro-level environmental factors can provide a more comprehensive framework to define how environmental exposures can shape the gut microbiome and influence the development of allergic disease.

Development of the equine gut microbiota

Shortly after birth the mammalian gut is colonized, by a transient microbiota, highly susceptible to environment and diet, that eventually stabilizes and becomes the resident gut microbiota. In a window of opportunity during the colonization, oral tolerance is established towards resident bacteria. In this study, the development of the equine gut microbiota was investigated in ten foals from parturition until post weaning. We found great differences in the core species of the gut microbiota composition between time-matched samples on Day 7 and 20 post-partum. Between day 20 and Day 50 post-partum, we saw the gut microbiota became increasingly dominated by fiber fermenting species. After Day 50, no significant changes in species abundance were observed. Gene expression analysis of pro- and anti-inflammatory cytokines in the blood revealed no significant changes before and after weaning. In summary, relative stability of the gut microbiota was reached within 50 days post-partum and, weaning did not have a major impact on the microbial composition.

The antidepressant-like effect of probiotics and their faecal abundance may be modulated by the cohabiting gut microbiota in rats

Numerous studies have been published describing the effect of various probiotics (PRO) on behaviours related to psychiatric disease. We have previously shown a robust antidepressant-like effect of PRO in rats, but over time, the treatment effect seems to vary significantly between different sets of rats from the same commercial vendor. Therefore, we hypothesised that the antidepressant-like response may be modulated by the cohabiting gut microbiota. The aims of the present study were (1) to investigate any differences in the gut microbiota composition between responders (Resp) and non-responders (Non-resp) to PRO with regards to depressive-like behaviour, and (2) to evaluate the effects of PRO on the microbiota composition. Two sets of 20 male Sprague-Dawley rats each were treated with multi-species PRO (nine Bifidobacterium, Lactococcus and Lactobacillus species) for eight weeks and subjected to a behavioural assessment. Faecal samples were collected for 16 s rRNA (VR4) gene amplicon sequencing (Illumina MiSeq). As previously reported, PRO-treated Resp animals showed a marked decrease in depressive-like behaviour, whereas no such response was seen in Non-resp. We observed profound differences in the gut microbiota composition between the two sets of rats, and the relative faecal abundance of the genera that comprised PRO was higher in Resp than in Non-resp although treated with the same dose of PRO. Particularly, the relative abundance of the Lactobacillus genus was not increased in PRO-treated Non-resp animals. In conclusion, the cohabiting microbiota and the faecal abundance of PRO may modulate the antidepressant-like effect of PRO in rats.

Assessing Transmission of Antimicrobial-Resistant Escherichia coli in Wild Giraffe Contact Networks

There is growing evidence that anthropogenic sources of antibiotics and antimicrobial-resistant bacteria can spill over into natural ecosystems, raising questions about the role wild animals play in the emergence, maintenance, and dispersal of antibiotic resistance genes. In particular, we lack an understanding of how resistance genes circulate within wild animal populations, including whether specific host characteristics, such as social associations, promote interhost transmission of these genes. In this study, we used social network analysis to explore the forces shaping population-level patterns of resistant Escherichia coli in wild giraffe (Giraffa camelopardalis) and assess the relative importance of social contact for the dissemination of resistant E. coli between giraffe. Of 195 giraffe sampled, only 5.1% harbored E. coli isolates resistant to one or more tested antibiotics. Whole-genome sequencing on a subset of resistant isolates revealed a number of acquired resistance genes with linkages to mobile genetic elements. However, we found no evidence that the spread of resistance genes among giraffe was facilitated by interhost associations. Giraffe with lower social degree were more likely to harbor resistant E. coli, but this relationship was likely driven by a correlation between an individual's social connectedness and age. Indeed, resistant E. coli was most frequently detected in socially isolated neonates, indicating that resistant E. coli may have a selective advantage in the gastrointestinal tracts of neonates compared to other age classes. Taken together, these results suggest that the maintenance of antimicrobial-resistant bacteria in wild populations may, in part, be determined by host traits and microbial competition dynamics within the host.IMPORTANCE Antimicrobial resistance represents a significant threat to human health, food security, and the global economy. To fully understand the evolution and dissemination of resistance genes, a complete picture of antimicrobial resistance in all biological compartments, including natural ecosystems, is required. The environment and wild animals may act as reservoirs for anthropogenically derived resistance genes that could be transferrable to clinically relevant bacteria of humans and domestic animals. Our study investigated the possible transmission mechanisms for antimicrobial-resistant bacteria within a wild animal population and, more broadly, contributes to our understanding of how resistance genes are spread and maintained in natural ecosystems.

Bacteria and fungi in day-old turkeys vary among companies, collection periods, and breeder flocks

Microbial colonization of the intestinal tract of commercial poultry is highly variable, likely due to the fact that poults and chicks are hatched and raised without exposure to adult birds and their microbiota. In industrial poultry production, it is hypothesized that most of the microbiota is obtained through horizontal transmission from the environment and very little by maternal transmission. The initial gut microbiota will therefore differ between flocks and companies based on environmental conditions at the hatchery. Day-old poults were collected from the hatchery of 2 companies at 3 different time points to monitor the initial colonizing microbiota by sequencing amplicons of marker genes for bacteria, lactic acid bacteria (LAB), fungi, and archaea. Bacterial colonizers were distinct by company (pseudo-F 38.7, P ≤ 0.05) with the predominant bacteria at Company A being clostridia, specifically Clostridium celatum group, C. paraputrificum, and C. tertium. Predominant bacteria at Company B were Enterobacteriaceae, belonging to 2 different groups, one that included Escherichia; Shigella and Salmonella and the other Klebsiella; Enterobacter; and others. The predominant LAB at both companies were Enterococcus faecalis and E. gallinarum, confirmed by sequencing the 16S ribosomal RNA (rRNA) gene of colonies picked from lactobacilli agar plate counts. The predominant fungi were Aspergillus niger and Saccharomyces cerevisiae, with Candida sake or Alterneria sp. in some samples of Company A. Archaeal sequences were detected only in a single poult from Company B. The initial gastrointestinal colonizers of poults vary across company and time, signifying a strong environmental effect on microbiota acquisition. There was an indication of maternal effects in certain breeder flocks from Company B. Further work is necessary to determine how this variability affects microbiota succession and impacts growth and production of the birds.

Bifidobacterial strains in the intestines of newborns originate from their mothers

The gastrointestinal tract is believed to be colonized rapidly with bacteria immediately from birth. The source of these intestinal microbes is an ongoing topic of interest because increasing evidence suggests that the composition of the initial intestinal bacterial colonization strongly affects health. In particular, the source of bifidobacteria has received marked attention because these bacteria are suggested to play a crucial role in protecting against susceptibility to diverse diseases later in life. However, the source of these microbes has remained unclear. Recently, it was confirmed that mothers transmit their unique bifidobacterial strains to their children shortly after birth. The transmitted strains predominate during early infancy, suggesting that maternal intestinal bifidobacteria are an important source of the infant gut microbiota. Accordingly, maintenance of a healthy, balanced gut microbiota during pregnancy has an important positive influence on the newborn gut microbiota.

Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?

Global comparisons reveal a decrease in gut microbiota diversity attributed to Western diets, lifestyle practices such as caesarian section, antibiotic use and formula-feeding of infants, and sanitation of the living environment. While gut microbial diversity is decreasing, the prevalence of chronic inflammatory diseases such as inflammatory bowel disease, diabetes, obesity, allergies and asthma is on the rise in Westernized societies. Since the immune system development is influenced by microbial components, early microbial colonization may be a key factor in determining disease susceptibility patterns later in life. Evidence indicates that the gut microbiota is vertically transmitted from the mother and this affects offspring immunity. However, the role of the external environment in gut microbiome and immune development is poorly understood. Studies show that growing up in microbe-rich environments, such as traditional farms, can have protective health effects on children. These health-effects may be ablated due to changes in the human lifestyle, diet, living environment and environmental biodiversity as a result of urbanization. Importantly, if early-life exposure to environmental microbes increases gut microbiota diversity by influencing patterns of gut microbial assembly, then soil biodiversity loss due to land-use changes such as urbanization could be a public health threat. Here, we summarize key questions in environmental health research and discuss some of the challenges that have hindered progress toward a better understanding of the role of the environment on gut microbiome development.

Pika Gut May Select for Rare but Diverse Environmental Bacteria

The composition of the mammalian gut bacterial communities can be influenced by the introduction of environmental bacteria in their respective habitats. However, there are no extensive studies examining the interactions between environmental bacteriome and gut bacteriome in wild mammals. Here, we explored the relationship between the gut bacterial communities of pika (Ochotona spp.) and the related environmental bacteria across host species and altitudinal sites using 16S rRNA gene sequencing. Plateau pikas (O. curzoniae) and Daurian pikas (O. daurica) were sampled at five different sites, and plant and soil samples were collected at each site as well. Our data indicated that Plateau pikas and Daurian pikas had distinct bacterial communities. The pika, plant and soil bacterial communities were also distinct. Very little overlap occurred in the pika core bacteria and the most abundant environmental bacteria. The shared OTUs between pikas and environments were present in the environment at relatively low abundance, whereas they were affiliated with diverse bacterial taxa. These results suggested that the pika gut may mainly select for low-abundance but diverse environmental bacteria in a host species-specific manner.

Gut Microbiotas and Host Evolution: Scaling Up Symbiosis

Our understanding of species evolution is undergoing restructuring. It is well accepted that host-symbiont coevolution is responsible for fundamental aspects of biology. However, the emerging importance of plant- and animal-associated microbiotas to their hosts suggests a scale of coevolutionary interactions many-fold greater than previously considered. This review builds on current understanding of symbionts and their contributions to host evolution to evaluate recent data demonstrating similar contributions of gut microbiotas. It further considers a multilayered model for microbiota to account for emerging themes in host-microbiota interactions. Drawing on the structure of bacterial genomes, this model distinguishes between a host-adapted core microbiota, and a flexible, environmentally modulated microbial pool, differing in constraints on their maintenance and in their contributions to host adaptation.

Nodavirus Colonizes and Replicates in the Testis of Gilthead Seabream and European Sea Bass Modulating Its Immune and Reproductive Functions

Viruses are threatening pathogens for fish aquaculture. Some of them are transmitted through gonad fluids or gametes as occurs with nervous necrosis virus (NNV). In order to be transmitted through the gonad, the virus should colonize and replicate inside some cell types of this tissue and avoid the subsequent immune response locally. However, whether NNV colonizes the gonad, the cell types that are infected, and how the immune response in the gonad is regulated has never been studied. We have demonstrated for the first time the presence and localization of NNV into the testis after an experimental infection in the European sea bass (Dicentrarchus labrax), and in the gilthead seabream (Sparus aurata), a very susceptible and an asymptomatic host fish species, respectively. Thus, we localized in the testis viral RNA in both species using in situ PCR and viral proteins in gilthead seabream by immunohistochemistry, suggesting that males might also transmit the virus. In addition, we were able to isolate infective particles from the testis of both species demonstrating that NNV colonizes and replicates into the testis of both species. Blood contamination of the tissues sampled was discarded by completely fish bleeding, furthermore the in situ PCR and immunocytochemistry techniques never showed staining in blood vessels or cells. Moreover, we also determined how the immune and reproductive functions are affected comparing the effects in the testis with those found in the brain, the main target tissue of the virus. Interestingly, NNV triggered the immune response in the European sea bass but not in the gilthead seabream testis. Regarding reproductive functions, NNV infection alters 17β-estradiol and 11-ketotestosterone production and the potential sensitivity of brain and testis to these hormones, whereas there is no disruption of testicular functions according to several reproductive parameters. Moreover, we have also studied the NNV infection of the testis in vitro to assess local responses. Our in vitro results show that the changes observed on the expression of immune and reproductive genes in the testis of both species are different to those observed upon in vivo infections in most of the cases.

Antimicrobial response is increased in the testis of European sea bass, but not in gilthead seabream, upon nodavirus infection

Antimicrobial peptides (AMPs) have a crucial role in the fish innate immune response, being considered a fundamental component of the first line of defence against pathogens. Moreover, AMPs have not been studied in the fish gonad since this is used by some pathogens as a vehicle or a reservoir to be transmitted to the progeny, as occurs with nodavirus (VNNV), which shows vertical transmission through the gonad and/or gonadal fluids, but no study has looked into the gonad of infected fish. In this framework, we have characterized the antimicrobial response triggered by VNNV in the testis of European sea bass, a very susceptible species of the virus, and in the gilthead seabream, which acts as a reservoir, both in vivo and in vitro, and compared with that present in the serum and brain (target tissue of VNNV). First, our data show a great antiviral response in the brain of gilthead seabream and in the gonad of European sea bass. In addition, for the first time, our results demonstrate that the antimicrobial activities (complement, lysozyme and bactericidal) and the expression of AMP genes such as complement factor 3 (c3), lysozyme (lyz), hepcidin (hamp), dicentracin (dic), piscidin (pis) or β-defensin (bdef) in the gonad of both species are very different, but generally activated in the European sea bass, probably related with the differences of susceptibility upon VNNV infection, and even differs to the brain response. Furthermore, the in vitro data suggest that some AMPs are locally regulated playing a local immune response in the gonad, while others are more dependent of the systemic immune system. Data are discussed in the light to ascertain their potential role in viral clearance by the gonad to avoid vertical transmission.

Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota

Objectives

Bifidobacterium species are one of the major components of the infant's intestine microbiota. Colonization with bifidobacteria in early infancy is suggested to be important for health in later life. However, information remains limited regarding the source of these microbes. Here, we investigated whether specific strains of bifidobacteria in the maternal intestinal flora are transmitted to their infant's intestine.

Materials and Methods

Fecal samples were collected from healthy 17 mother and infant pairs (Vaginal delivery: 12; Cesarean section delivery: 5). Mother's feces were collected twice before delivery. Infant's feces were collected at 0 (meconium), 3, 7, 30, 90 days after birth. Bifidobacteria isolated from feces were genotyped by multilocus sequencing typing, and the transitions of bifidobacteria counts in infant's feces were analyzed by quantitative real-time PCR.

Results

Stains belonging to Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium longum subsp. longum, and Bifidobacterium pseudocatenulatum, were identified to be monophyletic between mother's and infant's intestine. Eleven out of 12 vaginal delivered infants carried at least one monophyletic strain. The bifidobacterial counts of the species to which the monophyletic strains belong, increased predominantly in the infant's intestine within 3 days after birth. Among infants delivered by C-section, monophyletic strains were not observed. Moreover, the bifidobacterial counts were significantly lower than the vaginal delivered infants until 7 days of age.

Conclusions

Among infants born vaginally, several Bifidobacterium strains transmit from the mother and colonize the infant's intestine shortly after birth. Our data suggest that the mother's intestine is an important source for the vaginal delivered infant's intestinal microbiota.

Disturbance induced decoupling between host genetics and composition of the associated microbiome

BACKGROUND

Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host.

RESULTS

While the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains.

CONCLUSION

The decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.

Kin recognition in Drosophila: the importance of ecology and gut microbiota

The animal gut commonly contains a large reservoir of symbiotic microbes. Although these microbes have obvious functions in digestion and immune defence, gut microbes can also affect behaviour. Here, we explore whether gut microbiota has a role in kin recognition. We assessed whether relatedness, familiarity and food eaten during development altered copulation investment in three species of Drosophila with diverse ecologies. We found that a monandrous species exhibited true kin recognition, whereas familiarity determined kin recognition in a species living in dense aggregations. Finally, in a food generalist species, food eaten during development masked kin recognition. The effect of food type on copulation duration, in addition to the removal of this effect via antibiotic treatment, suggests the influence of bacteria associated with the gut. Our results provide the first evidence that varied ecologically determined mechanisms of kin recognition occur in Drosophila, and that gut bacteria are likely to have a key role in these mechanisms.

The intestinal microbiota in the rat model: major breakthroughs from new technologies

The mammalian intestine harbors a large and diverse community of micro-organisms, known as the intestinal microbiota. Recent developments in molecular profiling methods, mainly based on microbial 16S ribosomal RNA gene sequencing, have provided unprecedented insights into the make-up and diversity of intestinal microbial communities. Using these culture-independent analyses, gut microbiota of several mammals including laboratory rodents, have been revisited. The laboratory rat is one of the major species bred and kept for scientific research. Although this animal is bred in confined environments and subjected to procedures for satisfying health requirements that hamper natural colonization, some major features of mammalian gut microbiota are conserved. However, the gut microbiota varies according to the breeding conditions of the rats and this could impact reproducibility of the experimental models. Determining the non-pathogenic microbial community might be relevant in standards of quality control of laboratory animals. Molecular profiling techniques could be applied to document this information.

Influence of maternal bifidobacteria on the development of gut bifidobacteria in infants

Intestinal microbiota plays an important role in human health by influencing metabolic activities that result in the creation of energy and absorbable nutrients, a barrier to the colonization of pathogens, and stimulation of the immune system. The development of fecal microbiota in neonates is crucial because those bacteria are the first to colonize the sterile intestine of the neonates and, thus, have a significant effect on the host. Initial colonization is also relevant to the final composition of the permanent microbiota in adults. Bifidobacteria are predominant in the fecal microbiota of infants, and, therefore, they are important to an understanding of how commensal bifidobacteria is established in the intestine of infants. While the mother's bifidobacteria are considered to significantly influence the infant's bifidobacteria, it is not clear whether a specific bifidobacterial strain transmits vertically from mother to infant and what factors of the mother before delivery influence the establishment of intestinal bifidobacteria in infants. This review focuses on the impact of maternal bifidobacteria on the development of gut bifidobacteria in the infant and suggests that there is cumulative evidence regarding bifidobacterial transfer from the maternal gut or breast milk to the infant gut.

Transmission of intestinal Bifidobacterium longum subsp. longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism

The gastrointestinal tracts of neonates are colonized by bacteria immediately after birth. It has been discussed that the intestinal microbiota of neonates includes strains transferred from the mothers. Although some studies have indicated possible bacterial transfer from the mother to the newborn, this is the first report confirming the transfer of bifidobacteria at the strain level. Here, we investigated the mother-to-infant transmission of Bifidobacterium longum subsp. longum by genotyping bacterial isolates from the feces of mothers before delivery and of their infants after delivery. Two hundred seven isolates from 8 pairs of mothers and infants were discriminated by multilocus sequencing typing (MLST) and amplified fragment length polymorphism (AFLP) analysis. By both methods, 11 strains of B. longum subsp. longum were found to be monophyletic for the feces of the mother and her infant. This finding confirms that these strains were transferred from the intestine of the mother to that of the infant. These strains were found in the first feces (meconium) of the infant and in the feces at days 3, 7, 30, and 90 after birth, indicating that they stably colonize the infant's intestine immediately after birth. The strains isolated from each family did not belong to clusters derived from any of the other families, suggesting that each mother-infant pair might have unique family-specific strains.

Evolutionary relationships of wild hominids recapitulated by gut microbial communities

Although bacteria are continually acquired over the lifetime of an individual, the phylogenetic relationships of great ape species is mirrored in the compositions of their gut microbial communities.

Multiple factors over the lifetime of an individual, including diet, geography, and physiologic state, will influence the microbial communities within the primate gut. To determine the source of variation in the composition of the microbiota within and among species, we investigated the distal gut microbial communities harbored by great apes, as present in fecal samples recovered within their native ranges. We found that the branching order of host-species phylogenies based on the composition of these microbial communities is completely congruent with the known relationships of the hosts. Although the gut is initially and continuously seeded by bacteria that are acquired from external sources, we establish that over evolutionary timescales, the composition of the gut microbiota among great ape species is phylogenetically conserved and has diverged in a manner consistent with vertical inheritance.

The microbial communities that inhabit the gastrointestinal tract of humans and other mammals are complex, dynamic, and critical to both health and disease. The composition and constituents of these communities are influenced by multiple factors such as host diet, geography, physiology, and disease state. Given the central role of the gut microbiota in the physiology of the host, it is important to determine whether it is predictable and substantially determined by the host, or variable and largely determined by the external environment (including diet) experienced by the host. A valuable way of determining the relative contributions of such factors is by comparing gut microbial communities in closely related host species. Applying a high-throughput sequencing approach, we profiled the distal gut microbiotae of great ape species sampled in their native ranges and then employed a parsimony-based analysis of phylogenetically informative phylotypes (i.e., bacterial taxa residing in multiple individuals) to determine the relationships among the diverse microbial communities. Our analyses revealed a clear species-specific signature of microbial community structure. Moreover, the pattern of relationships among the five great ape species (Homo sapiens, Pan troglodytes, P. paniscus, Gorilla gorilla, and G. beringei) inferred from their fecal microbial communities was identical to that inferred from host mitochondrial DNA, indicating that host phylogeny shapes the gut microbiota over evolutionary timescales. It seems after all that you are not what you eat.

Health-beneficial effects of probiotics: Its mode of action

It is now widely recognized that probiotics have health-beneficial effects on humans and animals. Probiotics should survive in the intestinal tract to exert beneficial effects on the host's health. To keep a sufficient level of probiotic bacteria in the gastrointestinal tract, a shorter interval between doses may be required. Although adherence to the intestinal epithelial cell and mucus is not a universal property of probiotics, high ability to adhere to the intestinal surface might strongly interfere with infection of pathogenic bacteria and regulate the immune system. The administration of probiotic Lactobacillus stimulated indigenous Lactobacilli and the production of short-chain fatty acids. This alteration of the intestinal environment should contribute to maintain the host's health. The immunomodulatory effects of probiotics are related to important parts of their beneficial effects. Probiotics may modulate the intestinal immune response through the stimulation of certain cytokine and IgA secretion in intestinal mucosa. The health-beneficial effects, in particular the immunomodulation effect, of probiotics depend on the strain used. Differences in indigenous intestinal microflora significantly alter the magnitude of the effects of a probiotic. Specific probiotic strains suitable for each animal species and their life stage as well as each individual should be found.

Development of intestinal microbiota in mice and its possible interaction with the evolution of luminal IgA in the intestine

The development of the intestinal microbiota and the evolution of the fecal IgA in mice were analyzed from 18 to 40 days old by PCR temperature gradient gel electrophoresis (TGGE) and ELISA, respectively. There were two events for the diversification of the intestinal microbiota from suckling to maturity. The first change occurred between days 21 and 22 after birth, when the diversity of the intestinal microbiota showed a remarkable increase at this time. The second change occurred from days 27 to 30 after birth, and the increase in the diversity of the intestinal microbiota ceased. The amount of fecal IgA decreased from days 18 to 20, remained low until day 22, on day 23, it recovered and then continued to increase. This study suggests that there are possible interactions between the development of intestinal microbiota and the evolution of intestinal secretion of IgA in mice, the same as in rats, although the second change in mice intestinal microbiota occurred a few days later than in rats. The decline in maternal IgA supply as the suckling period proceeded presumably allowed the bacterial colonization. As a consequence of this increase in bacterial colonization, the secretion of the self-SIgA was accelerated in the pups.

Molecular analyses of the intestinal microbiota of chimpanzees in the wild and in captivity

Little information is available regarding the intestinal bacteria of chimpanzees in the wild, due to the technical difficulties of studying intestinal bacteria in the field. In this study, molecular-based bacterial analyses were performed to overcome this difficulty because polymerase chain reaction (PCR)-based methods, such as temperature gradient gel electrophoresis (TGGE) and amplified ribosomal DNA restriction analysis (ARDRA), of the bacterial 16S rRNA gene can be applied to ethanol-fixed fecal samples. The common presence of bacteria belonging to the Clostridium rRNA sub-group XIVa, such as Ruminococcus obeum and Eubacterium sp., was indicated for Bossou wild chimpanzees by ARDRA. TGGE on partial 16S rDNA followed by hierarchical clustering analysis showed a systematic difference in the composition of intestinal microbiota between wild and captive chimpanzees. However, several TGGE bands commonly shared by wild and captured chimpanzees were excised, and their sequences were obtained. They were suggested to be the Clostridium leptum subgroup bacteria, Lactobacillus gasseri-like bacterium, and Bifidobacterium pseudocatenulatum- or B. catenulatum-like bacterium. These may be considered as common intestinal bacteria for chimpanzees, and may be transmitted vertically over generations.

Stimulation of Indigenous Lactobacilli by Fermented Milk Prepared with Probiotic Bacterium, Lactobacillus delbrueckii subsp. bulgaricus Strain 2038, in the Pigs

The aim of this study was to evaluate the effect of feeding yoghurt, prepared with Lactobacillus delbrueckii subsp. bulgaricus strain 2038, on indigenous lactobacilli in the pig cecum. Three female pigs fistulated at the cecum were fed 250 g of this yoghurt that contained over 10(11) colony-forming units of L. delbrueckii subsp. bulgaricus strain 2038 with their daily meal for 2 wk. The relative abundance and the composition of cecal lactobacilli was monitored by analysis of bacterial 16S rDNA with real time PCR and amplified bacterial rDNA restriction analysis using Lactobacillus-group specific primers, respectively, for 2 wk prior to, at the end of 2 wk of and 2 wk after the administration of this yoghurt. The relative abundance of lactobacilli was significantly increased by feeding yoghurt (p<0.01), although the bacterial 16S rDNA matching L. delbrueckii subsp. bulgaricus strain 2038 was not detected by amplified bacterial rDNA restriction analysis during this study. The number of operational taxonomic units (OTUs) detected was increased with feeding of the yoghurt in all pigs. At the same time, the estimated cell number of each OTU was increased with feeding of the yoghurt. It is demonstrated that continuous consumption of the probiotic lactobacilli will stimulate the growth of some indigenous lactobacilli and alter the composition of the lactobacilli.

The Organic Acid Profiles in the Feces of Pigs at Brachyspira hyodysenteriae-or B. pilosicoli-Positive Farms

We observed a significant difference in the organic acid profile of diarrheal feces between pigs infected with and free from pathogenic spirochetes. Diarrhea and loose feces were collected from growing pigs, held at 15 different commercial farms. A total of 106 samples were measured for organic acid concentration by HPLC and were checked for the presence of B. hyodysenteriae and B. pilosicoli by PCR. B. hyodysenteriae was detected in 3 samples collected from one farm. B. pilosicoli was detected in 5 samples collected from another farm. Lower concentrations of iso-butyrate and iso-valerate were likely associated with development of pathogenic spirochete infection.

Detection of methanogens and proteobacteria from a single cell of rumen ciliate protozoa

Rumen ciliate-associated bacteria and methanogenic archaea were analyzed by a 16S rRNA gene retrieved from a single cell of Polyplastron multivesiculatum, Isotricha intestinalis, and Ophryoscolex purkynjei. Rumen fluid was taken from a ruminally fistulated goat to prepare a ciliate fraction. Ciliate mixtures were incubated under mixtures of antibiotics for 48 h to eliminate extracellular bacteria. Individual cells of rumen ciliates were selected under microscopic observation after fixation with ethanol. Bacterial and archaeal 16S rRNA gene sequences were retrieved from each cell of three genera of ciliate. Two archaeal sequences related to Methanobrevibacter smithii were distributed to nearly all ciliate cells tested. These two methanogenic archaea were likely to be endosymbiotic methanogens commonly carried by the rumen ciliate, although some other sequences similar to the other genera were detected. A range of proteobacteria was retrieved from cells of P. multivesiculatum. Some sequences showed similarities to the previously known endosymbiotic proteobacteria. However, there were no proteobacteria that were carried by all the ciliate cells tested.