Maternal prenatal stress is associated with the infant intestinal microbiota

Maternal prenatal stress has been often associated with infant physical development and health, as well as psychological functioning and behavior. However, the mechanisms underlying these relations remain elusive. The goal of the present study was to prospectively investigate the development of the intestinal microbiota as a potential pathway linking maternal prenatal stress and infant health. The development of the infant intestinal microbiota was followed over the first 110 days after birth in a healthy cohort of 56 vaginally born Dutch infants. Additionally, the relation between infant intestinal microbiota and gastrointestinal and allergic symptoms was examined. Results showed that maternal prenatal stress, i.e., either reported stress or elevated basal maternal salivary cortisol concentrations or both, was strongly and persistently associated with the infants' microbiota composition as determined by a phylogenetic microarray. Infants of mothers with high cumulative stress (i.e., high reported stress and high cortisol concentrations) during pregnancy had significantly higher relative abundances of Proteobacterial groups known to contain pathogens (related to Escherichia, Serratia, and Enterobacter), and lower relative abundances of lactic acid bacteria (i.e., Lactobacillus, Lactoccus, Aerococcus) and Bifidobacteria, altogether characteristics of a potentially increased level of inflammation. Furthermore, this aberrant colonization pattern was related to more maternally reported infant gastrointestinal symptoms and allergic reactions. In conclusion, clear links were found between maternal prenatal stress and the infant intestinal microbiota and health. Although causality cannot be concluded, the results suggest a possible mechanism by which maternal prenatal stress influences the offspring development. These results suggest a potential for bacterial interventions to enhance offspring health and development in pregnant women with stress.

Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena?

Irritable bowel syndrome (IBS) is a heterogeneous functional disorder with a multifactorial etiology that involves the interplay of both host and environmental factors. Among environmental factors relevant for IBS etiology, the diet stands out given that the majority of IBS patients report their symptoms to be triggered by meals or specific foods. The diet provides substrates for microbial fermentation, and, as the composition of the intestinal microbiota is disturbed in IBS patients, the link between diet, microbiota composition, and microbial fermentation products might have an essential role in IBS etiology. In this review, we summarize current evidence regarding the impact of diet and the intestinal microbiota on IBS symptoms, as well as the reported interactions between diet and the microbiota composition. On the basis of the existing data, we suggest pathways (mechanisms) by which diet components, via the microbial fermentation, could trigger IBS symptoms. Finally, this review provides recommendations for future studies that would enable elucidation of the role of diet and microbiota and how these factors may be (inter)related in the pathophysiology of IBS.

Use of non-growing Lactococcus lactis cell suspensions for production of volatile metabolites with direct relevance for flavour formation during dairy fermentations

Background

Lactococcus lactis is a lactic acid bacterium that has been used for centuries in the production of a variety of cheeses, as these bacteria rapidly acidify milk and greatly contribute to the flavour of the fermentation end-products. After a short growth phase during cheese ripening L. lactis enters an extended non-growing state whilst still strongly contributing to amino acid-derived flavour formation. Here, a research approach is presented that allows investigation of strain- and amino acid-specific flavour formation during the non-growing state.

Results

Non-growing cells of five selected L. lactis strains were demonstrated to degrade amino acids into flavour compounds that are relevant in food fermentations and differs greatly from production of flavour compounds using growing cells. As observed earlier in other research set-ups and with other microorganisms, addition of NADH, α-ketoglutarate and pyridoxal-5-phosphate was demonstrated to be essential for optimal flavour formation, suggesting that intracellular pools of these substrates are too low for the significant production of the flavour compounds. Production of flavours during the non-growing phase strongly depends on the individual amino acids that were supplied, on the presence of other amino acids (mixtures versus single compounds), and on the strain used. Moreover, we observed that the plasmid-free model strains L. lactis MG1363 and IL1403 produce relatively low amounts of flavour components under the various conditions tested.

Conclusions

By using this simplified and rapid approach to study flavour formation by non-growing lactic acid bacteria, lengthy ripening periods are no longer required to assess the capacity of strains to produce flavours in the long, non-growing state of dairy fermentation. In addition, this method also provides insight into the conversion of single amino acids versus the conversion of a mixture of amino acids as produced during protein degradation. The generated results are complementary to earlier generated datasets using growing cells, allowing assessment of the full flavour forming potential of strains used as starter cultures in industrial food fermentation processes.

Faecal microbiota composition and host-microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome

BACKGROUND

About 10% of patients with IBS report the start of the syndrome after infectious enteritis. The clinical features of postinfectious IBS (PI-IBS) resemble those of diarrhoea-predominant IBS (IBS-D). While altered faecal microbiota has been identified in other IBS subtypes, composition of the microbiota in patients with PI-IBS remains uncharacterised.

OBJECTIVE

To characterise the microbial composition of patients with PI-IBS, and to examine the associations between the faecal microbiota and a patient's clinical features.

DESIGN

Using a phylogenetic microarray and selected qPCR assays, we analysed differences in the faecal microbiota of 57 subjects from five study groups: patients with diagnosed PI-IBS, patients who 6 months after gastroenteritis had either persisting bowel dysfunction or no IBS symptoms, benchmarked against patients with IBS-D and healthy controls. In addition, the associations between the faecal microbiota and health were investigated by correlating the microbial profiles to immunological markers, quality of life indicators and host gene expression in rectal biopsies.

RESULTS

Microbiota analysis revealed a bacterial profile of 27 genus-like groups, providing an Index of Microbial Dysbiosis (IMD), which significantly separated patient groups and controls. Within this profile, several members of Bacteroidetes phylum were increased 12-fold in patients, while healthy controls had 35-fold more uncultured Clostridia. We showed correlations between the IMD and expression of several host gene pathways, including amino acid synthesis, cell junction integrity and inflammatory response, suggesting an impaired epithelial barrier function in IBS.

CONCLUSIONS

The faecal microbiota of patients with PI-IBS differs from that of healthy controls and resembles that of patients with IBS-D, suggesting a common pathophysiology. Moreover, our analysis suggests a variety of host-microbe associations that may underlie intestinal symptoms, initiated by gastroenteritis.

Abstract SS01-03: Can variations in the intestinal microbiota explain differences in colon cancer risk?

Humans harbor a very complex and diverse collection of microbes, mostly bacteria, in their intestines that are collectively called the intestinal microbiota. It is known that we cannot live without the microbiota but on the other hand, the microbiota is associated to a number of intestinal and systemic diseases, including colorectal cancer (CRC). Nevertheless, the mechanisms underlying the key roles of the microbiota in health and disease are largely unknown. Compared to human populations in the Western countries, native Africans have a very low incidence and mortality of sporadic colorectal cancer (CRC). In contrast, African Americans, who are genetically similar to Africans, have a very high rate of CRC compared to other ethnic groups in the USA. Therefore, we hypothesize that differences in CRC risk between these groups is that the differential diets consumed by both groups (high fat and protein diets by African Americans; high starch and fibers diets by native Africans) impact the microbiota which as a result contributes to the differential CRC risk development.

To test this hypothesis, we compared and contrasted the microbiota between African Americans, urbanized Africans (who live in a more Western semi-urban environment) and rural Africans at baseline, followed by a longitudinal study focusing on healthy middle aged African and African Americans volunteers who were subjected to reciprocal diet exchange under strict controlled in-house conditions over two weeks. Fresh fecal samples were collected and frozen immediately at baseline, and before and after diet exchange. DNA was isolated from these samples and subsequently used for microbiota profiling using the Human Intestinal Tract Chip (HITChip), which is a 16S ribosomal RNA-based phylogenetic microarray covering over 1,000 of the currently known bacterial species from the human intestine.

HITChip profiling demonstrated that the microbiota composition is significantly different between the three groups at baseline with Prevotella (average abundance 22%), Oscillospira (average abundance 16%) and Bacteroides (28%) as key genera in urbanized Africans, rural Africans and African Americans, respectively. Co-occurrence analysis of microbial groups demonstrated that despite the differences in composition, the microbiota connectivity was similar between urban and rural Africans with potential butyrate producing and fiber consuming groups co-occurring at high correlation (p>0.8) in both groups. Remarkably, these groups did not show strong co-occurrences within African Americans. We speculate that these co-occurrences represent interacting bacterial groups that form the structural core

Compared to differences at baseline, the microbiota compositional changes were subtle after the short dietary exchange with only ten and two bacterial groups changing significantly (p<0.01) in Africans and African Americans, respectively. Remarkably, the co-occurrence between bacterial groups changed reciprocally upon the diet exchange with more highly correlated (p>0.8) co-occurring groups after consumption of the traditional African diet. We speculate that the decrease of co-occurring groups in the Western diet is associated to a weaker microbiota structure, which is more vulnerable for pertubations.

In conclusion, our study demonstrated that long-term dietary patterns are likely responsible for the microbiota compositional differences observed between Africans and Americans, but that a short term dietary exchange can modify microbiota composition and structure. The fact that the microbiota structure changes reciprocally upon diet exchange holds promise for the prevention of diet-microbiota induced CRC risk.

Citation Format: Erwin G. Zoetendal, Leo Lahti, Sebastian Tims, Philippe G.B. Puylaert, Junhai Ou, Kishore Vipperla, Willem M. de Vos, Stephen J. O'Keefe. Can variations in the intestinal microbiota explain differences in colon cancer risk?. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr SS01-03. doi:10.1158/1538-7755.DISP13-SS01-03

The first 1000 cultured species of the human gastrointestinal microbiota

The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.

Functional genomics of lactic acid bacteria: from food to health

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.

Aberrant gut microbiota composition at the onset of type 1 diabetes in young children

AIMS/HYPOTHESIS

Recent studies indicate that an aberrant gut microbiota is associated with the development of type 1 diabetes, yet little is known about the microbiota in children who have diabetes at an early age. To this end, the microbiota of children aged 1-5 years with new-onset type 1 diabetes was compared with the microbiota of age-matched healthy controls.

METHODS

A deep global analysis of the gut microbiota composition was established by phylogenetic microarray analysis using a Human Intestinal Tract Chip (HITChip).

RESULTS

Principal component analyses highlighted the importance of age when comparing age-matched pairs. In pairs younger than 2.9 years, the combined abundance of the class Bacilli (notably streptococci) and the phylum Bacteroidetes was higher in diabetic children, whereas the combined abundance of members of Clostridium clusters IV and XIVa was higher in the healthy controls. Controls older than 2.9 years were characterised by a higher fraction of butyrate-producing species within Clostridium clusters IV and XIVa than was seen in the corresponding diabetic children or in children from the younger age groups, while the diabetic children older than 2.9 years could be differentiated by having an increased microbial diversity.

CONCLUSIONS/INTERPRETATION

The results from both age groups suggest that non-diabetic children have a more balanced microbiota in which butyrate-producing species appear to hold a pivotal position.

Tipping elements in the human intestinal ecosystem

The microbial communities living in the human intestine can have profound impact on our well-being and health. However, we have limited understanding of the mechanisms that control this complex ecosystem. Here, based on a deep phylogenetic analysis of the intestinal microbiota in a thousand western adults, we identify groups of bacteria that exhibit robust bistable abundance distributions. These bacteria are either abundant or nearly absent in most individuals, and exhibit decreased temporal stability at the intermediate abundance range. The abundances of these bimodally distributed bacteria vary independently, and their abundance distributions are not affected by short-term dietary interventions. However, their contrasting alternative states are associated with host factors such as ageing and overweight. We propose that the bistable groups reflect tipping elements of the intestinal microbiota, whose critical transitions may have profound health implications and diagnostic potential.

Intestinal microbes can have important effects on our health. Here, the authors analyse the gut microbiota composition in 1,000 western adults and find that certain bacteria are either abundant or nearly absent, and that these alternative states are associated with ageing and overweight.

vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense

The glycopeptide vancomycin was until recently considered a drug of last resort against Gram-positive bacteria. Increasing numbers of bacteria, however, are found to carry genes that confer resistance to this antibiotic. So far, 10 different vancomycin resistance clusters have been described. A chromosomal vancomycin resistance gene cluster was previously described for the anaerobic Desulfitobacterium hafniense Y51. We demonstrate that this gene cluster, characterized by its d-Ala-d-Lac ligase-encoding vanI gene, is present in all strains of D. hafniense, D. chlororespirans and some strains of Desulfosporosinus spp. This gene cluster was not found in vancomycin-sensitive Desulfitobacterium or Desulfosporosinus spp., and we show that this antibiotic resistance can be exploited as an intrinsic selection marker for Desulfitobacterium hafniense and D. chlororespirans. The gene cluster containing vanI is phylogenetically only distantly related with those described from soil and gut bacteria, but clusters instead with vancomycin resistance genes found within the phylum Actinobacteria that include several vancomycin-producing bacteria. It lacks a vanH homologue, encoding a D-lactate dehydrogenase, previously thought to always be present within vancomycin resistance gene clusters. The location of vanH outside the resistance gene cluster likely hinders horizontal gene transfer. Hence, the vancomycin resistance cluster in D. hafniense should be regarded a novel one that we here designated vanI after its unique d-Ala-d-Lac ligase.

Inulin-type fructans modulate intestinal Bifidobacterium species populations and decrease fecal short-chain fatty acids in obese women

BACKGROUND & AIMS

Inulin-type fructans (ITF) prebiotics promote changes in the composition and activity of the gut microbiota. The aim of this study was to determine variations on fecal short chain fatty acids (SCFA) concentration in obese women treated with ITF and to explore associations between Bifidobacterium species, SCFA and host biological markers of metabolism.

METHODS

Samples were obtained in a randomized, double blind, parallel, placebo-controlled trial, with 30 obese women randomly assigned to groups that received either 16 g/day ITF (n = 15) or maltodextrin (n = 15) for 3 months. The qualitative and quantitative analysis of Bifidobacterium spp. was performed in feces by PCR-DGGE and q-PCR, and SCFA profile was analyzed by gas chromatography. Spearman correlation analysis was performed between the different variables analyzed.

RESULTS

The species Bifidobacterium longum, Bifidobacterium pseudocatenulatum and Bifidobacterium adolescentis were significantly increased at the end of the treatment in the prebiotic group (p < 0.01) with being B. longum negatively correlated with serum lipopolysaccharide (LPS) endotoxin (p < 0.01). Total SCFA, acetate and propionate, that positively correlated with BMI, fasting insulinemia and homeostasis model assessment (HOMA) (p < 0.05), were significantly lower in prebiotic than in placebo group after the treatment period.

CONCLUSIONS

ITF consumption selectively modulates Bifidobacterium spp. and decreases fecal SCFA concentration in obese women. ITF could lessen metabolic risk factors associated with higher fecal SCFA concentration in obese individuals.

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

There is growing interest in understanding how diet affects the intestinal microbiota, including its possible associations with systemic diseases such as metabolic syndrome. Here we report a comprehensive and deep microbiota analysis of 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet. We analyzed the composition, diversity and dynamics of the fecal microbiota on each dietary regime by phylogenetic microarray and quantitative PCR (qPCR) analysis. In addition, we analyzed fecal short chain fatty acids (SCFAs) as a proxy of colonic fermentation, and indices of insulin sensitivity from blood samples. The diet explained around 10% of the total variance in microbiota composition, which was substantially less than the inter-individual variance. Yet, each of the study diets induced clear and distinct changes in the microbiota. Multiple Ruminococcaceae phylotypes increased on the RS diet, whereas mostly Lachnospiraceae phylotypes increased on the NSP diet. Bifidobacteria decreased significantly on the WL diet. The RS diet decreased the diversity of the microbiota significantly. The total 16S ribosomal RNA gene signal estimated by qPCR correlated positively with the three major SCFAs, while the amount of propionate specifically correlated with the Bacteroidetes. The dietary responsiveness of the individual's microbiota varied substantially and associated inversely with its diversity, suggesting that individuals can be stratified into responders and non-responders based on the features of their intestinal microbiota.

Functional identification of conserved residues involved in Lactobacillus rhamnosus strain GG sortase specificity and pilus biogenesis

In Gram-positive bacteria, sortase-dependent pili mediate the adhesion of bacteria to host epithelial cells and play a pivotal role in colonization, host signaling, and biofilm formation. Lactobacillus rhamnosus strain GG, a well known probiotic bacterium, also displays on its cell surface mucus-binding pilus structures, along with other LPXTG surface proteins, which are processed by sortases upon specific recognition of a highly conserved LPXTG motif. Bioinformatic analysis of all predicted LPXTG proteins encoded by the L. rhamnosus GG genome revealed a remarkable conservation of glycine residues juxtaposed to the canonical LPXTG motif. Here, we investigated and defined the role of this so-called triple glycine (TG) motif in determining sortase specificity during the pilus assembly and anchoring. Mutagenesis of the TG motif resulted in a lack or an alteration of the L. rhamnosus GG pilus structures, indicating that the TG motif is critical in pilus assembly and that they govern the pilin-specific and housekeeping sortase specificity. This allowed us to propose a regulatory model of the L. rhamnosus GG pilus biogenesis. Remarkably, the TG motif was identified in multiple pilus gene clusters of other Gram-positive bacteria, suggesting that similar signaling mechanisms occur in other, mainly pathogenic, species.

Faecal microbiota composition in adults is associated with the FUT2 gene determining the secretor status

The human intestine is colonised with highly diverse and individually defined microbiota, which likely has an impact on the host well-being. Drivers of the individual variation in the microbiota compositions are multifactorial and include environmental, host and dietary factors. We studied the impact of the host secretor status, encoded by fucosyltransferase 2 (FUT2) -gene, on the intestinal microbiota composition. Secretor status determines the expression of the ABH and Lewis histo-blood group antigens in the intestinal mucosa. The study population was comprised of 14 non-secretor (FUT2 rs601338 genotype AA) and 57 secretor (genotypes GG and AG) adult individuals of western European descent. Intestinal microbiota was analyzed by PCR-DGGE and for a subset of 12 non-secretor subjects and 12 secretor subjects additionally by the 16S rRNA gene pyrosequencing and the HITChip phylogenetic microarray analysis. All three methods showed distinct clustering of the intestinal microbiota and significant differences in abundances of several taxa representing dominant microbiota between the non-secretors and the secretors as well as between the FUT2 genotypes. In addition, the non-secretors had lower species richness than the secretors. The soft clustering of microbiota into enterotypes (ET) 1 and 3 showed that the non-secretors had a higher probability of belonging to ET1 and the secretors to ET3. Our study shows that secretor status and FUT2 polymorphism are associated with the composition of human intestinal microbiota, and appears thus to be one of the key drivers affecting the individual variation of human intestinal microbiota.

Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity

BACKGROUND & AIMS

Obesity has been associated with changes in the composition and function of the intestinal microbiota. Modulation of the microbiota by antibiotics also alters bile acid and glucose metabolism in mice. Hence, we hypothesized that short term administration of oral antibiotics in humans would affect fecal microbiota composition and subsequently bile acid and glucose metabolism.

METHODS

In this single blinded randomized controlled trial, 20 male obese subjects with metabolic syndrome were randomized to 7 days of amoxicillin 500 mg t.i.d. or 7 days of vancomycin 500 mg t.i.d. At baseline and after 1 week of therapy, fecal microbiota composition (Human Intestinal Tract Chip phylogenetic microarray), fecal and plasma bile acid concentrations as well as insulin sensitivity (hyperinsulinemic euglycemic clamp using [6,6-(2)H2]-glucose tracer) were measured.

RESULTS

Vancomycin reduced fecal microbial diversity with a decrease of gram-positive bacteria (mainly Firmicutes) and a compensatory increase in gram-negative bacteria (mainly Proteobacteria). Concomitantly, vancomycin decreased fecal secondary bile acids with a simultaneous postprandial increase in primary bile acids in plasma (p<0.05). Moreover, changes in fecal bile acid concentrations were predominantly associated with altered Firmicutes. Finally, administration of vancomycin decreased peripheral insulin sensitivity (p<0.05). Amoxicillin did not affect any of these parameters.

CONCLUSIONS

Oral administration of vancomycin significantly impacts host physiology by decreasing intestinal microbiota diversity, bile acid dehydroxylation and peripheral insulin sensitivity in subjects with metabolic syndrome. These data show that intestinal microbiota, particularly of the Firmicutes phylum contributes to bile acid and glucose metabolism in humans. This trial is registered at the Dutch Trial Register (NTR2566).

Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals

BACKGROUND

Interactions between the diet and intestinal microbiota play a role in health and disease, including obesity and related metabolic complications. There is great interest to use dietary means to manipulate the microbiota to promote health. Currently, the impact of dietary change on the microbiota and the host metabolism is poorly predictable and highly individual. We propose that the responsiveness of the gut microbiota may depend on its composition, and associate with metabolic changes in the host.

METHODOLOGY

Our study involved three independent cohorts of obese adults (n = 78) from Belgium, Finland, and Britain, participating in different dietary interventions aiming to improve metabolic health. We used a phylogenetic microarray for comprehensive fecal microbiota analysis at baseline and after the intervention. Blood cholesterol, insulin and inflammation markers were analyzed as indicators of host response. The data were divided into four training set - test set pairs; each intervention acted both as a part of a training set and as an independent test set. We used linear models to predict the responsiveness of the microbiota and the host, and logistic regression to predict responder vs. non-responder status, or increase vs. decrease of the health parameters.

PRINCIPAL FINDINGS

Our models, based on the abundance of several, mainly Firmicute species at baseline, predicted the responsiveness of the microbiota (AUC  =  0.77-1; predicted vs. observed correlation  =  0.67-0.88). Many of the predictive taxa showed a non-linear relationship with the responsiveness. The microbiota response associated with the change in serum cholesterol levels with an AUC of 0.96, highlighting the involvement of the intestinal microbiota in metabolic health.

CONCLUSION

This proof-of-principle study introduces the first potential microbial biomarkers for dietary responsiveness in obese individuals with impaired metabolic health, and reveals the potential of microbiota signatures for personalized nutrition.

Anaerostipes rhamnosivorans sp. nov., a human intestinal, butyrate-forming bacterium

A novel butyrate-producing bacterium, strain 1y-2T, was isolated from a stool sample of a 1-year-old, healthy Dutch infant. The isolate was obtained by using lactate and acetate as sources of carbon and energy. The strain was Gram-variable, strictly anaerobic and spore-forming and formed curly rod-shaped cells that fermented glucose into butyrate, lactate, formate and acetate as main products. The DNA G+C content of the strain was 44.5 mol% and its major cellular fatty acids were C12 : 0, iso-C19 : 1 I and C16 : 0. Strain 1y-2T was related to Anaerostipes caccae DSM 14662T based on 16S rRNA gene sequence analysis, with 3 % divergence, but hybridization studies of their genomic DNA revealed only 33 % relatedness. Moreover, strain 1y-2T showed marked physiological and biochemical differences from known species of the genus Anaerostipes . Based on phylogenetic, chemotypic and phenotypic criteria, we propose that strain 1y-2T should be classified in the genus Anaerostipes within a novel species, Anaerostipes rhamnosivorans sp. nov. The type strain is 1y-2T ( = DSM 26241T = KCTC 15316T).

Stability of (bio)functionalized porous aluminum oxide

Porous aluminum oxide (PAO), a nanostructured support for, among others, culturing microorganisms, was chemically modified in order to attach biomolecules that can selectively interact with target bacteria. We present the first comprehensive study of monolayer-modified PAO using conditions that are relevant to microbial growth with a range of functional groups (carboxylic acid, α-hydroxycarboxylic acid, alkyne, alkene, phosphonic acid, and silane). Their stability was initially assessed in phosphate-buffered saline (pH 7.0) at room temperature. The most stable combination (PAO with phosphonic acids) was further studied over a range of physiological pHs (4-8) and temperatures (up to 80 °C). Varying the pH had no significant effect on the stability, but it gradually decreased with increasing temperature. The stability of phosphonic acid-modified PAO surfaces was shown to depend strongly on the other terminal group of the monolayer structure: in general, hydrophilic monolayers were less stable than hydrophobic monolayers. Finally, an alkyne-terminated PAO surface was reacted with an azide-linked mannose derivative. The resulting mannose-presenting PAO surface showed the clearly increased adherence of a mannose-binding bacterium, Lactobacillus plantarum, and also allowed for bacterial outgrowth.

Impact of diet on human intestinal microbiota and health

Our intestinal microbiota is involved in the breakdown and bioconversion of dietary and host components that are not degraded and taken up by our own digestive system. The end products generated by our microbiota fuel our enterocytes and support growth but also have signaling functions that generate systemic immune and metabolic responses. Due to the immense metabolic capacity of the intestinal microbiota and its relatively high plasticity, there is great interest in identifying dietary approaches that allow intentional and predictable modulation of the microbiota. In this article, we review the current insights on dietary influence on the human intestinal microbiota based on recent high-throughput molecular studies and interconnections with health. We focus especially on the emerging data that identify the amount and type of dietary fat as significant modulators of the colonic microbiota and its metabolic output.

[The gut microbiota in sickness and health]

The human gut microbiota, formerly known as 'gut flora', may be regarded as an external organ with many physiological functions in metabolism, development of the immune system and defense against pathogens. The adult gut microbiota consist of 1013-1014 micro-organisms. The aggregate genome of these, known as the microbiome, is 100 times larger than the human genome. The gut microbiotica may be involved in the pathogenesis of a range of syndromes, such as inflammatory bowel disease, obesity, diabetes mellitus and atopic disorders. It should be noted that until now most of the studies conducted have been association studies, without proof of causality. This increasing insight has led to identification of new therapeutic strategies, which are currently being investigated in clinical studies. Although the implications of this knowledge for individual patients have yet to become clear, various interventions are conceivable, such as supplementation of nutritional elements, prebiotics or probiotics and feces transplantation.

Human intestinal microbiota composition is associated with local and systemic inflammation in obesity

OBJECTIVE

Intestinal microbiota have been suggested to contribute to the development of obesity, but the mechanism remains elusive. The relationship between microbiota composition, intestinal permeability, and inflammation in nonobese and obese subjects was investigated.

DESIGN AND METHODS

Fecal microbiota composition of 28 subjects (BMI 18.6-60.3 kg m(-2) ) was analyzed by a phylogenetic profiling microarray. Fecal calprotectin and plasma C-reactive protein levels were determined to evaluate intestinal and systemic inflammation. Furthermore, HbA1c , and plasma levels of transaminases and lipids were analyzed. Gastroduodenal, small intestinal, and colonic permeability were assessed by a multisaccharide test.

RESULTS

Based on microbiota composition, the study population segregated into two clusters with predominantly obese (15/19) or exclusively nonobese (9/9) subjects. Whereas intestinal permeability did not differ between clusters, the obese cluster showed reduced bacterial diversity, a decreased Bacteroidetes/Firmicutes ratio, and an increased abundance of potential proinflammatory Proteobacteria. Interestingly, fecal calprotectin was only detectable in subjects within the obese microbiota cluster (n = 8/19, P = 0.02). Plasma C-reactive protein was also increased in these subjects (P = 0.0005), and correlated with the Bacteroidetes/Firmicutes ratio (rs = -0.41, P = 0.03).

CONCLUSIONS

Intestinal microbiota alterations in obese subjects are associated with local and systemic inflammation, suggesting that the obesity-related microbiota composition has a proinflammatory effect.

Immunostimulatory CpG motifs in the genomes of gut bacteria and their role in human health and disease

Toll-like receptor (TLR) signalling plays an important role in epithelial and immune cells of the intestine. TLR9 recognizes unmethylated CpG motifs in bacterial DNA, and TLR9 signalling maintains the gut epithelial homeostasis. Here, we carried out a bioinformatic analysis of the frequency of CpG motifs in the genomes of gut commensal bacteria across major bacterial phyla. The frequency of potentially immunostimulatory CpG motifs (all CpG hexamers) or purine-purine-CG-pyrimidine-pyrimidine hexamers was linearly dependent on the genomic G+C content. We found that species belonging to Proteobacteria, Bacteroidetes and Actinobacteria (including bifidobacteria) carried high counts of GTCGTT, the optimal motif stimulating human TLR9. We also found that Enterococcus faecalis, Lactobacillus casei, Lactobacillus plantarum and Lactobacillus rhamnosus, whose strains have been marketed as probiotics, had high counts of GTCGTT motifs. As gut bacterial species differ significantly in their genomic content of CpG motifs, the overall load of CpG motifs in the intestine depends on the species assembly of microbiota and their cell numbers. The optimal CpG motif content of microbiota may depend on the host's physiological status and, consequently, on an adequate level of TLR9 signalling. We speculate that microbiota with increased numbers of microbes with CpG motif-rich DNA could better support mucosal functions in healthy individuals and improve the T-helper 1 (Th1)/Th2 imbalance in allergic diseases. In autoimmune disorders, CpG motif-rich DNA could, however, further increase the Th1-type immune responsiveness. Estimation of the load of microbe-associated molecular patterns, including CpG motifs, in gut microbiota could shed new light on host-microbe interactions across a range of diseases.