Metagenomics: key to human gut microbiota

Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus

BACKGROUND

Type 2 diabetes mellitus (T2DM) is an independent risk factor for colorectal cancer (CRC), and the patients with CRC and T2DM have worse survival. The human gut microbiota (GM) is linked to the development of CRC and T2DM, respectively. However, the GM characteristics in patients with CRC and T2DM remain unclear.

METHODS

We performed fecal metagenomic and targeted metabolomics studies on 36 samples from CRC patients with T2DM (DCRC group, n = 12), CRC patients without diabetes (CRC group, n = 12), and healthy controls (Health group, n = 12). We analyzed the fecal microbiomes, characterized the composition and function based on the metagenomics of DCRC patients, and detected the short-chain fatty acids (SCFAs) and bile acids (BAs) levels in all fecal samples. Finally, we performed a correlation analysis of the differential bacteria and metabolites between different groups.

RESULTS

Compared with the CRC group, LefSe analysis showed that there is a specific GM community in DCRC group, including an increased abundance of Eggerthella , Hungatella , Peptostreptococcus , and Parvimonas , and decreased Butyricicoccus , Lactobacillus , and Paraprevotella . The metabolomics analysis results revealed that the butyric acid level was lower but the deoxycholic acid and 12-keto-lithocholic acid levels were higher in the DCRC group than other groups ( P < 0.05). The correlation analysis showed that the dominant bacterial abundance in the DCRC group ( Parvimonas , Desulfurispora , Sebaldella , and Veillonellales , among others) was negatively correlated with butyric acid, hyodeoxycholic acid, ursodeoxycholic acid, glycochenodeoxycholic acid, chenodeoxycholic acid, cholic acid and glycocholate. However, the abundance of mostly inferior bacteria was positively correlated with these metabolic acid levels, including Faecalibacterium , Thermococci , and Cellulophaga .

CONCLUSIONS

Unique fecal microbiome signatures exist in CRC patients with T2DM compared to those with non-diabetic CRC. Alterations in GM composition and SCFAs and secondary BAs levels may promote CRC development.

Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study

BACKGROUND

Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique.

RESULTS

Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and amino acids pathways were aberrantly upregulated in CRC patients. Proteomics and metabolomics profiles of CRC patients showed different proteins and metabolites, a total of 360 and 158 proteins and metabolites, respectively were highly expressed compared to healthy control with fold change ≥ 1.2. Among the highly expressed proteins were transketolase, sushi domain-containing protein, sulfide quinone oxidoreductase protein, AAA family ATPase protein, carbonic anhydrase, IgG Fc-binding protein, nucleoside diphosphate kinase protein, arylsulfatase, alkaline phosphatase protein, phosphoglycerate kinase, protein kinase domain-containing protein, non-specific serine/threonine protein kinase, Acyl-CoA synthetase and EF-hand domain-containing protein. Some of the differential metabolites, Taurine, Taurocholic acid, 7-ketodeoxycholic acid, Glycochenodeoxycholic acid, Glycocholic acid, and Taurochenodeoxycholic acid that belong to bile acids metabolites.

CONCLUSIONS

Some bacterial species, proteins, and metabolites could be used as diagnostic biomarkers for CRC. Our study paves an insight into using multi-omics technology to address the relationship between gut microbiota and CRC.

A Preliminary Study of Gut Microbiota in Airline Pilots: Comparison With Construction Workers and Fitness Instructors

INTRODUCTION

The term "WORKbiota" has been used to describe the impact of occupational exposure and work types on human microbiota composition. Airline pilots, construction workers, and fitness instructors encompass three diverse professional groups, each with distinct work environments and lifestyle factors that may significantly influence their intestinal "WORKbiota."

OBJECTIVES

The current preliminary investigation was aimed to compare the relative abundance of specific gut microbes among airline pilots, construction workers, and fitness instructors to shed light on any significant differences. By scrutinizing these diverse professional groups, our objective was to enhance our understanding of how occupational factors influence gut microbiota while identifying possible implications for occupational medicine.

METHODS

A convenience sample consisting of 60 men representing three different professional domains - airline pilots, construction workers, and fitness instructors (with 20 individuals in each group) - was selected during regular outpatient occupational health consultations. The abundance of selected gut microbiota constituents, including Escherichia coli, Methanobrevibacter smithii, Akkermansia muciniphila, Faecalibacterium prausnitzii, Lactobacillus spp., Bifidobacterium spp., and Bacteroides spp., was quantified using quantitative SYBR Green quantitative real-time polymerase chain reaction (qRT-PCR) in stool samples.

RESULTS

There were no significant variations among the groups concerning Escherichia coli, Methanobrevibacter smithii, Bifidobacterium spp., and Bacteroides spp. However, Lactobacillus spp. and Faecalibacterium prausnitzii were significantly more abundant in the microbiota of fitness instructors compared to both airline pilots and construction workers, with no significant differences observed between the latter two groups. Notably, the abundance of Akkermansia muciniphila demonstrated a progressive decline from fitness instructors to construction workers and ultimately to airline pilots, who exhibited the lowest levels.

CONCLUSION

Airline pilots' gut microbiota was characterized by a lower abundance of health-promoting bacterial species, including Lactobacillus spp., Faecalibacterium prausnitzii, and Akkermansia muciniphila. Future research is essential to determine whether targeted interventions, such as probiotic and prebiotic supplementation, could potentially enhance gut microbiota composition and overall health in particular occupational groups.

Omics biomarkers and an approach for their practical implementation to delineate health status for personalized nutrition strategies

Personalized nutrition (PN) has gained much attention as a tool for empowerment of consumers to promote changes in dietary behavior, optimizing health status and preventing diet related diseases. Generalized implementation of PN faces different obstacles, one of the most relevant being metabolic characterization of the individual. Although omics technologies allow for assessment the dynamics of metabolism with unprecedented detail, its translatability as affordable and simple PN protocols is still difficult due to the complexity of metabolic regulation and to different technical and economical constrains. In this work, we propose a conceptual framework that considers the dysregulation of a few overarching processes, namely Carbohydrate metabolism, lipid metabolism, inflammation, oxidative stress and microbiota-derived metabolites, as the basis of the onset of several non-communicable diseases. These processes can be assessed and characterized by specific sets of proteomic, metabolomic and genetic markers that minimize operational constrains and maximize the information obtained at the individual level. Current machine learning and data analysis methodologies allow the development of algorithms to integrate omics and genetic markers. Reduction of dimensionality of variables facilitates the implementation of omics and genetic information in digital tools. This framework is exemplified by presenting the EU-Funded project PREVENTOMICS as a use case.

Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection

Background

Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI.

Methods

We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples.

Results

We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients.

Conclusion

IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.

Association between Microbiome-Related Human Genetic Variants and Fasting Plasma Glucose in a High-Cardiovascular-Risk Mediterranean Population

Background and Objectives: The gut microbiota has been increasingly recognized as a relevant factor associated with metabolic diseases. However, directly measuring the microbiota composition is a limiting factor for several studies. Therefore, using genetic variables as proxies for the microbiota composition is an important issue. Landmark microbiome-host genome-wide association studies (mbGWAS) have identified many SNPs associated with gut microbiota. Our aim was to analyze the association between relevant microbiome-related genetic variants (Mi-RSNPs) and fasting glucose and type 2 diabetes in a Mediterranean population, exploring the interaction with Mediterranean diet adherence. Materials and Methods: We performed a cross-sectional study in a high-cardiovascular-risk Mediterranean population (n = 1020), analyzing the association of Mi-RSNPs (from four published mbGWAS) with fasting glucose and type 2 diabetes. A single-variant approach was used for fitting fasting glucose and type 2 diabetes to a multivariable regression model. In addition, a Mendelian randomization analysis with multiple variants was performed as a sub-study. Results: We obtained several associations between Mi-RSNPs and fasting plasma glucose involving gut Gammaproteobacteria_HB, the order Rhizobiales, the genus Rumminococcus torques group, and the genus Tyzzerella as the top ranked. For type 2 diabetes, we also detected significant associations with Mi-RSNPs related to the order Rhizobiales, the family Desulfovibrionaceae, and the genus Romboutsia. In addition, some Mi-RSNPs and adherence to Mediterranean diet interactions were detected. Lastly, the formal Mendelian randomization analysis suggested combined effects. Conclusions: Although the use of Mi-RSNPs as proxies of the microbiome is still in its infancy, and although this is the first study analyzing such associations with fasting plasma glucose and type 2 diabetes in a Mediterranean population, some interesting associations, as well as modulations, with adherence to the Mediterranean diet were detected in these high-cardiovascular-risk subjects, eliciting new hypotheses.

New horizons in developing cell lysis methods: A Review

Cell lysis is an essential step in many studies related to biology and medicine. Based on the scale and medium that cell lysis is carried out, there are three main types of the cell lysis: 1) lysis of the cells in the surrounding environment, 2) lysis of the isolated or cultured cells and 3) Single cell lysis. Conventionally, several cell lysis methods have been developed, such as freeze-thawing, bead beating, incursion in liquid nitrogen, sonication and enzymatic and chemical based approaches. In recent years, various novel technologies have been employed to develop new methods of cell lysis. The aim of studies in this field is to introduce more precise and efficient tools or to reduce the costs of cell lysis procedures. Nanostructure based lysis methods, acoustic oscillation, electrical current, irradiation, bacteria-mediated cell lysis, magnetic ionic liquids, bacteriophage genes, monolith columns, hydraulic forces and steam explosion are some examples of new developed cell lysis methods. Beside the significant advances in this field, there are still many challenges and the tools must be further improved. This article is protected by copyright. All rights reserved.

Metagenomic Analysis of Intestinal Microbiota in Florated Rats

Changes in gut microbiota have shown that it plays an important role in animal health and metabolic diseases. The intestinal microbiota is a complex structure that functions as an organ system with the presence of trillions of microorganisms. In this study, changes in the intestinal microbiota of Wistar rats with high fluorine were evaluated. Water containing 100 ppm NaF was given to 14 male Wistar albino rats as drinking water for 12 weeks. Fluorine is known to be an inducer of protein oxidation, lipid peroxidation, modulation of intracellular redox homeostasis, and oxidative stress. In this study, it was determined that the level of MDA (molandialdehyde), one of the oxidative stress parameters, increased significantly in the intestinal tissue after fluorine intoxication. The decrease in CAT (catalase) and SOD (superoxide dismutase) enzyme activities was found to be statistically significant. Intestinal tissues were taken under aseptic conditions and microorganisms found in flora were replicated by V3-V4 16S rRNA gene-specific primers. As a result of the sequence analysis, a statistical comparison of the control group and the fluorine applied group was made. The study we have done showed that there was a significant difference in species diversity in the intestinal microbiota of mice treated with fluorine. As a result, the composition of the intestinal microflora, especially Lactobacillus species, was significantly changed in rats with high fluorine.

Avian leukosis virus subgroup J infection influences the gut microbiota composition in Huiyang bearded chickens

Avian leukosis virus (ALV) poses a major threat to poultry. The chicken gut microbiota plays critical roles in host performance, health and immunity. However, the effect of viral infection on the microbiota of Chinese local chickens is not well understood. In this study, we performed high-throughput 16S rRNA gene sequencing and evaluated the gut microbiota profiles using faeces from ALV subgroup J (ALV-J)-infected and healthy Huiyang bearded chickens (Chinese local chickens). At the phylum level, ALV-J infection mainly increased the abundance of Bacteroidetes and Proteobacteria and decreased that of Firmicutes. An analysis at the order, family and genus levels showed that the abundance of Lactobacillales, Lactobacillaceae and Lactobacillus was the highest in normal chicken faeces, accounting for 89·07%, 86·47% and 86·46%, respectively, of phylotypes. Moreover, samples from ALV-J-infected chickens were enriched with Bacteroidales, Clostridiales, Bacteroidaceae, Ruminococcaceae, Lachnospiraceae and Bacteroides. Our findings highlight that ALV-J infection alters the gut microbiota and disrupts the host-microbial homeostasis in chickens, which may be involved in the pathogenesis of ALV-J infection.

Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study design

BACKGROUND

The effect of vegan diets on metabolic processes in the body is still controversial in ultra endurance athletes. The study aims to determine gut microbiome adaptation to extreme exercise according to vegan or omnivore diet consumed in ultra-marathoners. We also seek to evaluate long-term vegan diets' effects on redox homeostasis, and muscle fatigue, and assess energy availability.

METHODS

Seventy participants will be assigned to the study, including 35 vegan ultra-marathoners and 35 omnivores competing in the Sri-Chinmoy ultra marathon race. Research data will be collected from the participants at four steps (three visits to the research laboratory and the race day) throughout the study. At the first visit (seven days before the race), fecal samples, and anthropometric measurements will be collected. Body composition will be measured using DXA. Participants will be informed about keeping detailed food records and will be asked to record their diet data and activity logs during the entire study period. At second visit, maximum oxygen consumption will be measured on treadmill. On race day, blood samples will be collected immediately before, and 0. min, 2 hours, and 24 hours after the race. Body weight will be measured before and after the race. The blood and fecal samples will be stored at -80 C until analysis. Plasma malondialdehyde, reactive oxygen metabolites, total antioxidant capacity, Heatshockprotein-70, and serum Orosomucoid-1 will be analyzed in blood samples. Fecal samples will be analyzed with shotgun metagenomic analysis and interpreted using bioinformatics pipeline (HumanN2). Statistical tests will be analyzed using SPSS version 23.0 and R Software.

DISCUSSION

Study findings will determine the effects of the vegan diet on sports performance, revealing the multiple interactions between host and gut microbiome at the whole metagenomic level. Additionally, results will show the possible adaptation throughout the race by analyzing blood and fecal samples. Furthermore, by assessing energy availability and determining host-metabolite crosstalk for ultra-endurance athletes, possible nutritional deficiencies can be identified. Thus, advanced nutritional strategies can be developed based on metabolic needs.

TRIAL REGISTRATION

Current controlled trials, ISRCTN registry 69541705. Registered on 8 December 2019.

Metagenome Analysis of Intestinal Bacteria in Healthy People, Patients With Inflammatory Bowel Disease and Colorectal Cancer

Objectives

Several reports suggesting that the intestinal microbiome plays a key role in the development of inflammatory bowel disease (IBD) or colorectal cancer (CRC), but the changes of intestinal bacteria in healthy people, patients with IBD and CRC are not fully explained. The study aimed to investigate changes of intestinal bacteria in healthy subjects, patients with IBD, and patients with CRC.

Materials

We collected data from the European Nucleotide Archive on healthy people and patients with colorectal cancer with the study accession number PRJEB6070, PRJEB7774, PRJEB27928, PRJEB12449, and PRJEB10878, collected IBD patient data from the Integrated Human Microbiome Project from the Human Microbiome Project Data Portal. We performed metagenome-wide association studies on the fecal samples from 290 healthy subjects, 512 IBD patients, and 285 CRC patients. We used the metagenomics dataset to study bacterial community structure, relative abundance, functional prediction, differentially abundant bacteria, and co-occurrence networks.

Results

The bacterial community structure in both IBD and CRC was significantly different from healthy subjects. Our results showed that IBD patients had low intestinal bacterial diversity and CRC patients had high intestinal bacterial diversity compared to healthy subjects. At the phylum level, the relative abundance of Firmicutes in IBD decreased significantly, while the relative abundance of Bacteroidetes increased significantly. At the genus level, the relative abundance of Bacteroides in IBD was higher than in healthy people and CRC. Compared with healthy people and CRC, the main difference of intestinal bacteria in IBD patients was Bacteroidetes, and compared with healthy people and IBD, the main difference of intestinal bacteria in CRC patients was in Fusobacteria, Verrucomicrobia, and Proteobacteria. The main differences in the functional composition of intestinal bacteria in healthy people, IBD and CRC patients were L-homoserine and L-methionine biosynthesis, 5-aminoimidazole ribonucleotide biosynthesis II, L-methionine biosynthesis I, and superpathway of L-lysine, L-threonine, and L-methionine biosynthesis I. The results of stratified showed that the abundance of Firmicutes, Bacteroidetes, and Actinobacteria involved in metabolic pathways has significantly changed. Besides, the association network of intestinal bacteria in healthy people, IBD, and CRC patients has also changed.

Conclusions

In conclusion, compared with healthy people, the taxonomic and functional composition of intestinal bacteria in IBD and CRC patients was significantly changed.

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

In this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

Enterococcus faecalis Is a Better Competitor Than Other Lactic Acid Bacteria in the Initial Colonization of Colon of Healthy Newborn Babies at First Week of Their Life

Initial colonization of human gut by bacteria is an important step in controlling its microbiota and health status. This study followed the initial colonization by lactic acid bacteria (LAB) in colon of new born babies through following its occurrence in their stool at first week of their life. The LAB occurrence in the neonates' stool was followed on MRS agar medium. The isolated LAB from male and female newborn babies of normal birth and cesarean section surgical delivery were molecular biologically identified by phylogenetic analysis of 16S rRNA gene sequence. From the 24 investigated newborn babies, three LAB taxa, Lactobacillaceae, Enterococcus, and Streptococcus, were detected in their stool at first week of their life. Lactobacillaceae represented 20.8% of total colonized LAB in newborn babies in the culture-dependent approach used in this study and included three species namely Limosilactobacillus reuteri (previously known as Lactobacillus reuteri), Lacticaseibacillus rhamnosus (previously known as Lactobacillus rhamnosus) and Ligilactobacillus agilis (previously known as Lactobacillus agilis). Enterococcus faecalis and E. faecium were detected where E. faecalis was the highest dominant, representing 62.5% of total LAB colonizing newborn babies. This result suggests that this bacterium has high potency for colonization and might be important for controlling the initial settlement of microbiota in healthy newborn babies. Only one species of Streptococcus namely Streptococcus agalactiae was detected in 8.33% total of the investigated newborn babies indicating high competency by other LAB for colonization and that this bacteria, in spite of its pathogenicity, is commensal in its low existence in healthy babies. The explored potency of natural initial colonization of the LAB species E. faecalis, E. faecium, L. reuteri, L. rhamnosus, and L. agilis of which many health beneficial strains were previously reported, would be important for future applications. Despite the controversy in evaluating its health benefits, E. faecalis as a potent competitor to other LAB refers to its importance in initial colonization of healthy babies colon at first week of their life. Further future studies, with more number of samples and characterization, would be of importance for evaluating the potential use of beneficial Enterococcus strains which could improve intestinal ecosystem.

Oxalobacter formigenes reduce the risk of kidney stones in patients exposed to oral antibiotics: a case-control study

This is the first prospective study to investigate the association between kidney stones, bone mineral density, serum testosterone, colon cancer and O. formigenes colonization. 40 kidney stone patients and 85 controls were enrolled. O. formigenes colonization was established. BMD was examined from T- and Z-scores using dual energy absorptiometry. O. formigenes was found in 28 of 40 cases and 80 of 85 controls. BMD was significantly reduced in patients (p < 0.05). The evaluation revealed a significant association between lowered O. formigenes colonization and low testosterone. Urinary calcium and oxalates levels were greater in patient. Serum testosterone and urinary citrate concentrations was reduced in patients with a significant difference. Also an association between O. formigenes and colon cancer was noted. Absence of O. formigenes might stand for a pathogenic factor in calcium oxalate stone, low bone mineral density, low testosterone levels and also colon cancer, when antibiotics are prescribed generously.

Potential proton pump inhibitor-related adverse effects

Proton pump inhibitors (PPIs) are one of the most common medications taken by patients worldwide. PPIs are used to treat acid-related disorders, including gastroesophageal reflux disease, peptic ulcer disease, Helicobacter pylori infection, and nonsteroidal anti-inflammatory drug/stress ulceration. For some of these diseases, long-term treatment is necessary. With such prolonged use, concern and investigation into potential adverse effects has increased. In addition, data are available regarding potential anticancer effects of PPIs, especially regarding solid tumors. The aim of this review is to assess the literature on PPIs with regard to common concerns, such as drug-drug interactions, the intestinal microbiome, dementia and central nervous system disease, and osteoporosis, as well as to highlight potential negative and positive impacts of the drug in cancer.

Comparison of microbiota in the cloaca, colon, and magnum of layer chicken

Anatomically terminal parts of the urinary, reproductive, and digestive systems of birds all connect to the cloaca. As the feces drain through the cloaca in chickens, the cloacal bacteria were previously believed to represent those of the digestive system. To investigate similarities between the cloacal microbiota and the microbiota of the digestive and reproductive systems, microbiota inhabiting the colon, cloaca, and magnum, which is a portion of the chicken oviduct of 34-week-old, specific-pathogen-free hens were analyzed using a 16S rRNA metagenomic approach using the Ion torrent sequencer and the Qiime2 bioinformatics platform. Beta diversity via unweighted and weighted unifrac analyses revealed that the cloacal microbiota was significantly different from those in the colon and the magnum. Unweighted unifrac revealed that the cloacal microbiota was distal from the microbiota in the colon than from the microbiota in the magnum, whereas weighted unifrac revealed that the cloacal microbiota was located further away from the microbiota in the magnum than from the microbiota inhabiting the colon. Pseudomonas spp. were the most abundant in the cloaca, whereas Lactobacillus spp. and Flavobacterium spp. were the most abundant species in the colon and the magnum. The present results indicate that the cloaca contains a mixed population of bacteria, derived from the reproductive, urinary, and digestive systems, particularly in egg-laying hens. Therefore, sampling cloaca to study bacterial populations that inhabit the digestive system of chickens requires caution especially when applied to egg-laying hens. To further understand the physiological role of the microbiota in chicken cloaca, exploratory studies of the chicken’s cloacal microbiota should be performed using chickens of different ages and types.

Necrotizing Enterocolitis: A Multi-omic Approach and the Role of the Microbiome

Necrotizing enterocolitis (NEC) is a poorly defined disease that primarily affects preterm infants. There has not been much progress in the prevention or treatment of NEC since it became recognized as a common problem in preterm infants. Reasons for this lack of progress include the likelihood that different diseases are being put under the same moniker of "NEC," similar to using "diabetes" for the different diseases it represents. In order to make progress, better delineation of the phenotypes that present as NEC will be necessary to clearly establish their pathophysiology, find specific and sensitive biomarkers, and establish preventative regimens. In this review, we summarize some of the entities that are being called NEC, discuss the pathophysiology of the most classic form of NEC, and provide an overview of how we might proceed in the future to make progress in this field.

Crosstalk Between the Gut Microbiota and the Brain: An Update on Neuroimaging Findings

An increasing amount of evidence suggests that bidirectional communication between the gut microbiome and the central nervous system (CNS), which is also known as the microbiota-gut-brain axis, plays a key role in the development and function of the brain. For example, alterations or perturbations of the gut microbiota (GM) are associated with neurodevelopmental, neurodegenerative, and psychiatric disorders and modulation of the microbiota-gut-brain axis by probiotics, pre-biotics, and/or diet induces preventative and therapeutic effects. The current interpretation of the mechanisms underlying this relationship are mainly based on, but not limited to, parallel CNS, endocrine, and immune-related molecular pathways that interact with each other. Although many studies have revealed the peripheral aspects of this axis, there is a paucity of data on how structural and functional changes in the brain correspond with gut microbiotic states in vivo. However, modern neuroimaging techniques and other imaging modalities have been increasingly applied to study the structure, function, and molecular aspects of brain activity in living healthy human and patient populations, which has resulted in an increased understanding of the microbiota-gut-brain axis. The present review focuses on recent studies of healthy individuals and patients with diverse neurological disorders that employed a combination of advanced neuroimaging techniques and gut microbiome analyses. First, the technical information of these imaging modalities will be briefly described and then the included studies will provide primary evidence showing that the human GM profile is significantly associated with brain microstructure, intrinsic activities, and functional connectivity (FC) as well as cognitive function and mood.

Gut microbiome of Moroccan colorectal cancer patients

Although colorectal cancer is the third leading cause of death in Morocco, there are no studies of the microbiome changes associated with the disease in the Moroccan population. The aim of our study was to compare the stool microbiome of Moroccan cancer patients with healthy individuals. We analyzed the microbiome composition of samples from 11 CRC patients and 12 healthy individuals by 16S rRNA amplicon sequencing. Principal coordinate analysis of samples revealed defined cancer versus healthy clusters. Our findings showed that cancer samples had higher proportions of Firmicutes (T = 50.5%; N = 28.4%; p = 0.04), specifically of Clostridia (T = 48.3%; N = 19.0%; p = 0.002), and Fusobacteria (T = 0.1%; N = 0.0%; p = 0.02), especially of Fusobacteriia (T = 0.1%; N = 0.0%; p = 0.02), while Bacteroidetes were enriched in healthy samples (T = 35.1%; N = 62.8%; p = 0.06), particularly the class Bacteroidia (T = 35.1%; N = 62.6%; p = 0.06). Porphyromonas, Clostridium, Ruminococcus, Selenomonas, and Fusobacterium were significantly overrepresented in diseased patients, similarly to other studies. Predicted functional information showed that bacterial motility proteins, flagellar assembly, and fatty acid biosynthesis metabolism were significantly overrepresented in cancer patients, while amino acid metabolism and glycan biosynthesis were overrepresented in controls. This suggests that involvement of these functional metagenomes is similar and relevant in the carcinogenesis process, independent of the origin of the samples. Results from this study allowed identification of bacterial taxa relevant to the Moroccan population and encourages larger studies to facilitate population-directed therapeutic approaches.

Microbiomic Analysis of Intra-Abdominal Infections by Using Denaturing High-Performance Liquid Chromatography: A Prospective Observational Study

BACKGROUND

Intra-abdominal infections represent a subgroup of septic syndromes with high death rates and the need for prompt and appropriate antimicrobial therapy. Conventional culture-based microbial identification has notable shortcomings in the diagnostics of polymicrobial infections. Modern culture-independent molecular methods may represent a new diagnostic approach. The current study aimed to compare the results obtained from the denaturing high-performance liquid chromatography WAVE^® system as a culture-independent diagnostic tool with those obtained from standard culture-based microbiologic testing in the clinical setting of severe intra-abdominal sepsis.

PATIENTS AND METHODS

The study included 42 samples of pathologic intra-abdominal fluids, collected from 37 patients with intra-abdominal sepsis. Micro-organisms grown in culture and detected by the WAVE system were compared. Further, we recorded clinical data including baseline characteristics and the use of antibiotic agents.

RESULTS

In 38.1% of the analyzed samples, the classic, culture-based methods showed no bacterial growth on agar plates, in comparison with the microbiomic analysis in which the proportion of samples with negative signal was 31%. In about 40% of the patients, both methods detected one microbiologic agent, whereas in approximately one quarter of the samples, two or more agents were identified. The detection rate of certain bacteria such as Enterobacteriacae or Enterococcus faecium was significantly higher using the microbiomic analysis. Bacteria such as Haemophilus, Lactobacillus, Clostridium, Methylobacterium, Collinsella aerofaciens, and Solobacterium moorei were detected exclusively using microbiomic analysis.

CONCLUSION

The culture independent molecular WAVE system provided additional information, especially concerning unusual, fastidious bacteria in patients with intra-abdominal infections. Further, it has a higher detection rate for polymicrobial infection and delivers results much sooner than conventional microbiologic methods.

Fecal bacterial microbiome diversity in chronic HIV-infected patients in China

The purpose of this study was to identify fecal bacterial microbiome changes in patients with chronic human immunodeficiency virus (HIV) infection in China. Bacterial 16S rRNA genes were amplified, sequenced (454 pyrosequencing), and clustered into operational taxonomic units using the QIIME software. Relative abundance at the phylum and genus levels were calculated. Alpha diversity was determined by Chao 1 and observed-species indices, and beta diversity was determined by double principal component analysis using the estimated phylogeny-based unweighted Unifrac distance matrices. Fecal samples of the patients with chronic HIV-infection tended to be enriched with bacteria of the phyla Firmicutes (47.20%±0.43 relative abundance) and Proteobacteria (37.21%±0.36) compared with those of the non-HIV infected controls (17.95%±0.06 and 3.81%±0.02, respectively). Members of the genus Bilophila were exclusively detected in samples of the non-HIV infected controls. Bacteroides and arabacteroides were more abundant in the chronic HIV-infected patients. Our study indicated that chronic HIV-infected patients in China have a fecal bacterial microbiome composition that is largely different from that found in non-HIV infected controls, and further study is needed to evaluate whether microbiome changes play a role in disease complications in the distal gut, including opportunistic infections.

Helicobacter pylori and gut microbiota modulate energy homeostasis prior to inducing histopathological changes in mice

Helicobacter pylori have been shown to influence physiological regulation of metabolic hormones involved in food intake, energy expenditure and body mass. It has been proposed that inducing H. pylori-induced gastric atrophy damages hormone-producing endocrine cells localized in gastric mucosal layers and therefore alter their concentrations. In a recent study, we provided additional proof in mice under controlled conditions that H. pylori and gut microbiota indeed affects circulating metabolic gut hormones and energy homeostasis. In this addendum, we presented data from follow-up investigations that demonstrated H. pylori and gut microbiota-associated modulation of metabolic gut hormones was independent and precedes H. pylori-induced histopathological changes in the gut of H. pylori-infected mice. Thus, H. pylori-associated argumentation of energy homeostasis is not caused by injury to endocrine cells in gastric mucosa.

Could the gut microbiota reconcile the oral bioavailability conundrum of traditional herbs?

ETHNOPHARMACOLOGICAL RELEVANCE

A wealth of information is emerging about the impact of gut microbiota on human health and diseases such as cardiovascular diseases, obesity and diabetes. As we learn more, we find out the gut microbiota has the potential as new territory for drug targeting. Some novel therapeutic approaches could be developed through reshaping the commensal microbial structure using combinations of different agents. The gut microbiota also affects drug metabolism, directly and indirectly, particularly towards the orally administered drugs. Herbal products have become the basis of traditional medicines such as traditional Chinese medicine and also been being considered valuable materials in modern drug discovery. Of note, low oral bioavailability but high bioactivity is a conundrum not yet solved for some herbs. Since most of herbal products are orally administered, the herbs' constituents are inevitably exposed to the intestinal microbiota and the interplays between herbal constituents and gut microbiota are expected. Emerging explorations of herb-microbiota interactions have an opportunity to revolutionize the way we view herbal therapeutics. The present review aims to provide information regarding the health promotion and/or disease prevention by the interplay between traditional herbs with low bioavailability and gut microbiota through gut microbiota via two different types of mechanisms: (1) influencing the composition of gut microbiota by herbs and (2) metabolic reactions of herbal constituents by gut microbiota.

MATERIALS AND METHODS

The major data bases (PubMed and Web of Science) were searched using "gut microbiota", "intestinal microbiota", "gut flora", "intestinal flora", "gut microflora", "intestinal microflora", "herb", "Chinese medicine", "traditional medicine", or "herbal medicine" as keywords to find out studies regarding herb-microbiota interactions. The Chinese Pharmacopoeia (2010 edition, Volume I) was also used to collect the data of commonly used medicinal herbs and their quality control approaches.

RESULTS

Among the 474 monographs of herbs usually used in the Chinese Pharmacopoeia, the quality control approach of 284 monographs is recommended to use high-performance liquid chromatography approach. Notably, the major marker compounds (>60%) for quality control are polyphenols, polysaccharides and saponins, with significant oral bioavailability conundrum. Results from preclinical and clinical studies on herb-microbiota interactions showed that traditional herbs could exert heath promotion and disease prevention roles via influencing the gut microbiota structure. On the other hand, herb constituents such as ginsenoside C-K, hesperidin, baicalin, daidzin and glycyrrhizin could exert their therapeutic effects through gut microbiota-mediated bioconversion.

CONCLUSIONS

Herb-microbiota interaction studies provide novel mechanistic understanding of the traditional herbs that exhibit poor oral bioavailability. "Microbiota availability" could be taken consideration into describing biological measurements in the therapeutic assessment of herbal medicine. Our review should be of value in stimulating discussions among the scientific community on this relevant theme and prompting more efforts to complement herb-microbiota interactions studies.

Acidic Food pH Increases Palatability and Consumption and Extends Drosophila Lifespan

BACKGROUND

Despite the prevalent use of Drosophila as a model in studies of nutrition, the effects of fundamental food properties, such as pH, on animal health and behavior are not well known.

OBJECTIVES

We examined the effect of food pH on adult Drosophila lifespan, feeding behavior, and microbiota composition and tested the hypothesis that pH-mediated changes in palatability and total consumption are required for modulating longevity.

METHODS

We measured the effect of buffered food (pH 5, 7, or 9) on male gustatory responses (proboscis extension), total food intake, and male and female lifespan. The effect of food pH on germfree male lifespan was also assessed. Changes in fly-associated microbial composition as a result of food pH were determined by 16S ribosomal RNA gene sequencing. Male gustatory responses, total consumption, and male and female longevity were additionally measured in the taste-defective Pox neuro (Poxn) mutant and its transgenic rescue control.

RESULTS

An acidic diet increased Drosophila gustatory responses (40-230%) and food intake (5-50%) and extended survival (10-160% longer median lifespan) compared with flies on either neutral or alkaline pH food. Alkaline food pH shifted the composition of fly-associated bacteria and resulted in greater lifespan extension (260% longer median survival) after microbes were eliminated compared with flies on an acidic (50%) or neutral (130%) diet. However, germfree flies lived longer on an acidic diet (5-20% longer median lifespan) compared with those on either neutral or alkaline pH food. Gustatory responses, total consumption, and longevity were unaffected by food pH in Poxn mutant flies.

CONCLUSIONS

Food pH can directly influence palatability and feeding behavior and affect parameters such as microbial growth to ultimately affect Drosophila lifespan. Fundamental food properties altered by dietary or drug interventions may therefore contribute to changes in animal physiology, metabolism, and survival.

Cell-Nonautonomous Mechanisms Underlying Cellular and Organismal Aging

Cell-autonomous mechanisms underlying cellular and organismal aging in evolutionarily distant eukaryotes have been established; these mechanisms regulate longevity-defining processes within a single eukaryotic cell. Recent findings have provided valuable insight into cell-nonautonomous mechanisms modulating cellular and organismal aging in eukaryotes across phyla; these mechanisms involve a transmission of various longevity factors between different cells, tissues, and organisms. Herein, we review such cell-nonautonomous mechanisms of aging in eukaryotes. We discuss the following: (1) how low molecular weight transmissible longevity factors modulate aging and define longevity of cells in yeast populations cultured in liquid media or on solid surfaces, (2) how communications between proteostasis stress networks operating in neurons and nonneuronal somatic tissues define longevity of the nematode Caenorhabditis elegans by modulating the rates of aging in different tissues, and (3) how different bacterial species colonizing the gut lumen of C. elegans define nematode longevity by modulating the rate of organismal aging.

Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain

Colorectal cancer (CRC) is the third most common cancer in the world and the second leading cause of cancer deaths in the US and Spain. The molecular mechanisms involved in the etiology of CRC are not yet elucidated due in part to the complexity of the human gut microbiota. In this study, we compared the microbiome composition of 90 tumor and matching adjacent tissue (adjacent) from cohorts from the US and Spain by 16S rRNA amplicon sequencing in order to determine the impact of the geographic origin on the CRC microbiome. Data showed a significantly (P < 0.05) higher Phylogenetic Diversity (PD) for the US (PD Adjacent = 26.3 ± 5.3, PD Tumor = 23.3 ± 6.2) compared to the Spanish cohort (PD Adjacent = 18.9 ± 5.9, PD Tumor = 18.7 ± 6.6) while no significant differences in bacterial diversity were observed between tumor and adjacent tissues for individuals from the same country. Adjacent tissues from the Spanish cohort were enriched in Firmicutes (SP = 43.9% and US = 22.2%, P = 0.0001) and Actinobacteria (SP = 1.6% and US = 0.5%, P = 0.0018) compared to US adjacent tissues, while adjacent tissues from the US had significantly higher abundances of Fusobacteria (US = 8.1% and SP = 1.5%, P = 0.0023) and Sinergistetes (US = 0.3% and SP = 0.1%, P = 0.0097). Comparisons between tumor and adjacent tissues in each cohort identified the genus Eikenella significantly over represented in US tumors (T = 0.024% and A = 0%, P = 0.03), and the genera Fusobacterium (T = 10.4% and A = 1.5%, P = <0.0001), Bulleida (T = 0.36% and A = 0.09%, P = 0.02), Gemella (T = 1.46% and A = 0.19%, P = 0.03), Parvimonas (T = 3.14% and A = 0.86%, P = 0.03), Campylobacter (T = 0.15% and A = 0.008%, P = 0.047), and Streptococcus (T = 2.84% and A = 2.19%, P = 0.05) significantly over represented in Spanish tumors. Predicted metagenome functional content from 16S rRNA surveys showed that bacterial motility proteins and proteins involved in flagellar assembly were over represented in adjacent tissues of both cohorts, while pathways involved in fatty acid biosynthesis, the MAPK signaling pathway, and bacterial toxins were over represented in tumors. Our study suggests that microbiome compositional and functional dissimilarities by geographic location should be taken in consideration when approaching CRC therapeutic options.

Functional impacts of the intestinal microbiome in the pathogenesis of inflammatory bowel disease

: The human intestinal microbiome plays a critical role in human health and disease, including the pathogenesis of inflammatory bowel disease (IBD). Numerous studies have identified altered bacterial diversity and abundance at varying taxonomic levels through biopsies and fecal samples of patients with IBD and diseased model animals. However, inconsistent observations regarding the microbial compositions of such patients have hindered the efforts in assessing the etiological role of specific bacterial species in the pathophysiology of IBD. These observations highlight the importance of minimizing the confounding factors associated with IBD and the need for a standardized methodology to analyze well-defined microbial sampling sources in early IBD diagnosis. Furthermore, establishing the linkage between microbiota compositions with their function within the host system can provide new insights on the pathogenesis of IBD. Such research has been greatly facilitated by technological advances that include functional metagenomics coupled with proteomic and metabolomic profiling. This review provides updates on the composition of the microbiome in IBD and emphasizes microbiota dysbiosis-involved mechanisms. We highlight functional roles of specific bacterial groups in the development and management of IBD. Functional analyses of the microbiome may be the key to understanding the role of microbiota in the development and chronicity of IBD and reveal new strategies for therapeutic intervention.

From food to cell: nutrient exploitation strategies of enteropathogens

Upon entering the human gastrointestinal tract, foodborne bacterial enteropathogens encounter, among numerous other stress conditions, nutrient competition with the host organism and the commensal microbiota. The main carbon, nitrogen and energy sources exploited by pathogens during proliferation in, and colonization of, the gut have, however, not been identified completely. In recent years, a huge body of literature has provided evidence that most enteropathogens are equipped with a large set of specific metabolic pathways to overcome nutritional limitations in vivo, thus increasing bacterial fitness during infection. These adaptations include the degradation of myo-inositol, ethanolamine cleaved from phospholipids, fucose derived from mucosal glycoconjugates, 1,2-propanediol as the fermentation product of fucose or rhamnose and several other metabolites not accessible for commensal bacteria or present in competition-free microenvironments. Interestingly, the data reviewed here point to common metabolic strategies of enteric pathogens allowing the exploitation of nutrient sources that not only are present in the gut lumen, the mucosa or epithelial cells, but also are abundant in food. An increased knowledge of the metabolic strategies developed by enteropathogens is therefore a key factor to better control foodborne diseases.

Unraveling the ties between irritable bowel syndrome and intestinal microbiota

Irritable bowel syndrome (IBS) is the most prevalent functional gastrointestinal disorder. It is a multifactorial disorder. Intestinal microbiota may cause the pathogenesis of IBS by contributing to abnormal gastrointestinal motility, low-grade inflammation, visceral hypersensitivity, communication in the gut-brain axis, and so on. Previous attempts to identify the intestinal microbiota composition in IBS patients have yielded inconsistent and occasionally contradictory results. This inconsistency may be due to the differences in the molecular techniques employed, the sample collection and handling methods, use of single samples that are not linked to fluctuating symptoms, or other factors such as patients’ diets and phenotypic characterizations. Despite these difficulties, previous studies found that the intestinal microbiota in some IBS patients was completely different from that in healthy controls, and there does appear to be a consistent theme of Firmicutes enrichment and reduced abundance of Bacteroides. Based on the differences in intestinal microbiota composition, many studies have addressed the roles of microbiota-targeted treatments, such as antibiotics and probiotics, in alleviating certain symptoms of IBS. This review summarizes the current knowledge of the associations between intestinal microbiota and IBS as well as the possible modes of action of intestinal microbiota in the pathogenesis of IBS. Improving the current level of understanding of host-microbiota interactions in IBS is important not only for determining the role of intestinal microbiota in IBS pathogenesis but also for therapeutic modulation of the microbiota.

Problems and prospects of current studies on the microecology of tongue coating

Tongue diagnosis in traditional Chinese medicine (TCM) assesses the health by investigation of tongue coating. The science and technology of tongue coating analysis have become a significant issue for modernization of TCM. The relationship between microecology of tongue coating and TCM was relevant to the syndrome differentiation in TCM, such as the cold/hot syndrome may exhibit different specific microbiota patterns in the tongue coating. This article provides a review on the microbiota research of tongue coating.

Compositional differences in fecal microbiota between rats with colorectal cancer and normal rats

AIM: To investigate the compositional differences in fecal flora between rats with colorectal cancer and normal rats.

METHODS: A rat model of colorectal cancer was developed by intraperitoneal injection of 1, 2-dimethyl hydrazine (DMH). Fecal samples were collected from rats with colorectal cancer and normal controls, and the microbiota was isolated by PCR-DGGE technique to perform flora similarity analysis (cluster analysis) and polymorphism analysis (richness, uniformity, Shannon-Wiener index, Simpson index) and to compare with the GenBank to identify the genus so as to study the variation.

RESULTS: Compared with normal rats, the abundance of Lachnospiraceae, Ruminococcaceae, Lactobacillus intestinalis, Paraprevotella, Lactobacillus murinus, Lactobacillus, Prevotella, Lactobacillus crispatus and Lachnospiracea incertae sedis was significantly reduced and that of Coprobacillus was significantly increased in rats with colorectal cancer. Although the flora diversity between the two groups showed no statistical difference, there was a significant difference in flora composition.

CONCLUSION: The composition of fecal microflora changes in rats with colorectal cancer compared with normal rats, with the number of beneficial bacteria reduced and that of potential pathogens increased.

Role of "Western diet" in inflammatory autoimmune diseases

Developed societies, although having successfully reduced the burden of infectious disease, constitute an environment where metabolic, cardiovascular, and autoimmune diseases thrive. Living in westernized countries has not fundamentally changed the genetic basis on which these diseases emerge, but has strong impact on lifestyle and pathogen exposure. In particular, nutritional patterns collectively termed the "Western diet", including high-fat and cholesterol, high-protein, high-sugar, and excess salt intake, as well as frequent consumption of processed and 'fast foods', promote obesity, metabolic syndrome, and cardiovascular disease. These factors have also gained high interest as possible promoters of autoimmune diseases. Underlying metabolic and immunologic mechanisms are currently being intensively explored. This review discusses the current knowledge relative to the association of "Western diet" with autoimmunity, and highlights the role of T cells as central players linking dietary influences to autoimmune pathology.

Moving fecal microbiota transplantation into the mainstream

In recent years, fecal microbiota transplantation (aka fecal transplantation, fecal bacteriotherapy, FMT) has become increasing utilized to treat recurrent and refractory Clostridium difficile infection (CDI). Almost 600,000 cases of CDI occur each year in the United States. Of these, an estimated 15,000 patients have a recurrence. The management of recurrent disease has been challenging for patients and clinicians. Increasingly, FMT has been recognized as an effective option for these patients. This article explores why FMT has reemerged as a practical therapeutic modality. In the process, the logistics by which the procedure is performed and the factors that may affect quality, safety, and patient outcomes will be described.

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

Background

Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation of which requires a reliable bioinformatic pipeline. In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy.

Results

The metatranscriptome pipeline developed here enabled effective removal of rRNA derived sequences, followed by confident assignment of the predicted function and taxonomic origin of the mRNA reads. Phylogenetic analysis of the small intestine metatranscriptome datasets revealed a strong similarity with the community composition profiles obtained from 16S rDNA and rRNA pyrosequencing, indicating considerable congruency between community composition (rDNA), and the taxonomic distribution of overall (rRNA) and specific (mRNA) activity among its microbial members. Reproducibility of the metatranscriptome sequencing approach was established by independent duplicate experiments. In addition, comparison of metatranscriptome analysis employing single- or paired-end sequencing methods indicated that the latter approach does not provide improved functional or phylogenetic insights. Metatranscriptome functional-mapping allowed the analysis of global, and genus specific activity of the microbiota, and illustrated the potential of these approaches to unravel syntrophic interactions in microbial ecosystems.

Conclusions

A reliable pipeline for metatransciptome data analysis was developed and evaluated using RNA-seq datasets obtained for the human small intestine microbiota. The set-up of the pipeline is very generic and can be applied for (bacterial) metatranscriptome analysis in any chosen niche.

Autism and dietary therapy: case report and review of the literature

We report the history of a child with autism and epilepsy who, after limited response to other interventions following her regression into autism, was placed on a gluten-free, casein-free diet, after which she showed marked improvement in autistic and medical symptoms. Subsequently, following pubertal onset of seizures and after failing to achieve full seizure control pharmacologically she was advanced to a ketogenic diet that was customized to continue the gluten-free, casein-free regimen. On this diet, while still continuing on anticonvulsants, she showed significant improvement in seizure activity. This gluten-free casein-free ketogenic diet used medium-chain triglycerides rather than butter and cream as its primary source of fat. Medium-chain triglycerides are known to be highly ketogenic, and this allowed the use of a lower ratio (1.5:1) leaving more calories available for consumption of vegetables with their associated health benefits. Secondary benefits included resolution of morbid obesity and improvement of cognitive and behavioral features. Over the course of several years following her initial diagnosis, the child's Childhood Autism Rating Scale score decreased from 49 to 17, representing a change from severe autism to nonautistic, and her intelligence quotient increased 70 points. The initial electroencephalogram after seizure onset showed lengthy 3 Hz spike-wave activity; 14 months after the initiation of the diet the child was essentially seizure free and the electroencephalogram showed only occasional 1-1.5 second spike-wave activity without clinical accompaniments.

Gut microbiota and obesity: lessons from the microbiome

The distal gut harbours microbial communities that outnumber our own eukaryotic cells. The contribution of the gut microbiota to the development of several diseases (e.g. obesity, type 2 diabetes, steatosis, cardiovascular diseases and inflammatory bowel diseases) is becoming clear, although the causality remains to be proven in humans. Global changes in the gut microbiota have been observed by a number of culture-dependent and culture-independent methods, and while the latter have mostly included 16S ribosomal RNA gene analyses, more recent studies have utilized DNA sequencing of whole-microbial communities. Altogether, these high-throughput methods have facilitated the identification of novel candidate bacteria and, most importantly, metabolic functions that might be associated with obesity and type 2 diabetes. This review discusses the association between specific taxa and obesity, together with the techniques that are used to characterize the gut microbiota in the context of obesity and type 2 diabetes. Recent results are discussed in the framework of the interactions between gut microbiota and host metabolism.

The use of metagenomic approaches to analyze changes in microbial communities

Microbes are the most abundant biological entities found in the biosphere. Identification and measurement of microorganisms (including viruses, bacteria, archaea, fungi, and protists) in the biosphere cannot be readily achieved due to limitations in culturing methods. A non-culture based approach, called “metagenomics”, was developed that enabled researchers to comprehensively analyse microbial communities in different ecosystems. In this study, we highlight recent advances in the field of metagenomics for analyzing microbial communities in different ecosystems ranging from oceans to the human microbiome. Developments in several bioinformatics approaches are also discussed in context of microbial metagenomics that include taxonomic systems, sequence databases, and sequence-alignment tools. In summary, we provide a snapshot for the recent advances in metagenomics approach for analyzing changes in the microbial communities in different ecosystems.

IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation

IBS is a prevalent functional gastrointestinal disorder, in which the microbiota has been demonstrated to play a role. An increasing number of studies have suggested how probiotics may alleviate IBS symptoms and several mechanisms of action have been proposed.   In the present study we characterized the intestinal microbiota of 19 subjects suffering from diagnosed IBS using a fully validated High Taxonomic Fingerprint Microbiota Array (HTF-Microbi.Array). We demonstrated that the IBS microbiota is different from that of healthy individuals due to an unbalance in a number of commensal species, with an increase in relative abundance of lactobacilli, B. cereus and B. clausii, bifidobacteria, Clostridium cluster IX and E. rectale, and a decrease in abundance of Bacteroides/Prevotella group and Veillonella genus. Additionally, we demonstrated that some bacterial groups of the human intestinal microbiota, recently defined as pathobionts, are increased in concentration in the IBS microbiota. Furthermore, we aimed at investigating if the daily administration of a novel probiotic yogurt containing B. animalis subsp lactis Bb12 and K. marxianus B0399, recently demonstrated to have beneficial effects in the management of IBS symptoms, could impact on the biostructure of IBS microbiota, modulating its composition to counteract putative dysbiosis found in IBS subjects. Notably, we demonstrated that the beneficial effects associated to the probiotic preparation are not related to significant modifications in the composition of the human intestinal microbiota.