Dysbiotic drift: mental health,environmental grey space,and microbiota

Advances in research concerning the mental health implications of dietary patterns and select nutrients have been remarkable. At the same time, there have been rapid increases in the understanding of the ways in which non-pathogenic microbes can potentially influence many aspects of human health, including those in the mental realm. Discussions of nutrition and microbiota are often overlapping. A separate, yet equally connected, avenue of research is that related to natural (for example, green space) and built environments, and in particular, how they are connected to human cognition and behaviors. It is argued here that in Western industrial nations a ‘disparity of microbiota’ might be expected among the socioeconomically disadvantaged, those whom face more profound environmental forces. Many of the environmental forces pushing against the vulnerable are at the neighborhood level. Matching the developing microbiome research with existing environmental justice research suggests that grey space may promote dysbiosis by default. In addition, the influence of Westernized lifestyle patterns, and the marketing forces that drive unhealthy behaviors in deprived communities, might allow dysbiosis to be the norm rather than the exception in those already at high risk of depression, subthreshold (subsyndromal) conditions, and subpar mental health. If microbiota are indeed at the intersection of nutrition, environmental health, and lifestyle medicine (as these avenues pertain to mental health), then perhaps the rapidly evolving gut-brain-microbiota conversation needs to operate through a wider lens. In contrast to the more narrowly defined psychobiotic, the term eco-psychotropic is introduced.     

Nutritional psychiatry research: an emerging discipline and its intersection with global urbanization,environmental challenges and the evolutionary mismatch

In 21st-century public health, rapid urbanization and mental health disorders are a growing global concern. The relationship between diet, brain function and the risk of mental disorders has been the subject of intense research in recent years. In this review, we examine some of the potential socioeconomic and environmental challenges detracting from the traditional dietary patterns that might otherwise support positive mental health. In the context of urban expansion, climate change, cultural and technological changes and the global industrialization and ultraprocessing of food, findings related to nutrition and mental health are connected to some of the most pressing issues of our time. The research is also of relevance to matters of biophysiological anthropology. We explore some aspects of a potential evolutionary mismatch between our ancestral past (Paleolithic, Neolithic) and the contemporary nutritional environment. Changes related to dietary acid load, advanced glycation end products and microbiota (via dietary choices and cooking practices) may be of relevance to depression, anxiety and other mental disorders. In particular, the results of emerging studies demonstrate the importance of prenatal and early childhood dietary practices within the developmental origins of health and disease concept. There is still much work to be done before these population studies and their mirrored advances in bench research can provide translation to clinical medicine and public health policy. However, the clear message is that in the midst of a looming global epidemic, we ignore nutrition at our peril.     

Impact of microbial transformation of food on health - from fermented foods to fermentation in the gastro-intestinal tract

Fermentation of food components by microbes occurs both during certain food production processes and in the gastro-intestinal tract. In these processes specific compounds are produced that originate from either biotransformation reactions or biosynthesis, and that can affect the health of the consumer. In this review, we summarize recent advances highlighting the potential to improve the nutritional status of a fermented food by rational choice of food-fermenting microbes. The vast numbers of microbes residing in the human gut, the gut microbiota, also give rise to a broad array of health-active molecules. Diet and functional foods are important modulators of the gut microbiota activity that can be applied to improve host health. A truly multidisciplinary approach is required to increase our understanding of the molecular mechanisms underlying health beneficial effects that arise from the interaction of diet, microbes and the human body.     

Preventive and therapeutic aspects of fermented foods

In recent times, the status of some fermented foods which are considered as functional foods that confer health benefits in certain disease conditions has grown rapidly. The health benefits of fermented foods are due to the presence of probiotic microbes and the bioactive compounds formed during fermentation. Microbes involved and metabolites produced by them are highly species specific and contribute to the authenticity of the fermented foods. Several studies pertaining to the effect of fermented foods on various disease conditions have been conducted in recent years using both animal models and clinical trials on humans. This review focuses on the impact of fermented foods on conditions such as diabetes, cardiovascular disease, obesity, gastrointestinal disorder, cancer and neurodegenerative disorders.     

Influence of dietary fat on intestinal microbes,inflammation, barrier function and metabolic outcomes

Recent studies using germ-free, gnotobiotic microbial transplantation/conventionalization or antibiotic treatment in rodent models have highlighted the critical role of intestinal microbes on gut health and metabolic functions of the host. Genetic and environmental factors influence the abundance and type of mutualistic vs. pathogenic bacteria, each of which has preferred substrates for growth and unique products of fermentation. Whereas some fermentation products or metabolites promote gut function and health, others impair gut function, leading to compromised nutrient digestion and barrier function that adversely impact the host. Such products may also influence food intake, energy harvest and expenditure, and insulin action, thereby influencing adiposity and related metabolic outcomes. Diet composition influences gut microbiota and subsequent fermentation products that impact the host, as demonstrated by prebiotic studies using oligosaccharides or other types of indigestible fiber. Recent studies also show that dietary lipids affect specific populations of gut microbes and their metabolic end products. This review will focus on studies examining the influence of dietary fat amount and type on the gut microbiome, intestinal health and positive and negative metabolic consequences. The protective role of omega-3-rich fatty acids on intestinal inflammation will also be examined.     

Bioactivity of soy-based fermented foods: A review

For centuries, fermented soy foods have been dietary staples in Asia and, now, in response to consumer demand, they are available throughout the world. Fermentation bestows unique flavors, boosts nutritional values and increases or adds new functional properties. In this review, we describe the functional properties and underlying action mechanisms of soy-based fermented foods such as Natto, fermented soy milk, Tempeh and soy sauce. When possible, the contribution of specific bioactive components is highlighted. While numerous studies with in vitro and animal models have hinted at the functionality of fermented soy foods, ascribing health benefits requires well-designed, often complex human studies with analysis of diet, lifestyle, family and medical history combined with long-term follow-ups for each subject. In addition, the contribution of the microbiome to the bioactivities of fermented soy foods, possibly mediated through direct action or bioactive metabolites, needs to be studied. Potential synergy or other interactions among the microorganisms carrying out the fermentation and the host's microbial community may also contribute to food functionality, but the details still require elucidation. Finally, safety evaluation of fermented soy foods has been limited, but is essential in order to provide guidelines for consumption and confirm lack of toxicity.     

Impact of dietary protein on microbiota composition and activity in the gastrointestinal tract of piglets in relation to gut health: a review

In pigs, the microbial ecosystem of the gastrointestinal tract (GIT) is influenced by various factors; however, variations in diet composition have been identified as one of the most important determinants. Marked changes in fermentation activities and microbial ecology may occur when altering the diet, for example, from milk to solid feed during weaning. In that way, access of pathogens to the disturbed ecosystem is alleviated, leading to infectious diseases and diarrhea. Thus, there is increasing interest in improving intestinal health by use of dietary ingredients suitable to beneficially affect the microbial composition and activity. For example, fermentable carbohydrates have been shown to promote growth of beneficial Lactobacillus species and bifidobacteria, thereby enhancing colonization resistance against potential pathogens or production of short-chain fatty acids, which can be used as energy source for epithelial cells. On the other hand, fermentation of protein results in the production of various potentially toxic products, such as amines and NH₃, and is often associated with growth of potential pathogens. In that way, excessive protein intake has been shown to stimulate the growth of potentially pathogenic species such as Clostridium perfringens, and to reduce fecal counts of beneficial bifidobacteria. Therefore, it seems to be a promising approach to support growth and metabolic activity of the beneficial microbiota by developing suitable feeding strategies. For example, a reduction of dietary CP content and, at the same time, dietary supplementation with fermentable carbohydrates have proven to successfully suppress protein fermentation. In addition, the intestinal microbiota seems to be sensible to variations in dietary protein source, such as the use of highly digestible protein sources may reduce growth of protein-fermenting and potentially pathogenic species. The objective of the present review is to assess the impact of dietary protein on microbiota composition and activity in the GIT of piglets. Attention will be given to studies designed to determine the effect of variations in total protein supply, protein source and supplementation of fermentable carbohydrates to the diet on composition and metabolic activity of the intestinal microbiota.     

Traditional fermented beverages from Mexico as a potential probiotic source

Fermentation is one of the oldest ways of processing food. Some fermented food is produced industrially, but can also be produced in an artisanal way by certain ethnic groups, called traditional fermented foods. In Mexico, there are a variety of traditional fermented beverages which are produced in an artisanal way. They include those made with maize (atole agrio, pozol, and tesgüino), fruit (tepache and colonche), and obtained by plant fermentation (pulque, tuba, and taberna). These beverages have been used since ancient times for religious and medicinal purposes. The medicinal effect may be due to fermented microorganisms. The presence of beneficial microorganisms known as probiotics provides beneficial effects to consumer health, improving the balance of intestinal host, and reducing the risk of gastrointestinal diseases, mainly. Most probiotics belong to the genus Lactobacillus, but Bifidobacterium, Bacillus, and yeast are also found. Therefore, it is important that the microbiological diversity of the beverages is studied and documented. This review includes information on the microbial diversity and probiotic potential of the most important traditional fermented beverages from Mexico.     

Dysbiotic drift and biopsychosocial medicine: how the microbiome links personal,public and planetary health

The emerging concept of planetary health emphasizes that the health of human civilization is intricately connected to the health of natural systems within the Earth’s biosphere; here, we focus on the rapidly progressing microbiome science - the microbiota-mental health research in particular - as a way to illustrate the pathways by which exposure to biodiversity supports health. Microbiome science is illuminating the ways in which stress, socioeconomic disadvantage and social polices interact with lifestyle and behaviour to influence the micro and macro-level biodiversity that otherwise mediates health. Although the unfolding microbiome and mental health research is dominated by optimism in biomedical solutions (e.g. probiotics, prebiotics), we focus on the upstream psychosocial and ecological factors implicated in dysbiosis; we connect grand scale biodiversity in the external environment with differences in human-associated microbiota, and, by extension, differences in immune function and mental outlook. We argue that the success of planetary health as a new concept will be strengthened by a more sophisticated understanding of the ways in which individuals develop emotional connections to nature (nature relatedness) and the social policies and practices which facilitate or inhibit the pro-environmental values that otherwise support personal, public and planetary health.     

We and herbivores eat endophytes

Health depends on the diet and a vegetal diet promotes health by providing fibres, vitamins and diverse metabolites. Remarkably, plants may also provide microbes. Fungi and bacteria that reside inside plant tissues (endophytes) seem better protected to survive digestion; thus, we investigated the reported evidence on the endophytic origin of some members of the gut microbiota in animals such as panda, koala, rabbits and tortoises and several herbivore insects. Data examined here showed that some members of the herbivore gut microbiota are common plant microbes, which derived to become stable microbiota in some cases. Endophytes may contribute to plant fibre or antimetabolite degradation and synthesis of metabolites with the plethora of enzymatic activities that they display; some may have practical applications, for example, Lactobacillus plantarum found in the intestinal tract, plants and in fermented food is used as a probiotic that may defend animals against bacterial and viral infections as other endophytic-enteric bacteria do. Clostridium that is an endophyte and a gut bacterium has remarkable capabilities to degrade cellulose by having cellulosomes that may be considered the most efficient nanomachines. Cellulose degradation is a challenge in animal digestion and for biofuel production. Other endophytic-enteric bacteria may have cellulases, pectinases, xylanases, tannases, proteases, nitrogenases and other enzymatic capabilities that may be attractive for biotechnological developments, indeed many endophytes are used to promote plant growth. Here, a cycle of endophytic-enteric-soil-endophytic microbes is proposed which has relevance for health and comprises the fate of animal faeces as natural microbial inoculants for plants that constitute bacterial sources for animal guts.     

Fermentation of prebiotics by human colonic microbiota in vitro and short-chain fatty acids production: a critical review

Prebiotics are known for their health benefits to man, including reducing cardiovascular disease and improving gut health. This review takes a critical assessment of the impact of dietary fibres and prebiotics on the gastrointestinal microbiota in vitro. The roles of colonic organisms, slow fermentation of prebiotics, production of high butyric and propionic acids and positive modulation of the host health were taken into cognizance. Also, the short-chain fatty acids (SCFAs) molecular signalling mechanisms associated with their prebiotic substrate structural conformations and the phenotypic responses related to the gut microbes composition were discussed. Furthermore, common dietary fibres such as resistant starch, pectin, hemicelluloses, β-glucan and fructan in context of their prebiotic potentials for human health were also explained. Finally, the in vitro human colonic fermentation depends on prebiotic type and its physicochemical characteristics, which will then affect the rate of fermentation, selectivity of micro-organisms to multiply, and SCFAs concentrations and compositions.     

中国传统发酵食品微生物组研究进展

传统发酵食品风味独特、营养丰富,多采用自然接种方式进行生产,部分类型的生产技艺已具有数千年的历史。近年来应用新技术手段对传统发酵食品发酵过程进行的研究表明,传统发酵食品微生物组具有丰富的科学内涵和重要的应用价值。本文就我国传统发酵食品微生物组的基本特征、研究进展和发展方向进行了简要的评述。     

Botulism among Alaska Natives. The role of changing food preparation and consumption practices.

Alaska Natives have one of the highest rates of food-borne botulism worldwide. All outbreaks have been associated with the consumption of native foods, but in recent years outbreaks have occurred in previously unaffected areas and have involved new food items. Five botulism outbreaks occurred between 1975 and 1985 in an area of southwestern Alaska without previous confirmed outbreaks and among one ethnic group, the Yupik Eskimo. Of the 5 outbreaks, 3 were associated with fermented beaver tail, a nontraditional native food recently introduced into the region. Preparation techniques vary widely within villages and among ethnic groups. Traditional fermentation techniques have changed over the past 50 years; current preparation methods used by some families and ethnic groups may be more favorable for Clostridium botulinum growth. Prevention efforts should be targeted at high-risk subgroups of Alaska Natives who appear to have modified traditional practices and increased their risk of food-borne botulism.     

Impact of supplementation with a food-derived microbial community on obesity-associated inflammation and gut microbiota composition

Background

Obesity is a complex pathology associated with dysbiosis, metabolic alterations, and low-grade chronic inflammation promoted by immune cells, infiltrating and populating the adipose tissue. Probiotic supplementation was suggested to be capable of counteracting obesity-associated immune and microbial alterations, based on its proven immunomodulatory activity and positive effect on gut microbial balance. Traditional fermented foods represent a natural source of live microbes, including environmental strains with probiotic features, which could transiently colonise the gut. The aim of our work was to evaluate the impact of supplementation with a complex foodborne bacterial consortium on obesity-associated inflammation and gut microbiota composition in a mouse model.

Methods

C57BL/6J mice fed a 45% high fat diet (HFD) for 90 days were supplemented with a mixture of foodborne lactic acid bacteria derived from the traditional fermented dairy product “Mozzarella di Bufala Campana” (MBC) or with the commercial probiotic GG strain of Lactobacillus rhamnosus (LGG). Inflammation was assessed in epididymal white adipose tissue (WAT) following HFD. Faecal microbiota composition was studied by next-generation sequencing.

Results

Significant reduction of epididymal WAT weight was observed in MBC-treated, as compared to LGG and control, animals. Serum metabolic profiling showed correspondingly reduced levels of triglycerides and higher levels of HDL cholesterol, as well as a trend toward reduction of LDL-cholesterol levels. Analysis of the principal leucocyte subpopulations in epididymal WAT revealed increased regulatory T cells and CD4⁺ cells in MBC microbiota-supplemented mice, as well as decreased macrophage and CD8⁺ cell numbers, suggesting anti-inflammatory effects. These results were associated with lower levels of pro-inflammatory cytokines and chemokines in WAT explants. Faecal bacterial profiling demonstrated increased Firmicutes/Bacteroidetes ratio in all mice groups following HFD.

Conclusions

Taken together, these results indicate a protective effect of MBC microbiota supplementation toward HFD-induced fat accumulation and triglyceride and cholesterol levels, as well as inflammation, suggesting a stronger effect of a mixed microbial consortium vs single-strain probiotic supplementation. The immunomodulatory activity exerted by the MBC microbiota could be due to synergistic interactions within the microbial consortium, highlighting the important role of dietary microbes with yet uncharacterised probiotic effect.

     

Gut Microbiota,Prebiotics, Probiotics,and Synbiotics in Management of Obesity and Prediabetes: Review of Randomized Controlled Trials

Objective: To review the data from randomized controlled trials (RCTs) for the roles of microbiota, pre-, pro- and synbiotics in metabolic conditions (obesity, prediabetes, and diabetes mellitus type 2 [DM2]).Methods: Primary literature was reviewed on the topics including RCTs of pre-, pro- and synbiotics use for metabolic disease.Results: Gut bacteria (microbiota) benefit digestion and have multiple other functions. Microbiota could increase harvesting of energy from the food and cause subclinical inflammation seen in metabolic disorders. Diet-related interventions including prebiotics, probiotics, and synbiotics (combining pre-and probiotics) may benefit metabolic conditions. Prebiotics are complex carbohydrates (i.e., dietary fiber). Results of RCTs of prebiotics suggested a neutral effect on body weight, decreased fasting and postprandial glucose, and improved insulin sensitivity and lipid profile. Some inflammation markers were reduced, sometimes substantially (20–30%). RCTs for probiotics demonstrated significant but small effects on body weight (<3%) and metabolic parameters. The effect was seen mostly with fermented milk or yogurt compared to capsule form, consumption for at least 8 weeks, and use of multiple rather than a single bacterial strain. Changes in microbiota were seen at times with both pre- and probiotics. Pickled and fermented foods, particularly vegetables and beans, could serve as a dietary source of pre-, pro-, and synbiotics. These foods showed possible benefits for morbidity and mortality in prospective cohort studies.Conclusion: Pre-, pro-, and synbiotics could prove useful, but further research is needed to clarify their clinical relevance for the prevention and management of metabolic disease.Abbreviations:A1c = glycohemoglobin A1cCI = confidence intervalCVD = cardiovascular diseaseGMB = gut (large bowel) microbiotaDM2 = diabetes mellitus type 2HOMA-IR = homeostatic model assessment of insulin resistanceLDL = low-density lipoproteinLPS = lipopolysaccharideNAFLD = nonalcoholic fatty liver diseaseRCT = randomized controlled trialSMD = standardized mean differenceTG = triglycerides     

Molecular Paths Linking Metabolic Diseases,Gut Microbiota Dysbiosis and Enterobacteria Infections

Alterations of both ecology and functions of gut microbiota are conspicuous traits of several inflammatory pathologies, notably metabolic diseases such as obesity and type 2 diabetes. Moreover, the proliferation of enterobacteria, subdominant members of the intestinal microbial ecosystem, has been shown to be favored by Western diet, the strongest inducer of both metabolic diseases and gut microbiota dysbiosis. The inner interdependence between the host and the gut microbiota is based on a plethora of molecular mechanisms by which host and intestinal microbes modify each other. Among these mechanisms are as follows: (i) the well-known metabolic impact of short chain fatty acids, produced by microbial fermentation of complex carbohydrates from plants; (ii) a mutual modulation of miRNAs expression, both on the eukaryotic (host) and prokaryotic (gut microbes) side; (iii) the production by enterobacteria of virulence factors such as the genotoxin colibactin, shown to alter the integrity of host genome and induce a senescence-like phenotype in vitro; (iv) the microbial excretion of outer-membrane vesicles, which, in addition to other functions, may act as a carrier for multiple molecules such as toxins to be delivered to target cells. In this review, I describe the major molecular mechanisms by which gut microbes exert their metabolic impact at a multi-organ level (the gut barrier being in the front line) and support the emerging triad of metabolic diseases, gut microbiota dysbiosis and enterobacteria infections.     

In vitro evaluation of the microbiota modulation abilities of different sized whole oat grain flakes

Epidemiological studies and healthy eating guidelines suggest a positive correlation between ingestion of whole grain cereal and food rich in fibre with protection from chronic diseases. The prebiotic potential of whole grains may be related, however, little is known about the microbiota modulatory capability of oat grain or the impact processing has on this ability. In this study the fermentation profile of whole grain oat flakes, processed to produce two different sized flakes (small and large), by human faecal microbiota was investigated in vitro. Simulated digestion and subsequent fermentation by gut bacteria was investigated using pH controlled faecal batch cultures inoculated with human faecal slurry. The different sized oat flakes, Oat 23’s (0.53–0.63 mm) and Oat 25’s/26’s (0.85–1.0 mm) were compared to oligofructose, a confirmed prebiotic, and cellulose, a poorly fermented carbohydrate. Bacterial enumeration was carried out using the culture independent technique, fluorescent in situ hybridisation, and short chain fatty acid (SCFA) production monitored by gas chromatography. Significant changes in total bacterial populations were observed after 24 h incubation for all substrates except Oat 23’s and cellulose. Oats 23’s fermentation resulted in a significant increase in the Bacteroides–Prevotella group. Oligofructose and Oats 25’s/26’s produced significant increases in Bifidobacterium in the latter stages of fermentation while numbers declined for Oats 23’s between 5 h and 24 h. This is possibly due to the smaller surface area of the larger flakes inhibiting the simulated digestion, which may have resulted in increased levels of resistant starch (Bifidobacterium are known to ferment this dietary fibre). Fermentation of Oat 25’s/26’s resulted in a propionate rich SCFA profile and a significant increase in butyrate, which have both been linked to benefiting host health. The smaller sized oats did not produce a significant increase in butyrate concentration. This study shows for the first time the impact of oat grain on the microbial ecology of the human gut and its potential to beneficially modulate the gut microbiota through increasing Bifidobacterium population.     

Microbial diversity and dynamics of microbial communities during back-slop soaking of soybeans as determined by PCR–DGGE and molecular cloning

Tempe is a traditional fermented food in Indonesia. The manufacture process is quite complex, which comprises two stages, preparatory soaking of soybeans and fungal solid state fermentation. Daily addition of previous soak water (back-slopping) during the soybean soaking step is considered to be crucial in the manufacture of high quality tempe. The microbial diversity and dynamics of the microbial communities evolving during back-slop soaking of soybeans for tempe making was investigated by culture-independent PCR–DGGE and molecular cloning. Both DNA and total RNA were isolated and included in this study, to obtain a view on the succession of total and viable bacteria in the complex microbiota. DGGE profiles indicated that Enterobacter sp., Enterococcus sp., Pseudomonas putida, Leuconostoc fallax, Pediococcus pentosaceus, and Weissella cibaria, were the predominant bacteria. Their occurrence shifted dramatically during the back-slop soaking procedure. This study combined with previous culture-dependent studies could gain a better understanding of the complex microbiota of traditional fermented food and give useful information for its quality control.     

Panose, a new prebiotic candidate

Aims:  To investigate the prebiotic potential of two novel candidates, sophorose and panose, with in vitro methods.
Methods and Results:  The growth of single microbial strains was first assessed for both substrates in pure cultures, and panose was further analysed in the simulated colon model with mixed human faecal culture. Quantitative PCR and flow cytometry were used to determine the microbial group and strain densities after the simulated colonic fermentation of panose, and chromatographic methods were utilized to analyse metabolite concentrations. In pure cultures, sophorose and panose were both fermented only by few beneficial strains, and in the colon simulator, panose gave a significant increase in the numbers of Bifidobacterium and Bifidobacterium lactis , concomitantly decreasing Bacteroides group. Butyrate and acetate production was significantly increased together with decreased markers of protein fermentation as a result of panose fermentation.
Conclusions:  Panose had bifidogenic activities in vitro , and these potential beneficial effects should be further assessed in vitro and in vivo .
Significance and Impact of the Study:  The current study has provided the first data on pure panose fermentation by the endogenous microbiota and extends our knowledge of the selective fermentation of oligosaccharides by the intestinal microbes.     

Simulated colon fiber metabolome regulates genes involved in cell cycle, apoptosis, and energy metabolism in human colon cancer cells

High level of dietary fiber has been epidemiologically linked to protection against the risk for developing colon cancer. The mechanisms of this protection are not clear. Fermentation of dietary fiber in the colon results in production of for example butyrate that has drawn attention as a chemopreventive agent. Polydextrose, a soluble fiber that is only partially fermented in colon, was fermented in an in vitro colon simulator, in which the conditions mimic the human proximal, ascending, transverse, and distal colon in sequence. The subsequent fermentation metabolomes were applied on colon cancer cells, and the gene expression changes studied. Polydextrose fermentation down-regulated gene ontology classes linked with cell cycle, and affected number of metabolically active cells. Furthermore, up-regulated effects on classes linked with apoptosis, with increased caspase 2 and 3 activity, implicate that polydextrose fermentation plays a role in induction of apoptosis in colon cancer cells. The up-regulated genes involved also key regulators of lipid metabolism, such as PPARα and PGC-1α. These results offer hypotheses for the mechanisms of two health benefits linked with consumption of dietary fiber, reducing risk of development of colon cancer, and dyslipidemia.