Effects of Microbiota on GI Health: Gnotobiotic Research

Gut microbiome-targeted therapies and bone health across the lifespan: a scoping review

Emerging evidence suggests that bone turnover is influenced by the gut microbiome through critical bone signaling pathways. The purpose of this scoping review is to examine prebiotic, probiotic, and synbiotic interventions on bone outcomes in humans across the lifespan. PubMed, Scopus, and EBSCOhost were searched until January 2023 to identify clinical trials examining bone mineral density (BMD) or bone mineral content (BMC) with gut microbiome interventions. Of three prebiotic interventions, one reported higher areal BMD (aBMD) in adolescents. In two studies in postmenopausal women, no changes in aBMD were observed despite decreased biomarkers of bone resorption. Probiotic interventions in perimenopausal or postmenopausal women demonstrated increased aBMD or attenuated bone loss in various bone regions. All studies observed attenuated bone loss (n = 4) or increased aBMD (n = 1). One study assessed a synbiotic intervention on aBMD and observed decreased biomarkers of bone resorption but no changes in aBMD. Results suggest potential for microbiome-targeted therapies (prebiotics, probiotics and synbiotics) to attenuate bone loss. However, changes in biomarkers of bone turnover were not always accompanied by changes in bone mineralization. Future studies should utilize longer duration interventions to investigate the influence of prebiotic, probiotic, and synbiotic interventions across diverse age, sex, and ethnic cohorts.

SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data

Assessment of bioinformatics tools for the metagenomics analysis from the whole genome sequencing data requires realistic benchmark sets. We developed an effective and simple generator of artificial metagenomes from real sequencing experiments. The tool (SEQ2MGS) analyzes the input FASTQ files, precomputes genomic content, and blends shotgun reads from different sequenced isolates, or spike isolate(s) in real metagenome, in desired proportions. SEQ2MGS eliminates the need for simulation of sequencing platform variations, reads distributions, presence of plasmids, viruses, and contamination. The tool is especially useful for a quick generation of multiple complex samples that include new or understudied organisms, even without assembled genomes. For illustration, we first demonstrated the ease of SEQ2MGS use for the simulation of altered Schaedler flora (ASF) in comparison with de novo metagenomics generators Grinder and CAMISIM. Next, we emulated the emergence of a pathogen in the human gut microbiome and observed that Kraken, Centrifuge, and MetaPhlAn, while correctly identified Klebsiella pneumoniae, produced inconsistent results for the rest of real metagenome. Finally, using the MG-RAST platform, we affirmed that SEQ2MGS properly transfers genomic information from an isolate into the simulated metagenome by the correct identification of antimicrobial resistance genes anticipated to appear compared to the original metagenome.

Differential Immune Response of Lactobacillus plantarum 286 Against Salmonella Typhimurium Infection in Conventional and Germ-Free Mice

We aimed at evaluating in vivo the probiotic potential of Lactobacillus plantarum 286 against Salmonella enterica serov. Typhimurium. Colonization capacity and antagonistic activity were determined in feces of gnotobiotic mice. Survival to infection, translocation, histopathology, IgA and cytokine levels (IL-10, IL-6, IFN-γ, TNF-α, TGF-β) were determined both in conventional and germ-free mice followed L. plantarum 286 administration and Salmonella infection. L. plantarum 286 colonized the intestine of gnotobiotic mice, where it produced antagonistic substances against S. Typhimurium. In conventional animals, the administration of this strain increased intestinal IgA levels and reduced the inflammatory response and the tissue damage caused by S. Typhimurium. Reduction of tissue damage in the intestine and liver of germ-free animals was also observed, however the immune response elicited was different in either model. L. plantarum 286 showed in vivo probiotic properties in both murine models. Probiotic capacity results may depend on the animal model chosen.

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets

BACKGROUND

Immediately after birth, the porcine intestine rapidly develops morphologically, functionally, and immunologically. The jejunum, the second part of the small intestine, is of importance for nutrient uptake and immune surveillance. To study the early postnatal development of the jejunum, a meta-analysis was performed on different transcriptomic datasets. These datasets were acquired from different experimental in-house studies or from experiments described in literature of porcine jejunum mucosa. Gene expression was measured under different experimental interventions, such as nutritional intervention, at various time-points (age).

RESULTS

The studies included in the meta-analysis provided gene expression data for various time-points (piglet ages) for piglets that had received a treatment versus control piglets. In separate studies, treatments were administered to the sow (i.e. amoxicillin), or nutritional supplementation directly to the piglets with medium chain fatty acids (MCFAs), and oral administration of fructooligosaccharides (FOS) or a high dose of zinc-oxide, respectively. In the meta-analysis, genes were grouped into 16 clusters according to their temporal gene expression profiles for control piglets, i.e. the changes of gene expression level over time. Functional analysis showed that these temporal profile clusters had different dominant processes, such as immune related processes or barrier function. Transcriptomics data of treatment piglets was subsequently superimposed over the control temporal profiles. In this way we could investigate which temporal profile clusters (and which biological processes) were modulated by the treatments. Interestingly, not all 16 temporal profiles were modulated.

CONCLUSIONS

We showed that it is possible to re-use (publicly available) transcriptomics data and produce temporal gene expression profiles for control piglets with overexpression of genes representing specific biological processes. Subsequently, by superimposing gene expression data from (nutritional) intervention studies we observed deviations from some of these reference profile(s) and thus the plasticity of the system. By employing this meta-analysis approach we highlighted the importance of birth and weaning and the underlying biological processes.

An Okinawan-based Nordic diet improves glucose and lipid metabolism in health and type 2 diabetes, in alignment with changes in the endocrine profile, whereas zonulin levels are elevated

The Okinawan-based Nordic diet has been developed to improve glucose metabolism. The aim of the present study was to summarize all anthropometric, subjective, and biochemical findings obtained following two different studies investigating this diet. The diet was administered i) as a single breakfast to healthy volunteers and ii) as a 12-week dietary intervention to patients with type 2 diabetes. The degree of satiety, sweet cravings, gastrointestinal symptoms, and health-related quality of life were estimated. Weight and blood pressures of participants were measured, and analyses including circulating levels of inflammatory and metabolic biomarkers, hormones, and short-chain fatty acids (SCFA), and microbial diversity and amount of Enterobacteriaceae in feces, were performed. A single breakfast of the diet increased satiety (P<0.001), improved glucose homeostasis (P<0.001), and lowered levels of glucose-dependent insulinotropic polypeptide (GIP) (P=0.002), compared with a standard breakfast. A 12-week intervention in type 2 diabetes increased satiety and decreased sweet cravings, at the same time as health-related quality of life and gastrointestinal symptoms were improved. There were reductions in body mass index (P<0.001), waist circumference (P<0.001), and levels of glucose (P<0.001), cholesterol (P<0.001), and triglycerides (P=0.009), in alignment with the endocrine profile. These improvements were maintained at follow-up 16 weeks later, along with lower levels of ghrelin (P=0.012), polypeptide YY (P=0.002), and visfatin (P=0.021), compared with the parameters recorded at the study start. Levels of haptoglobin, interleukin-18 and thrombocytes were lowered, whereas some other inflammatory biomarkers were unaffected and zonulin levels elevated. Gut microbiota and SCFAs levels were mainly unaffected. The mechanisms governing the anthropometric and metabolic improvements appear to be mediated through alterations in the endocrine profile, yet not in the gut microbiota.

Caulerpa lentilliferapolysaccharides enhance the immunostimulatory activity in immunosuppressed mice in correlation with modulating gut microbiota

Caulerpa lentilliferapolysaccharides could serve as novel prebiotics and immunostimulators, since they improve the immune-related factors and modulate the gut microbiota in cytoxan-induced immunosuppressed mice.

The effect of storage at ambient temperature on the feline fecal microbiota

BACKGROUND

Feline fecal microbiota analyses can potentially be impacted by a variety of factors such as sample preparation, sequencing method and bioinformatics analyses. Another potential influence is changes in the microbiota from storage of samples prior to processing. This study examined the effect of ambient temperature exposure on the feline fecal microbiota composition. Fecal samples were collected from 12 healthy cats, within 15 min after defecation. Samples were aliquoted and the first aliquot was frozen at -80 °C within 1 hour of defecation. Remaining aliquots were maintained at ambient temperature (20 to 23 °C) and frozen at -80 °C at 6, 12, 24, 36, 48, 72 and 96 h after collection. DNA was extracted from all aliquots, and polymerase chain reaction (PCR). The PCR products were sequenced with next-generation sequencing (Illumina MiSeq).

RESULTS

No significant differences were observed in alpha and beta biodiversity indexes, as well as relative abundance of different taxa over time (P > 0.05 for all tests between time points). Principal coordinate analyses demonstrated that samples cluster mainly by cat, with no significant differences between time points (AMOVA, P > 0.05; HOMOVA, P > 0.05). Linear discriminant analysis effect size method was performed and failed to detect any enriched taxa, between time points. Random forest algorithm analysis indicated homogeneity across time points.

CONCLUSIONS

Although existing evidence from human fecal storage studies is contradictory, a recent study in companion animals agreed with the current study, demonstrating that maintenance of feline fecal samples at ambient temperature for up to 4 days has no effect on the bacterial membership and structure.

Hypotheses of the origin of natural antibodies: a glycobiologist's opinion

It is generally accepted that the generation of antibodies proceeds due to immunization of an organism by alien antigens, and the level and affinity of antibodies are directly correlated to the presence of immunogen. At the same time, vast experimental material has been obtained providing evidence of antibodies whose level remains unchanged and affinity is constant during a lifetime. In contrast to the first, adaptive immunoglobulins, the latter are named natural antibodies (nAbs). The nAbs are produced by B1 cells, whereas adaptive Abs are produced by B2. This review summarizes general data on nAbs and presents in more detail data on antigens of carbohydrate origin. Hypotheses on the origin of nAbs and their activation mechanisms are discussed. We present our thoughts on this matter supported by our experimental data on nAbs to glycans.

Effect of in ovo-delivered prebiotics and synbiotics on the morphology and specific immune cell composition in the gut-associated lymphoid tissue

The purpose of this study was to examine how pre- and synbiotic administration in ovo into the air chamber at d 12 of egg incubation influenced the specific immune cell composition and distribution in the ileum, cecal tonsils (CT) and bursa of Fabricius of broilers. The experiment was performed on 800 hatching eggs of the meat-type chickens (Ross 308). Hatching eggs were treated with: prebiotic, consisting of inulin (Pre1) or Bi(2)tos(®) (Pre2); symbiotic, composed of inulin and Lactococcus lactis subsp. lactis IBB SL1 (Syn1) or Bi(2)tos and Lactococcus lactis subsp. cremoris IBB SC1 (Syn2); or physiological saline as a control group. Seven chickens from each treatment group were randomly selected on , 1, 7, and 21 after hatch for tissue collection. Ileum, cecal tonsil and bursa of Fabricius samples were immunohistochemically stained and the proportions of Bu-1(+), CD3(+), CD4(+), CD8α(+) and TCRγδ(+) cells were estimated. It was indicated that the pre- and synbiotics do not adversely affect the development of the GALT of the chicken. The temporary decrease in B-cell number in bursa on d 7 after hatch suggested an increased colonization rate of the peripheral lymphoid organs by these cells after Pre1, Pre2, and Syn2 treatment. In CT at d 7 after hatch more potent colonization of the GALT by T cells was observed in all pre- and synbiotic treated groups and by B cells in both synbiotic-treated groups than those in respective controls. Then, on d 21 in both synbiotic-treated groups, an increase in T-cell number in ileum was also noticed with faster colonization of the CT by B cells. In 21-day-old chickens, both synbiotics exerted stronger stimulatory effect on the GALT colonization by T cells then prebiotics respectively. Similarly, the colonization by B cells was more pronounced in the Syn2 than in the Pre2 group. The data obtained in this study indicated that prebiotics and particularly synbiotics administrated in ovo stimulated GALT development after hatch.

Human norovirus infection and the acute serum cytokine response

Noroviruses (NoV) are the most common cause of epidemic gastroenteritis worldwide. The acute immune response to NoV in humans is poorly understood, hindering research on prevention and treatment. To elucidate the acute immune response and test for cytokine predictors of susceptibility to infection, serum samples from two human NoV challenge studies were tested for 16 cytokines. Subjects who became infected (n = 26) were age-matched with subjects who remained uninfected following NoV challenge (n = 26). Samples were tested from prechallenge and days 1-4 post-challenge. Cytokine responses were compared between infected and uninfected groups. Overall, infected individuals exhibited an elevation in T helper type 1 (Th1) and Th2 cytokines, as well as chemokines interleukin (IL)-8 and monocyte chemoattractant protein (MCP-1), compared to uninfected individuals (all P < 0.05). Most cytokines peaked on day 2 post-challenge in infected subjects, and tumour necrosis factor (TNF)-α, IL-8, and IL-10 remained elevated to day 3. The only cytokine elevated significantly among infected subjects to day 4 post-challenge was IL-10 (P = 0.021). Prechallenge cytokine concentrations were not predictive of infection status post-challenge. There were no significant changes in serum cytokines among NoV-challenged subjects who remained uninfected. These results suggest that NoV infection elicits a Th1-type response, with some Th2 activation. Persistent elevation of IL-10 among infected subjects is consistent with activation of adaptive immune responses, such as B cell expansion, as well as down-regulation of Th1 cytokines. This study presents the first comprehensive description of the acute cytokine response to GI.1 NoV in humans.

Long-lasting effects of early-life antibiotic treatment and routine animal handling on gut microbiota composition and immune system in pigs

BACKGROUND

In intensive pig husbandry systems, antibiotics are frequently administrated during early life stages to prevent respiratory and gastro-intestinal tract infections, often in combination with stressful handlings. The immediate effects of these treatments on microbial colonization and immune development have been described recently. Here we studied whether the early life administration of antibiotics has long-lasting effects on the pig's intestinal microbial community and on gut functionality.

METHODOLOGY/PRINCIPAL FINDINGS

To investigate the long-lasting effect of early-life treatment, piglets were divided into three different groups receiving the following treatments: 1) no antibiotics and no stress, 2) antibiotics and no stress, and 3) antibiotics and stress. All treatments were applied at day four after birth. Sampling of jejunal content for community scale microbiota analysis, and jejunal and ileal tissue for genome-wide transcription profiling, was performed at day 55 (~8 weeks) and day 176 (~25 weeks) after birth. Antibiotic treatment in combination with or without exposure to stress was found to have long-lasting effects on host intestinal gene expression involved in a multitude of processes, including immune related processes.

CONCLUSIONS/SIGNIFICANCE

The results obtained in this study indicate that early life (day 4 after birth) perturbations have long-lasting effects on the gut system, both in gene expression (day 55) as well as on microbiota composition (day 176). At day 55 high variance was observed in the microbiota data, but no significant differences between treatment groups, which is most probably due to the newly acquired microbiota during and right after weaning (day 28). Based on the observed difference in gene expression at day 55, it is hypothesized that due to the difference in immune programming during early life, the systems respond differently to the post-weaning newly acquired microbiota. As a consequence, the gut systems of the treatment groups develop into different homeostasis.

Effects of synbiotics injected in ovo on regulation of immune-related gene expression in adult chickens

OBJECTIVE

To determine immunomodulatory effects of synbiotics administered in ovo on immune-related gene expression in adult chickens.

ANIMALS

30 Green-legged Partridgelike chickens.

PROCEDURES

On incubation day 12, eggs were injected with 3 synbiotics (Lactococcus lactis subsp lactis IBB SL1 with raffinose family oligosaccharides [RFOs; S1], Lactococcus lactis subsp cremoris IBB SC1 with RFOs [S2], and Lactobacillus acidophilus and Streptococcus faecium with lactose [S3]). Control eggs were injected with RFOs prebiotic or saline (0.9% NaCl) solution. Gene expression of 6 cytokines (interleukin [IL]-4, IL-6, IL-12p40, IL-18, interferon [IFN]-β, and IFN-γ) and 1 chemokine (IL-8) was analyzed in the cecal tonsils and spleen of 6-week-old chickens by means of reverse transcription quantitative PCR assays.

RESULTS

Gene expression for IL-4, IL-6, IFN-β, and IL-18 was significantly upregulated in the spleen of chickens in groups S2 and S3. In contrast, IL-12 expression was downregulated in group S2 and IFN-γ expression was downregulated in group S3. Expression of IL-8 did not change in chickens treated with synbiotics in ovo. Gene expression of all cytokines, except for IL-18, was downregulated in cecal tonsils.

CONCLUSIONS AND CLINICAL RELEVANCE

In ovo administration of synbiotics activated the immune system in adult chickens. The intestinal immune system (cecal tonsils) had downregulation of expression for the cytokines evaluated, which indicated an increase in oral tolerance, whereas in the peripheral part of the immune system (spleen), expression of IL-4 and IL-6 was upregulated. Evaluation of immune-related gene expression patterns may be useful when monitoring the effectiveness of synbiotic selection with respect to immunobiotic properties.

New insights and challenges in microscopic colitis

Microscopic colitis (MC) is described as an inflammatory bowel disease characterized by chronic, bloodless diarrhea with normal or close to normal endoscopic findings. Histopathological examination reveals two subtypes: collagenous colitis (CC) and lymphocytic colitis (LC), which are indistinguishable clinically. The disease debuts typically in middle-aged patients, but can occur at all ages, including children. A female predominance is found in both CC and LC, but is not confirmed by others in LC. The etiology is unclear, but the disease has been assumed to be of autoimmune origin. However, several etiologies may render a microscopic inflammation in the mucosa; this is a common, universal reaction to a variety of irritants in contact with the intestinal lumen. Furthermore, some patients with a microscopic inflammation in their colonic mucosa have no symptoms, or are suffering from constipation or abdominal pain, rather than diarrhea. Recently, a discussion was initiated calling into question the overdiagnosing of symptoms and pointing out the danger of exacerbating people's perception of their ailments, of weakening their eligibility in health insurance, of overprescription of drugs, and thus the increasing cost to the society of health care. In the light of this discussion, this review will highlight histopathological and clinical features of MC, and discuss the diagnosis and management of this disease. Perhaps, the intestinal mucosa has no other mode by which to react than an inflammatory response, irrespective of the presence or absence of autoimmunity. Thus, to better identify and classify subgroups of MC, and to clarify and correctly handle the inflammatory changes, this field of research stands to benefit from a review of the results and experience gained to date.

Immune-directed support of rich microbial communities in the gut has ancient roots

The animal gut serves as a primary location for the complex host-microbe interplay that is essential for homeostasis and may also reflect the types of ancient selective pressures that spawned the emergence of immunity in metazoans. In this review, we present a phylogenetic survey of gut host-microbe interactions and suggest that host defense systems arose not only to protect tissue directly from pathogenic attack but also to actively support growth of specific communities of mutualists. This functional dichotomy resulted in the evolution of immune systems much more tuned for harmonious existence with microbes than previously thought, existing as dynamic but primarily cooperative entities in the present day. We further present the protochordate Ciona intestinalis as a promising model for studying gut host-bacterial dialogue. The taxonomic position, gut physiology and experimental tractability of Ciona offer unique advantages in dissecting host-microbe interplay and can complement studies in other model systems.

Early-life environmental variation affects intestinal microbiota and immune development in new-born piglets

Background

Early-life environmental variation affects gut microbial colonization and immune competence development; however, the timing and additional specifics of these processes are unknown. The impact of early-life environmental variations, as experienced under real life circumstances, on gut microbial colonization and immune development has not been studied extensively so far. We designed a study to investigate environmental variation, experienced early after birth, to gut microbial colonization and intestinal immune development.

Methodology/Principal Findings

To investigate effects of early-life environmental changes, the piglets of 16 piglet litters were divided into 3 groups per litter and experimentally treated on day 4 after birth. During the course of the experiment, the piglets were kept with their mother sow. Group 1 was not treated, group 2 was treated with an antibiotic, and group 3 was treated with an antibiotic and simultaneously exposed to several routine, but stressful management procedures, including docking, clipping and weighing. Thereafter, treatment effects were measured at day 8 after birth in 16 piglets per treatment group by community-scale analysis of gut microbiota and genome-wide intestinal transcriptome profiling. We observed that the applied antibiotic treatment affected the composition and diversity of gut microbiota and reduced the expression of a large number of immune-related processes. The effect of management procedures on top of the use of an antibiotic was limited.

Conclusions/Significance

We provide direct evidence that different early-life conditions, specifically focusing on antibiotic treatment and exposure to stress, affect gut microbial colonization and intestinal immune development. This reinforces the notion that the early phase of life is critical for intestinal immune development, also under regular production circumstances.

Smoking- and alcohol habits in relation to the clinical picture of women with microscopic colitis compared to controls

Background

Microscopic colitis (MC) induces gastrointestinal symptoms, which are partly overlapping with irritable bowel syndrome (IBS), predominately in middle-aged and elderly women. The etiology is unknown, but association with smoking has been found. The aim of this study was to examine whether the increased risk for smokers to develop MC is a true association, or rather the result of confounding factors. Therefore, patients suffering from MC and population-based controls from the same geographic area were studied regarding smoking- and alcohol habits, and other simultaneous, lifestyle factors, concerning the clinical expression of the disease.

Methods

Women at the age of 73 years or younger, who had been treated for biopsy-verified MC at any of the Departments of Gastroenterology in Skåne, between 2002 and 2010, were invited to the study (240 patients). Women (737) from the population-based prospective cohort study, Malmö Diet and Cancer Study (MDCS), served as controls. A self-administered questionnaire about lifestyle factors, gastrointestinal symptoms, medical conditions and medication at the time for the study was sent by post.

Results

Altogether, 131 women with MC could be included after age-matching with controls (median age 56 years) and exclusion of secondary MC. Patients were divided into persistent MC (MC1) and transient MC (MC2). Past smoking was associated with increased risk to develop MC2 (OR = 2.67, 95 CI = 1.15–6.23), whereas current smoking was associated with increased risk to develop MC1 (OR = 3.18, 95 CI = 1.57–6.42). Concomitant symptoms of IBS were associated with smoking (OR = 4.24, 95 CI = 1.92–9.32). Alcohol drinking had no association with MC or IBS.

Conclusions

The results suggest that past smoking is associated with transient MC, whereas current smoking is associated with persistent MC. Smoking is associated with MC patients with concomitant IBS-like symptoms.

Effects of Lactobacillus kefiranofaciens M1 isolated from kefir grains on germ-free mice

Lactobacillus kefiranofaciens M1 is a novel probiotic strain that was isolated from kefir grains. Previously, we have demonstrated the immunoregulatory, anti-allergic, anti-asthmatic and anti-colitis abilities of L. kefiranofaciens M1 in a number of in-vitro and in-vivo experiments. However, whether the effects of L. kefiranofaciens M1 are elicited directly on the host or act by regulating the host's microbiota remains unknown. A number of studies have used germ-free or gnotobiotic animals to investigate the relationship between probiotics and colitis; therefore the aim of this study was to investigate the effects of L. kefiranofaciens M1 on germ-free mice. Such an approach should help in determining the direct effects of L. kefiranofaciens M1 on the host itself. Four-week-old female germ-free mice were inoculated intragastrically with 2×10(8) CFU/mouse L. kefiranofaciens M1 once or at 2-day intervals for 14 days. Bacterial colonization, the Th1/Th2 cytokine profile of the mice's splenocytes and the anti-colitis effect of L. kefiranofaciens M1 were investigated. The strongest response in terms of splenic Th1 cytokine IFN-γ and IL-12 production upon TLR activation was detected in the continuous treatment group when comparing to the single inoculation group and the germ-free control. In addition, continuous inoculation with L. kefiranofaciens M1 was found to ameliorate the symptoms of DSS-induced colitis in germ-free mice. However, L. kefiranofaciens M1 failed to colonize the host. Thus it would seem that L. kefiranofaciens M1 is likely to act directly on the host and not be involved in microbiota regulation.

Behavior of lactobacilli isolated from fermented slurry (ben-saalga) in gnotobiotic rats

Most bacterial strains, which have been studied so far for their probiotic functions, are extensively used by manufacturers in developed countries. In our work, we sought to study a mix (called BSL) comprising three strains belonging to Lactobacillus fermentum, L. paraplantarum and L. salivarius, that were isolated from a traditional African pearl millet based fermented slurry. Our objective was to study this BSL cocktail in gnotobiotic rats, to evaluate their survival and their behavior in the digestive tract conditions. After a single oral inoculation of germfree rats with BSL, the species established stably in the digestive tract with the following hierarchy of abundance: L. salivarius> L. plantarum> L. fermentum. BSL cocktail was metabolically active since it produced 50 mM lactate and it expressed genes involved in binding mechanism in the caecum. Furthermore, the global morphology of the colon epithelium was not disturbed by the BSL cocktail. BSL cocktail did not modify mucus content and host mucus-related genes (MUC1, MUC2, MUC3 or resistin-like molecule β). The cocktail of lactobacilli enhanced the proliferating cell nuclear antigen (PCNA) at a level comparable to what was observed in conventional rats. PCNA was involved in proliferation and DNA repair, but the presence of the cocktail did not provoke proliferative events (with Ki67 as indicator), so we suppose BSL may help gut preservation. This work is the first step towards the selection of strains that are derived from traditional fermented food to formulate new probiotic mixture.

Probiotics - do they have a role in the pig industry?

The delivery of certain living microorganisms in food has long been suggested as having positive health effects in humans. This practice has extended into food animal production, with a variety of microorganisms being used; lactic acid bacteria, various Bacillus species and the yeast Saccharomyces cerevisiae have been particularly used in the pig industry. The increased interest in probiotics is essentially due to the problem of microbial resistance to antibiotics and following the ban of the use of antibiotics in animal production, probiotics being considered an alternative means to reduce pathogen infection and improve animal health especially around the time of weaning. However, there is still a need to clarify the probiotic effectiveness in pigs, and the underlying mechanisms. When assessing the efficacy of probiotics one must consider the particular strain of organism being used and the production stage of the pigs being treated. The reproducible delivery of probiotics in industrial pig production is problematic as maintenance of viability is key to their beneficial activity, but difficult to achieve with commonly used feed processing technologies. One specific context where probiotics organisms may be reliably delivered is in systems utilising fermented liquid feeds. Liquid feed may be fermented by the activity of wild lactic acid bacteria or may be stimulated using specific isolates as 'starters'; the latter system has advantages in terms of reproducibility and speed of fermentation. The farm context in which the organism is used is likely to be critical; the use of probiotics is more likely to result in measurable economic gains in animals living in sub-optimal conditions rather than in those reared in the highest welfare and husbandry conditions. The establishment of a beneficial lactic acid bacteria population at birth may lead to healthier animals, this may be most effectively achieved by treating sows, which provide an amplification step and flood the neonatal pigs' environment with desirable bacterial strains. In contrast, it may be sufficient to provide a supportive, protective microbiota around the time of weaning as this is a time of major crisis with instability and loss of certain bacterial populations.

Sex effects on neurodevelopmental outcomes of innate immune activation during prenatal and neonatal life

Humans are exposed to potentially harmful agents (bacteria, viruses, toxins) throughout our lifespan; the consequences of such exposure can alter central nervous system development. Exposure to immunogens during pregnancy increases the risk of developing neurological disorders such as schizophrenia and autism. Further, sex hormones, such as estrogen, have strong modulatory effects on immune function and have also been implicated in the development of neuropathologies (e.g., schizophrenia and depression). Similarly, animal studies have demonstrated that immunogen exposure in utero or during the neonatal period, at a time when the brain is undergoing maturation, can induce changes in learning and memory, as well as dopamine-mediated behaviors in a sex-specific manner. Literature that covers the effects of immunogens on innate immune activation and ultimately the development of the adult brain and behavior is riddled with contradictory findings, and the addition of sex as a factor only adds to the complexity. This review provides evidence that innate immune activation during critical periods of development may have effects on the adult brain in a sex-specific manner. Issues regarding sex bias in research as well as variability in animal models of immune function are discussed.

Restricting microbial exposure in early life negates the immune benefits associated with gut colonization in environments of high microbial diversity

Background

Acquisition of the intestinal microbiota in early life corresponds with the development of the mucosal immune system. Recent work on caesarean-delivered infants revealed that early microbial composition is influenced by birthing method and environment. Furthermore, we have confirmed that early-life environment strongly influences both the adult gut microbiota and development of the gut immune system. Here, we address the impact of limiting microbial exposure after initial colonization on the development of adult gut immunity.

Methodology/Principal Findings

Piglets were born in indoor or outdoor rearing units, allowing natural colonization in the immediate period after birth, prior to transfer to high-health status isolators. Strikingly, gut closure and morphological development were strongly affected by isolator-rearing, independent of indoor or outdoor origins of piglets. Isolator-reared animals showed extensive vacuolation and disorganization of the gut epithelium, inferring that normal gut closure requires maturation factors present in maternal milk. Although morphological maturation and gut closure were delayed in isolator-reared animals, these hard-wired events occurred later in development. Type I IFN, IL-22, IL-23 and Th17 pathways were increased in indoor-isolator compared to outdoor-isolator animals during early life, indicating greater immune activation in pigs originating from indoor environments reflecting differences in the early microbiota. This difference was less apparent later in development due to enhanced immune activation and convergence of the microbiota in all isolator-reared animals. This correlated with elevation of Type I IFN pathways in both groups, although T cell pathways were still more affected in indoor-reared animals.

Conclusions/Significance

Environmental factors, in particular microbial exposure, influence expression of a large number of immune-related genes. However, the homeostatic effects of microbial colonization in outdoor environments require sustained microbial exposure throughout development. Gut development in high-hygiene environments negatively impacts on normal succession of the gut microbiota and promotes innate immune activation which may impair immune homeostasis.

Lack of commensal flora in Helicobacter pylori-infected INS-GAS mice reduces gastritis and delays intraepithelial neoplasia

BACKGROUND & AIMS

Transgenic FVB/N insulin-gastrin (INS-GAS) mice have high circulating gastrin levels, and develop spontaneous atrophic gastritis and gastrointestinal intraepithelial neoplasia (GIN) with 80% prevalence 6 months after Helicobacter pylori infection. GIN is associated with gastric atrophy and achlorhydria, predisposing mice to nonhelicobacter microbiota overgrowth. We determined if germfree INS-GAS mice spontaneously develop GIN and if H pylori accelerates GIN in gnotobiotic INS-GAS mice.

METHODS

We compared gastric lesions, levels of messenger RNA, serum inflammatory mediators, antibodies, and gastrin among germfree and H pylori-monoinfected INS-GAS mice. Microbiota composition of specific pathogen-free (SPF) INS-GAS mice was quantified by pyrosequencing.

RESULTS

Germfree INS-GAS mice had mild hypergastrinemia but did not develop significant gastric lesions until 9 months old and did not develop GIN through 13 months. H pylori monoassociation caused progressive gastritis, epithelial defects, oxyntic atrophy, marked foveolar hyperplasia, dysplasia, and robust serum and tissue proinflammatory immune responses (particularly males) between 5 and 11 months postinfection (P<0.05, compared with germfree controls). Only 2 of 26 female, whereas 8 of 18 male, H pylori-infected INS-GAS mice developed low to high-grade GIN by 11 months postinfection. Stomachs of H pylori-infected SPF male mice had significant reductions in Bacteroidetes and significant increases in Firmicutes.

CONCLUSIONS

Gastric lesions take 13 months longer to develop in germfree INS-GAS mice than male SPF INS-GAS mice. H pylori monoassociation accelerated gastritis and GIN but caused less severe gastric lesions and delayed onset of GIN compared with H pylori-infected INS-GAS mice with complex gastric microbiota. Changes in gastric microbiota composition might promote GIN in achlorhydric stomachs of SPF mice.

Prebiotic effects: metabolic and health benefits

The different compartments of the gastrointestinal tract are inhabited by populations of micro-organisms. By far the most important predominant populations are in the colon where a true symbiosis with the host exists that is a key for well-being and health. For such a microbiota, 'normobiosis' characterises a composition of the gut 'ecosystem' in which micro-organisms with potential health benefits predominate in number over potentially harmful ones, in contrast to 'dysbiosis', in which one or a few potentially harmful micro-organisms are dominant, thus creating a disease-prone situation. The present document has been written by a group of both academic and industry experts (in the ILSI Europe Prebiotic Expert Group and Prebiotic Task Force, respectively). It does not aim to propose a new definition of a prebiotic nor to identify which food products are classified as prebiotic but rather to validate and expand the original idea of the prebiotic concept (that can be translated in 'prebiotic effects'), defined as: 'The selective stimulation of growth and/or activity(ies) of one or a limited number of microbial genus(era)/species in the gut microbiota that confer(s) health benefits to the host.' Thanks to the methodological and fundamental research of microbiologists, immense progress has very recently been made in our understanding of the gut microbiota. A large number of human intervention studies have been performed that have demonstrated that dietary consumption of certain food products can result in statistically significant changes in the composition of the gut microbiota in line with the prebiotic concept. Thus the prebiotic effect is now a well-established scientific fact. The more data are accumulating, the more it will be recognised that such changes in the microbiota's composition, especially increase in bifidobacteria, can be regarded as a marker of intestinal health. The review is divided in chapters that cover the major areas of nutrition research where a prebiotic effect has tentatively been investigated for potential health benefits. The prebiotic effect has been shown to associate with modulation of biomarkers and activity(ies) of the immune system. Confirming the studies in adults, it has been demonstrated that, in infant nutrition, the prebiotic effect includes a significant change of gut microbiota composition, especially an increase of faecal concentrations of bifidobacteria. This concomitantly improves stool quality (pH, SCFA, frequency and consistency), reduces the risk of gastroenteritis and infections, improves general well-being and reduces the incidence of allergic symptoms such as atopic eczema. Changes in the gut microbiota composition are classically considered as one of the many factors involved in the pathogenesis of either inflammatory bowel disease or irritable bowel syndrome. The use of particular food products with a prebiotic effect has thus been tested in clinical trials with the objective to improve the clinical activity and well-being of patients with such disorders. Promising beneficial effects have been demonstrated in some preliminary studies, including changes in gut microbiota composition (especially increase in bifidobacteria concentration). Often associated with toxic load and/or miscellaneous risk factors, colon cancer is another pathology for which a possible role of gut microbiota composition has been hypothesised. Numerous experimental studies have reported reduction in incidence of tumours and cancers after feeding specific food products with a prebiotic effect. Some of these studies (including one human trial) have also reported that, in such conditions, gut microbiota composition was modified (especially due to increased concentration of bifidobacteria). Dietary intake of particular food products with a prebiotic effect has been shown, especially in adolescents, but also tentatively in postmenopausal women, to increase Ca absorption as well as bone Ca accretion and bone mineral density. Recent data, both from experimental models and from human studies, support the beneficial effects of particular food products with prebiotic properties on energy homaeostasis, satiety regulation and body weight gain. Together, with data in obese animals and patients, these studies support the hypothesis that gut microbiota composition (especially the number of bifidobacteria) may contribute to modulate metabolic processes associated with syndrome X, especially obesity and diabetes type 2. It is plausible, even though not exclusive, that these effects are linked to the microbiota-induced changes and it is feasible to conclude that their mechanisms fit into the prebiotic effect. However, the role of such changes in these health benefits remains to be definitively proven. As a result of the research activity that followed the publication of the prebiotic concept 15 years ago, it has become clear that products that cause a selective modification in the gut microbiota's composition and/or activity(ies) and thus strengthens normobiosis could either induce beneficial physiological effects in the colon and also in extra-intestinal compartments or contribute towards reducing the risk of dysbiosis and associated intestinal and systemic pathologies.

Novel perspectives in probiotic treatment: the efficacy and unveiled mechanisms of the physiological functions

Probiotics are defined as "live microorganisms which confer a health benefit on the host" when administered in adequate amounts, and have potential effects for maintaining intestinal development, nutrition, and treating intestinal inflammations, functional disorders, and other extra-intestinal diseases. Although the benefits of probiotics for human health were first noted over 100 years ago, the analysis of probiotic functions began in earnest only 20 years ago. Probiotics, such as some strains of Lactobacillus, Bifidobacterium, Escherichia coli, and Bacillus subtilis, inhibit the growth of pathogenic bacteria, induce competitive effects for the adherent of pathogenic bacteria and their toxins to intestinal epithelia, induce cytoprotective heat shock proteins, enhance the intestinal barrier function, and modulate the host immune responses. The crosstalk between the host and the probiotics appears to be mediated by bacteria-derived effectors, which can be sensed with multiple systems, including the Toll-like receptors and cell membrane transporters. Future analyses will identify more probiotic-derived effectors, the recognition mechanisms of these effectors, and the subsequent changes of the intestinal epithelia and immune cells for each probiotic treatment. For clinical use, a procedure that objectively evaluates the ability of each probiotic effect will help establish a standard for choosing the most valuable strain and its proper dose for each individual patient.

Lactobacillus reuteri modulates cytokines production in exhaled breath condensate of children with atopic dermatitis

We measured the concentration of interferon-gamma and interleukin-4 in the exhaled breath condensate of children with atopic and nonallergic dermatitis receiving a probiotic supplementation (Lactobacillus reuteri ATCC 55730) or placebo for 8 weeks. We demonstrated that the levels of these cytokines increased and decreased respectively only in atopic subjects receiving active treatment. Our data suggest that the oral administration of a specific probiotic strain in patients with atopic dermatitis can modulate in vivo the cytokine pattern at a different site from intestine.

Safety assessment of probiotics for human use

The safety of probiotics is tied to their intended use, which includes consideration of potential vulnerability of the consumer or patient, dose and duration of consumption, and both the manner and frequency of administration. Unique to probiotics is that they are alive when administered, and unlike other food or drug ingredients, possess the potential for infectivity or in situ toxin production. Since numerous types of microbes are used as probiotics, safety is also intricately tied to the nature of the specific microbe being used. The presence of transferable antibiotic resistance genes, which comprises a theoretical risk of transfer to a less innocuous member of the gut microbial community, must also be considered. Genetic stability of the probiotic over time, deleterious metabolic activities, and the potential for pathogenicity or toxicogenicity must be assessed depending on the characteristics of the genus and species of the microbe being used. Immunological effects must be considered, especially in certain vulnerable populations, including infants with undeveloped immune function. A few reports about negative probiotic effects have surfaced, the significance of which would be better understood with more complete understanding of the mechanisms of probiotic interaction with the host and colonizing microbes. Use of readily available and low cost genomic sequencing technologies to assure the absence of genes of concern is advisable for candidate probiotic strains. The field of probiotic safety is characterized by the scarcity of studies specifically designed to assess safety contrasted with the long history of safe use of many of these microbes in foods.

Probiotics: progress toward novel therapies for intestinal diseases

PURPOSE OF REVIEW

As the beneficial effects of probiotics on health and disease prevention and treatment have been well recognized, the demand for probiotics in clinical applications and as functional foods has significantly increased in spite of limited understanding of the mechanisms. This review focuses on the most recent advances in probiotic research from genetics to biological consequences regulated by probiotics and probiotic-derived factors.

RECENT FINDINGS

Genomic and proteomic studies reveal genes and proteins involved in probiotic adaptation in the host and while exerting their beneficial effects. Recent studies in cell culture and in animal models emphasize probiotic functions in intestinal development, nutrition, host microbial balance, cytoprotection, barrier function, innate immunity, and inflammation. Most importantly, several novel and known probiotic-derived factors have been characterized, which regulate host-signaling pathways and mediate probiotic function.

SUMMARY

Progress in understanding probiotic mechanisms of action will increase our basic understanding of biological crosstalk and provide the rationale to support the development of new hypothesis-driven studies to define the clinical efficacy of probiotics for intestinal disorders.