A healthy gastrointestinal microbiome is dependent on dietary diversity

Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review

Understanding how dietary nutrients modulate the gut microbiome is of great interest for the development of food products and eating patterns for combatting the global burden of non-communicable diseases. In this narrative review we assess scientific studies published from 2005 to 2019 that evaluated the effect of micro- and macro-nutrients on the composition of the gut microbiome using in vitro and in vivo models, and human clinical trials. The clinical evidence for micronutrients is less clear and generally lacking. However, preclinical evidence suggests that red wine- and tea-derived polyphenols and vitamin D can modulate potentially beneficial bacteria. Current research shows consistent clinical evidence that dietary fibers, including arabinoxylans, galacto-oligosaccharides, inulin, and oligofructose, promote a range of beneficial bacteria and suppress potentially detrimental species. The preclinical evidence suggests that both the quantity and type of fat modulate both beneficial and potentially detrimental microbes, as well as the Firmicutes/Bacteroides ratio in the gut. Clinical and preclinical studies suggest that the type and amount of proteins in the diet has substantial and differential effects on the gut microbiota. Further clinical investigation of the effect of micronutrients and macronutrients on the microbiome and metabolome is warranted, along with understanding how this influences host health.

Accumulation of polybrominated diphenyl ethers and microbiome response in the great pond snail Lymnaea stagnalis with exposure to nylon (polyamide) microplastics

Microplastics attract widespread attention, including for their potential to transport toxic chemicals in the form of plasticisers and associated hydrophobic organic chemicals, such as polybrominated diphenyl ethers (PBDEs). The aims of this study were to investigate how nylon (polyamide) microplastics may affect PBDE accumulation in snails, and the acute effects of nylon particles and PBDEs on survival, weight change and inherent microbiome diversity and community composition of the pond snail Lymnaea stagnalis. Snails were exposed for 96 h to BDEs-47, 99, 100 and 153 in the presence and absence of 1% w/w nylon microplastics in quartz sand sediment. No mortality was observed over the exposure period. Snails not exposed to microplastics lost significantly more weight compared to those exposed to microplastics. Increasing PBDE concentration in the sediment resulted in an increased PBDE body burden in the snails, however microplastics did not significantly influence total PBDE uptake. Based on individual congeners, uptake of BDE 47 by snails was significantly reduced in the presence of microplastics. The diversity and composition of the snail microbiome was not significantly altered by the presence of PBDEs nor by the microplastics, singly or combined. Significant effects on a few individual operational taxonomic units (OTUs) occurred when comparing the highest PBDE concentration with the control treatment, but in the absence of microplastics only. Overall within these acute experiments, only subtle effects on weight loss and slight microbiome alterations occurred. These results therefore highlight that L. stagnalis are resilient to acute exposures to microplastics and PBDEs, and that microplastics are unlikely to influence HOC accumulation or the microbiome of this species over short timescales.

Gut microbiota composition after diet and probiotics in overweight breast cancer survivors: a randomized open-label pilot intervention trial

OBJECTIVES

Breast cancer (BC) is the most diagnosed cancer in women. Increasing survival rates shift attention to preventive strategies. Obesity and intestinal microbiota composition may be associated with BC. A Mediterranean diet (MD) proved to be protective. The aim of this study was to assess the efficacy of probiotics in addition to an MD versus diet alone in influencing gut microbiota and metabolic profile in overweight BC survivors.

METHODS

A total of 34 BC survivors were randomly assigned to an MD for 4 mo plus 1 sachet/d of probiotics (Bifidobacterium longum BB536, Lactobacillus rhamnosus HN001) for the first 2 mo (intervention group, n = 16) or an MD alone for 4 mo (control group, n = 18). Anthropometric and nutritional assessments, adherence to the MD, compliance with physical activity, and metabolic parameters dosage were performed at baseline (T0), at 2 mo (T2), and at 4 mo (T4). Intestinal microbiota analysis was performed at T0 and T2.

RESULTS

After 2 mo of probiotic administration the number of bacterial species (P = 0.01) and the bacterial diversity assessed with the Chao1 index (P = 0.004) significantly increased; no significant variations were detected after diet alone. The Bacteroidetes-to-Firmicutes ratio significantly decreased in the intervention group and increased in controls (P = 0.004). Significant reductions of body weight, body mass index, fasting glucose, and homeostasis model assessment of insulin resistance were identified at T4 in both groups; in the intervention group waist circumference (P = 0.012), waist-to-hip ratio (P = 0.045), and fasting insulin (P = 0.017) also significantly decreased.

CONCLUSIONS

Probiotics in addition to an MD positively influence gut microbiota and improve metabolic and anthropometric parameters compared with an MD alone.

Effects of Added Dietary Fiber and Rearing System on the Gut Microbial Diversity and Gut Health of Chickens

It is of merit to study the appropriate amount of dietary fiber to add to free-range chickens' feed to improve their microbial diversity and gut health in times of plant fiber deprivation. Lignocellulose is a useful source of dietary fiber, and its positive effects on the growth performance and laying performance of chickens has already been proven. However, few researchers have researched the effects of adding it on the gut microbiota of chickens. In this research, we added three different levels of eubiotic lignocellulose (0%, 2%, and 4%) to the feed of caged and free-range Bian chickens from September to November, aiming to observe the effects of added dietary fiber and different rearing systems on the gut microbial diversity and gut health of chickens, as well as to determine an appropriate amount of lignocellulose. The results showed that adding dietary fiber increased the thickness of the cecum mucus layer and the abundance of Faecalibacterium and Faecalibacterium in caged chickens, and 4% lignocellulose was appropriate. In addition, adding lignocellulose increased the microbial diversity and the abundance of the butyrate-producing bacteria Faecalibacterium and Roseburia in fee-range chickens. The α-diversity and the length of the small intestine with 2% lignocellulose in free-range chickens were better than with 2% lignocellulose in caged chickens. Maybe it is necessary to add dietary fiber to the feed of free-range chickens when plant fibers are lacking, and 2% lignocellulose was found to be appropriate in this experiment. In addition, compared with caged chickens, the free-range chickens had a longer small intestine and a lower glucagon like peptide-1 (GLP-1) level. The significant difference of GLP-1 levels was mainly driven by energy rather than short chain fatty acids (SCFAs). There was no interaction between added dietary fiber and the rearing system on SCFAs, cecum inner mucus layer, and GLP-1.

Effect of time-restricted feeding on metabolic risk and circadian rhythm associated with gut microbiome in healthy males

Time-restricted feeding (TRF) confers protection against nutritional challenges that predispose obesity and metabolic risks through involvement of circadian locomotor output cycles protein kaput genes and gut microbiome, but the underlying mechanism is not clearly understood. Therefore, the present study examined the effects of TRF on metabolic markers and circadian rhythm associated with gut microbiota in healthy males. Two groups (TRF, n 56; non-TRF, n 24) of male adults were enrolled. The TRF group provided blood at pre-TRF and post-TRF, while non-TRF one time after 25 d of trial. Serum lipid and liver profiles were determined. Real time-PCR was applied for circadian and inflammatory gene expression. The 16S rRNA genes were sequenced on the Illumina Miseq v3 platform to comprehensively catalogue the composition and abundance of bacteria in stool. We showed that TRF ameliorated the serum lipid and liver profiles of the individuals. In the TRF group, gut microbial richness was significantly enhanced, with enrichment of Prevotellaceae and Bacteroideaceae. TRF enhanced circadian gene expression probably by activation of sirtuin-1, which is positively associated with gut microbiome richness. TRF could be a safe remedy for the prevention of metabolic diseases related to dyslipidaemia, as it regulates circadian rhythm associated with gut microbiome modulation.

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.

Colonic bacterial composition is sex-specific in aged CD-1 mice fed diets varying in fat quality

Evidence suggests that sex influences the effect of diet on the gut bacterial composition, yet, no studies have been performed assessing dietary fatty acid composition (i.e., fat quality) in this context. This study examined the effect of dietary fat quality on colonic bacterial composition in an aged, genetically-diverse mouse population. CD-1 mice were fed isoenergetic diets consisting of (1) control fat (CO; "Western-style" fat blend), (2) CO supplemented with 30% fish oil, (3) CO supplemented with 30% dairy fat, or (4) CO supplemented with 30% echium oil. Fecal samples were collected at mid-life and aged (reproductively senescent) time points. Overall, the abundance of Bacteroidetes was greater in mice fed echium oil compared to mice fed the control fat. Examination of colonic bacterial relative abundance also revealed sex differences, with 73 bacterial taxa being differentially expressed in males and females. Notably, results showed a strong interactive effect among the diet, sex, and age of mice which influenced colonic bacterial relative abundance and alpha diversity. In males, supplementation of the diet with dairy fat or echium oil caused the abundance of Bacteroidetes and Bacteroides to change with age. Additionally, supplementation of the diet with fish oil induced sex-dependent changes in the alpha diversity of aged mice compared to mid-life. This work supports that sex is a critical factor in colonic bacterial composition of an aged, genetically-heterogenous population. Moreover, this study establishes that the effectiveness of dietary interventions for health maintenance and disease prevention via direct or indirect manipulation of the gut microbiota is likely dependent on an individual's sex, age, and genetic background.

Diet in Parkinson's Disease: Critical Role for the Microbiome

Background: Parkinson's disease (PD) is the most common movement disorder affecting up to 1% of the population above the age of 60 and 4–5% of those above the age of 85. Little progress has been made on efforts to prevent disease development or halt disease progression. Diet has emerged as a potential factor that may prevent the development or slow the progression of PD. In this review, we discuss evidence for a role for the intestinal microbiome in PD and how diet-associated changes in the microbiome may be a viable approach to prevent or modify disease progression.

Methods: We reviewed studies demonstrating that dietary components/foods were related to risk for PD. We reviewed evidence for the dysregulated intestinal microbiome in PD patients including abnormal shifts in the intestinal microbiota composition (i.e., dysbiosis) characterized by a loss of short chain fatty acid (SCFA) bacteria and increased lipopolysaccharide (LPS) bacteria. We also examined several candidate mechanisms by which the microbiota can influence PD including the NLRP3 inflammasome, insulin resistance, mitochondrial function, vagal nerve signaling.

Results: The PD-associated microbiome is associated with decreased production of SCFA and increased LPS and it is believed that these changes may contribute to the development or exacerbation of PD. Diet robustly impacts the intestinal microbiome and the Western diet is associated with increased risk for PD whereas the Mediterranean diet (including high intake of dietary fiber) decreases PD risk. Mechanistically this may be the consequence of changes in the relative abundance of SCFA-producing or LPS-containing bacteria in the intestinal microbiome with effects on intestinal barrier function, endotoxemia (i.e., systemic LPS), NLRP3 inflammasome activation, insulin resistance, and mitochondrial dysfunction, and the production of factors such as glucagon like peptide 1 (GLP-1) and brain derived neurotrophic factor (BDNF) as well as intestinal gluconeogenesis.

Conclusions: This review summarizes a model of microbiota-gut-brain-axis regulation of neuroinflammation in PD including several new mechanisms. We conclude with the need for clinical trials in PD patients to test this model for beneficial effects of Mediterranean based high fiber diets.

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro-organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (Sciurus aberti) and fox squirrels (S. niger) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber-rich inner bark of ponderosa pine (Pinus ponderosa). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.

Gut Microbiota and Cardiometabolic Risk Factors in Hemodialysis Patients: A Pilot Study

The gut microbiota has been implicated in the pathogenesis and progression of kidney disease. However, little is known about the gut microbiota in hemodialysis (HD) patients. We assessed the gut microbiota and its relationship with clinical variables in ten HD patients. We found that the Firmicutes-to-Bacteroidetes ratio was positively associated with traditional risk factors for cardiovascular disease. Furthermore, Faecalibacterium was positively associated with carbohydrate intake and negatively associated with arterial stiffness. Finally, endotoxemia was inversely associated with butyrate producers. Future studies should assess if targeting the gut microbiota result in a lower burden for cardiovascular disease in HD patients.

Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration

The human gut is inhabited by trillions of microorganisms composing a dynamic ecosystem implicated in health and disease. The composition of the gut microbiota is unique to each individual and tends to remain relatively stable throughout life, yet daily transient fluctuations are observed. Diet is a key modifiable factor influencing the composition of the gut microbiota, indicating the potential for therapeutic dietary strategies to manipulate microbial diversity, composition, and stability. While diet can induce a shift in the gut microbiota, these changes appear to be temporary. Whether prolonged dietary changes can induce permanent alterations in the gut microbiota is unknown, mainly due to a lack of long-term human dietary interventions, or long-term follow-ups of short-term dietary interventions. It is possible that habitual diets have a greater influence on the gut microbiota than acute dietary strategies. This review presents the current knowledge around the response of the gut microbiota to short-term and long-term dietary interventions and identifies major factors that contribute to microbiota response to diet. Overall, further research on long-term diets that include health and microbiome measures is required before clinical recommendations can be made for dietary modulation of the gut microbiota for health.

"Photobiomics": Can Light, Including Photobiomodulation, Alter the Microbiome?

Objective: The objective of this review is to consider the dual effects of microbiome and photobiomodulation (PBM) on human health and to suggest a relationship between these two as a novel mechanism. Background: PBM describes the use of low levels of visible or near-infrared (NIR) light to heal and stimulate tissue, and to relieve pain and inflammation. In recent years, PBM has been applied to the head as an investigative approach to treat diverse brain diseases such as stroke, traumatic brain injury (TBI), Alzheimer's and Parkinson's diseases, and psychiatric disorders. Also, in recent years, increasing attention has been paid to the total microbial population that colonizes the human body, chiefly in the gut and the mouth, called the microbiome. It is known that the composition and health of the gut microbiome affects many diseases related to metabolism, obesity, cardiovascular disorders, autoimmunity, and even brain disorders. Materials and methods: A literature search was conducted for published reports on the effect of light on the microbiome. Results: Recent work by our research group has demonstrated that PBM (red and NIR light) delivered to the abdomen in mice, can alter the gut microbiome in a potentially beneficial way. This has also now been demonstrated in human subjects. Conclusions: In consideration of the known effects of PBM on metabolomics, and the now demonstrated effects of PBM on the microbiome, as well as other effects of light on the microbiome, including modulating circadian rhythms, the present perspective introduces a new term "photobiomics" and looks forward to the application of PBM to influence the microbiome in humans. Some mechanisms by which this phenomenon might occur are considered.

The role of the brain-gut-microbiota axis in psychology: The importance of considering gut microbiota in the development, perpetuation, and treatment of psychological disorders

INTRODUCTION

The prevalence of psychological disorders remains stable despite steady increases in pharmacological treatments suggesting the need for auxiliary treatment options. Consideration of the brain-gut-microbiota axis (BGMA) has made inroads into reconceptualizing psychological illness from a more holistic perspective. While our understanding of the precise role of gut microbiota (GM) in psychological illness is in its infancy, it represents an attractive target for novel interventions.

METHOD

An extensive review of relevant literature was undertaken.

RESULTS

Gut microbiota are proposed to directly and indirectly influence mood, cognition, and behavior which are key components of mental health. This paper outlines how GM may be implicated in psychological disorders from etiology through to treatment and prevention using the Four P model of case formulation.

CONCLUSION

Moving forward, integration of GM into the conceptualization and treatment of psychological illness will require the discipline of psychology to undergo a significant paradigm shift. While the importance of the GM in psychological well-being must be respected, it is not proposed to be a panacea, but instead, an additional arm to a multidisciplinary approach to treatment and prevention.

City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii)

Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non-model species - the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen-15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human-altered landscapes.

Dietary intake influences gut microbiota development of healthy Australian children from the age of one to two years

Early life nutrition is a vital determinant of an individual’s life-long health and also directly influences the ecological and functional development of the gut microbiota. However, there are limited longitudinal studies examining the effect of diet on the gut microbiota development in early childhood. Here, up to seven stool samples were collected from each of 48 healthy children during their second year of life, and microbiota dynamics were assessed using 16S rRNA gene amplicon sequencing. Children’s dietary information was also collected during the same period using a validated food frequency questionnaire designed for this age group, over five time points. We observed significant changes in gut microbiota community, concordant with changes in the children’s dietary pattern over the 12-month period. In particular, we found differential effects on specific Firmicutes-affiliated lineages in response to frequent intake of either processed or unprocessed foods. Additionally, the consumption of fortified milk supplemented with a Bifidobacterium probiotic and prebiotics (synbiotics) further increased the presence of Bifidobacterium spp., highlighting the potential use of synbiotics to prolong and sustain changes in these lineages and shaping the gut microbiota community in young children.

Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota

The diversity of the colonic microbial community has been linked with health in adults and diet composition is one possible determinant of diversity. We used carefully controlled conditions in vitro to determine how the complexity and multiplicity of growth substrates influence species diversity of the human colonic microbiota. In each experiment, five parallel anaerobic fermenters that received identical faecal inocula were supplied continuously with single carbohydrates (either arabinoxylan-oligosaccharides (AXOS), pectin or inulin) or with a '3-mix' of all three carbohydrates, or with a '6-mix' that additionally contained resistant starch, β-glucan and galactomannan as energy sources. Inulin supported less microbial diversity over the first 6 d than the other two single substrates or the 3- and 6-mixes, showing that substrate complexity is key to influencing microbiota diversity. The communities enriched in these fermenters did not differ greatly at the phylum and family level, but were markedly different at the species level. Certain species were promoted by single substrates, whilst others (such as Bacteroides ovatus, LEfSe P = 0.001) showed significantly greater success with the mixed substrate. The complex polysaccharides such as pectin and arabinoxylan-oligosaccharides promoted greater diversity than simple homopolymers, such as inulin. These findings suggest that dietary strategies intended to achieve health benefits by increasing gut microbiota diversity should employ complex non-digestible substrates and substrate mixtures.

Different Gut Microbial Profiles in Sub-Saharan African and South Asian Women of Childbearing Age Are Primarily Associated With Dietary Intakes

Background

To compare and characterize the gut microbiota in women of childbearing age from sub-Saharan Africa (the Democratic Republic of the Congo, DRC) and South Asia (India), in relation to dietary intakes.

Methods

Women of childbearing age were recruited from rural DRC and India as part of the Women First (WF) preconception maternal nutrition trial. Findings presented include fecal 16S rRNA gene-based profiling of women in the WF trial from samples obtained at the time of randomization, prior to initiation of nutrition intervention and to conception.

Results

Stool samples were collected from 217 women (DRC n = 117; India n = 100). Alpha diversity of the gut microbiota was higher in DRC than in India (Chao1: 91 ± 11 vs. 82 ± 12, P = 6.58E-07). The gut microbial community structure was not significantly affected by any demographical or environmental variables, such as maternal BMI, education, and water source. Prevotella, Succinivibrio, and Roseburia were at relatively high abundance without differences between sites. Bifidobacterium was higher in India (4.95 ± 1.0%) than DRC (0.3 ± 0.1%; P = 2.71E-27), as was Lactobacillus (DRC: 0.2 ± 0.0%; India: 1.2 ± 0.1%; P = 2.39E-13) and Faecalibacterium (DRC: 6.0 ± 1.7%; India: 8.4 ± 2.9%; P = 6.51E-7). Ruminococcus was higher in DRC (2.3 ± 0.7%) than in India (1.8 ± 0.4%; P = 3.24E-5) and was positively associated with consumption of flesh foods. Succinivibrio was positively associated with dairy intake in India and fish/insects in DRC. Faecalibacterium was positively associated with vitamin A-rich fruits and vegetables. Overall, these observations were consistent with India being primarily vegetarian with regular fermented dairy consumption and DRC regularly consuming animal-flesh foods.

Conclusion

Consumption of animal-flesh foods and fermented dairy foods were independently associated with the gut microbiota while demographic variables were not, suggesting that diet may have a stronger association with microbiota than demographic characteristics.

Gut microbes, ageing & organ function: a chameleon in modern biology?

All species, including humans, are cohabited by a myriad of microbial species, which massively influences body function in a diet‐, exercise‐ and age‐dependent manner. The microbiome composition differs between individuals, partly due to the polymorphic immune system, as well as the environment, making the microbe–host interplay unique in each one of us. Ageing is a gradual loss of function in part due to reduced repair mechanisms and accumulation of tissue damage through mechanisms largely unknown. Accumulating evidence suggests that our indigenous microbes, a known major regulator of human physiology, are also connected to regulate the ageing process through signalling pathways and metabolites though the biological mechanisms are unknown. At an ageing meeting in Singapore in 2018, investigators discussed the current understanding of microbe regulation and its impact on healthy ageing. This review summarizes the highlights from the meeting and conveys some of the new ideas that emerged around gut microbes and the biology of ageing. While highly speculative, an idea emerged in which gut microbes constantly respond and evolve to environmental cues, as part of an ageing process, thus serving as a second messenger to support and attenuate organ decline in a diet‐, gender‐ and age‐dependent manner.

Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective

Sponges establish tight associations with both micro- and macroorganisms. However, while studies on sponge microbiomes are numerous, nothing is currently known about the microbiomes of sponge-associated polychaetes and their relationships with those of their host sponges. We analyzed the bacterial communities of symbiotic polychaetes (Haplosyllis spp.) and their host sponges (Clathria reinwardti, Amphimedon paraviridis, Neofibularia hartmani, and Aaptos suberitoides) to assess the influence of the sponges on the polychaete microbiomes. We identified both eukaryote partners by molecular (16S and COI genes) and morphological features, and we identified their microbial communities by high-throughput sequencing of the 16S rRNA gene (V4 region). We unravel the existence of six Haplosyllis species (five likely undescribed) associated at very high densities with the study sponge species in Nha Trang Bay (central Vietnam). A single polychaete species inhabited A. paraviridis and was different from the single species that inhabited A. suberitoides Conversely, two different polychaete species were found in C. reinwardti and N. hartmani, depending on the two host locations. Regardless of the host sponge, polychaete microbiomes were species specific, which is a widespread feature in marine invertebrates. More than half of the polychaete bacteria were also found in the host sponge microbiome but at contrasting abundances. Thus, the associated polychaetes seemed to be able to select, incorporate, and enrich part of the sponge microbiome, a selection that appears to be polychaete species specific. Moreover, the bacterial diversity is similar in both eukaryotic partners, which additionally confirms the influence of food (host sponge) on the structure of the polychaete microbiome.IMPORTANCE The symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own bacterial communities. Here, we study the microbiomes of sponge-polychaete associations and confirm that polychaetes feed on their host sponges. The study worms select and enrich part of the sponge microbiome to shape their own species-specific bacterial communities. Moreover, worm microbiome diversity runs parallel to that of its food host sponge. Considering our results on symbiotic polychaetes and previous studies on fishes and mammals, diet appears to be an important source of bacteria for animals to shape their species-specific microbiomes.

Alzheimer's disease and symbiotic microbiota: an evolutionary medicine perspective

Microorganisms resident in our bodies participate in a variety of regulatory and pathogenic processes. Here, we describe how etiological pathways implicated in Alzheimer's disease (AD) may be regulated or disturbed by symbiotic microbial activity. Furthermore, the composition of symbiotic microbes has changed dramatically across human history alongside the rise of agriculturalism, industrialization, and globalization. We postulate that each of these lifestyle transitions engendered progressive depletion of microbial diversity and enhancement of virulence, thereby enhancing AD risk pathways. It is likely that the human life span extended into the eighth decade tens of thousands of years ago, yet little is known about premodern geriatric epidemiology. We propose that microbiota of the gut, oral cavity, nasal cavity, and brain may modulate AD pathogenesis, and that changes in the microbial composition of these body regions across history suggest escalation of AD risk. Dysbiosis may promote immunoregulatory dysfunction due to inadequate education of the immune system, chronic inflammation, and epithelial barrier permeability. Subsequently, proinflammatory agents-and occasionally microbes-may infiltrate the brain and promote AD pathogenic processes. APOE genotypes appear to moderate the effect of dysbiosis on AD risk. Elucidating the effect of symbiotic microbiota on AD pathogenesis could contribute to basic and translational research.

Newer perspectives in the treatment of chronic osteomyelitis: A preliminary outcome report

The prevalence of chronic osteomyelitis due to trauma and surgical complications does not seem to be diminishing in our society. In many African Nations, with the urbanization and shift to the larger cities that has been occurring, Trauma has been classified as the number one disease problem plaguing such societies. This brings along with it the ensuing infections. With our better understanding of how microbes gain attachment to sites in our body and morph from a planktonic state to the slow growing sessile phase of growth, combined with their formation of a highly structured biofilm colony, we have come to realize that we must resort to other forms of treatment. This means changing our philosophical approach to treatment utilized over the past nearly 70 years involving complete reliance on chemotherapeutic agents with their resultant questionable efficacy in the treatment of chronic osteomyelitis. We report on preliminary early outcome results in the treatment of 127 patients with chronic osteomyelitis treated by a single surgeon in which all patients except those with underlying immunological impairment were treated with in-hospital intravenous antibiotics only. Only 5.5% of the patient population then received intravenous antibiotics following hospital discharge, and with this treatment approach there remained a 98.4% cure rate in the treatment of this chronic infection.

Gut microbiota in ALS: possible role in pathogenesis?

Introduction: The gut microbiota has important roles in maintaining human health. The microbiota and its metabolic byproducts could play a role in the pathogenesis of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Areas covered: The authors evaluate the methods of assessing the gut microbiota, and also review how the gut microbiota affects the various physiological functions of the gut. The authors then consider how gut dysbiosis could theoretically affect the pathogenesis of ALS. They present the current evidence regarding the composition of the gut microbiota in ALS and in rodent models of ALS. Finally, the authors review therapies that could improve gut dysbiosis in the context of ALS. Expert opinion: Currently reported studies suggest some instances of gut dysbiosis in ALS patients and mouse models; however, these studies are limited, and more information with well-controlled larger datasets is required to make a definitive judgment about the role of the gut microbiota in ALS pathogenesis. Overall this is an emerging field that is worthy of further investigation. The authors advocate for larger studies using modern metagenomic techniques to address the current knowledge gaps.

Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi

Many colobine species-including the endangered Guizhou snub-nosed monkey (Rhinopithecus brelichi) are difficult to maintain in captivity and frequently exhibit gastrointestinal (GI) problems. GI problems are commonly linked to alterations in the gut microbiota, which lead us to examine the gut microbial communities of wild and captive R. brelichi. We used high-throughput sequencing of the 16S rRNA gene to compare the gut microbiota of wild (N = 7) and captive (N = 8) R. brelichi. Wild monkeys exhibited increased gut microbial diversity based on the Chao1 but not Shannon diversity metric and greater relative abundances of bacteria in the Lachnospiraceae and Ruminococcaceae families. Microbes in these families digest complex plant materials and produce butyrate, a short chain fatty acid critical to colonocyte health. Captive monkeys had greater relative abundances of Prevotella and Bacteroides species, which degrade simple sugars and carbohydrates, like those present in fruits and cornmeal, two staples of the captive R. brelichi diet. Captive monkeys also had a greater abundance of Akkermansia species, a microbe that can thrive in the face of host malnutrition. Taken together, these findings suggest that poor health in captive R. brelichi may be linked to diet and an altered gut microbiota.

Precision Nutrition and the Microbiome, Part I: Current State of the Science

The gut microbiota is a highly complex community which evolves and adapts to its host over a lifetime. It has been described as a virtual organ owing to the myriad of functions it performs, including the production of bioactive metabolites, regulation of immunity, energy homeostasis and protection against pathogens. These activities are dependent on the quantity and quality of the microbiota alongside its metabolic potential, which are dictated by a number of factors, including diet and host genetics. In this regard, the gut microbiome is malleable and varies significantly from host to host. These two features render the gut microbiome a candidate ‘organ’ for the possibility of precision microbiomics—the use of the gut microbiome as a biomarker to predict responsiveness to specific dietary constituents to generate precision diets and interventions for optimal health. With this in mind, this two-part review investigates the current state of the science in terms of the influence of diet and specific dietary components on the gut microbiota and subsequent consequences for health status, along with opportunities to modulate the microbiota for improved health and the potential of the microbiome as a biomarker to predict responsiveness to dietary components. In particular, in Part I, we examine the development of the microbiota from birth and its role in health. We investigate the consequences of poor-quality diet in relation to infection and inflammation and discuss diet-derived microbial metabolites which negatively impact health. We look at the role of diet in shaping the microbiome and the influence of specific dietary components, namely protein, fat and carbohydrates, on gut microbiota composition.

Overfeeding a High-Fat Diet Promotes Sex-Specific Alterations on the Gut Microbiota of the Zebrafish (Danio rerio)

Diet modulates the gut microbiota and is one of the main factors promoting obesity and overweight. In the present study, we investigated the effect of a high-fat diet (HFD) on the gut microbiota of the zebrafish (Danio rerio). Fish were separated into three groups and fed in different regimes: low fat, high fat, and high fat overfed; the experiments were performed on males and females separately. We analyzed more than 2.6 million sequences of variable region V3 of the 16S rRNA gene generated by the Illumina Miniseq platform, clustered to 97% similarity with vsearch and classified with the EzBioCloud database. The weight gain, condition factor (K), and body mass index were calculated as indicators of obesity. Multivariate analysis (PERMANOVA and ANOSIM) and diversity indices (Shannon and Dominance) revealed that overfeeding a HFD disturbs the gut microbiota differently in males and females suggesting that sex is a significant factor (p < 0.05) for the composition of the gut microbiota of zebrafish. The results also indicate that a HFD provided in a basal caloric regime does not promote obesity or alterations in the gut microbiota.

Vegetable oil and carbohydrate-rich diets marginally affected intestine histomorphology, digestive enzymes activities, and gut microbiota of gilthead sea bream juveniles

For an increased incorporation of plant ingredients in aquafeeds at the expense of fish meal (FM) and fish oil (FO), more knowledge is needed on the effects at the intestine level of dietary vegetable oils (VO) and carbohydrates (CH), and of possible interactions. For that purpose, in this study, the activities of digestive pancreatic enzymes (amylase, lipase, total alkaline proteases), gut microbiota, and histomorphology were assessed in gilthead sea bream (IBW 71.0 ± 1.5 g) fed four diets differing in lipid source (FO or a blend of VO) and carbohydrate content (0% or 20% gelatinized starch) for 81 days. No major changes in digestive enzyme activities were noticed in fish fed the experimental diets. Dietary VO, but not CH content, modified intestinal microbial profile, by increasing the similarity of bacterial communities. Especially when combined with CH, dietary VO promoted abnormal enterocyte architecture. Liver histology was also accessed, and an increased cytoplasmic vacuolization of hepatocytes was related with dietary CH inclusion, being only significantly different in fish fed FO-based diets. Overall, nutritional interactions between dietary lipid source and carbohydrate content were not observed on digestive enzyme activities and microbial profile. However, the intestine histological modifications observed in fish fed the VOCH+ diet suggest a negative interaction between dietary VO and CH. This requires a more in depth assessment in future studies as it can have negative consequences at a functional level.

Dynamics of the gut microbiota in developmental stages of Litopenaeus vannamei reveal its association with body weight

Increasing evidences have revealed a close interaction between the intestinal microbes and host growth performance. The shrimp (Litopenaeus vannamei) gut harbors a diverse microbial community, yet its associations with dietary, body weight and weaning age remain a matter of debate. In this study, we analyzed the effects of different dietary (fishmeal group (NC), krill meal group (KM)) and different growth stages (age from 42 day-old to 98 day-old) of the shrimp on the intestinal microbiota. High throughput sequencing of the 16S rRNA genes of shrimp intestinal microbes determined the novelty of bacteria in the shrimp gut microbiota and a core of 58 Operation Taxonomic Units (OTUs) was present among the shrimp gut samples. Analysis results indicated that the development of the shrimp gut microbiota is a dynamic process with three stages across the age according to the gut microbiota compositions. Furthermore, the dietary of KM group did not significantly change the intestinal microbiota of the shrimps compared with NC group. Intriguingly, compared to NC group, we observed in KM group that a fluctuation of the shrimp gut microbiota coincided with the shrimp body weight gain between weeks 6–7. Six OTUs associated with the microbiota change in KM group were identified. This finding strongly suggests that the shrimp gut microbiota may be correlated with the shrimp body weight likely by influencing nutrient uptake in the gut. The results obtained from this study potentially will be guidelines for manipulation to provide novel shrimp feed management approaches.

Dietary shifts influenced by livestock grazing shape the gut microbiota composition and co-occurrence networks in a local rodent species

The collapse of large wild herbivores with replacement of livestock is causing global plant community and diversity shifts, resulting in altered food availability and diet composition of other sympatric small herbivores in grasslands. How diet shifts affect the gut microbiota of small mammals and whether these changes may translate into complex interactions among coexisting herbivores remain largely unknown. We conducted both a field experiment and a laboratory diet manipulation experiment to test whether sheep grazing induces a diet shift and thus alters the gut microbiota of a small rodent species living in grassland. We found that enclosures subjected to grazing were mostly dominated by Stipa krylovii (accounting for 53.6% of the total biomass) and that voles consumed significantly more S. krylovii and less Cleistogenes squarrosa in grazed enclosures. Voles in grazing enclosures exhibited significantly lower abundances of Firmicutes, higher abundances of Bacteroidetes and significantly lower measurements of alpha diversity. The microbiota from voles in the grazed enclosures had a smaller and more simplified co-occurrence network with relatively higher percentage of positive interactions. Analysis based on dietary clusters indicated that grazing-induced changes in diet composition contributed to the distinct gut microbial community of voles in enclosures. We verified our findings using laboratory experiments, in which voles were exclusively fed C. squarrosa (high carbohydrate, high fibre and high in secondary compounds), S. krylovii (low carbohydrate, low fibre and low in secondary compounds) or Leymus chinensis (nutritionally intermediate). We observed that the gut microbiota of voles changed with the three different diets, supporting the idea that the effects of sheep grazing on the gut microbiota of Brandt's voles may be related to grazing-induced diet shifts. Our results highlighted the negative effects of livestock grazing on small mammals in grassland via changes in plant community and gut microbiota of small mammals and help to better understand the cascading consequences of realistic scenarios of world-wide decline in large wild herbivores.

Associations Between Race, Perceived Psychological Stress, and the Gut Microbiota in a Sample of Generally Healthy Black and White Women: A Pilot Study on the Role of Race and Perceived Psychological Stress

OBJECTIVE

Racial health disparities persist among black and white women for colorectal cancer. Understanding racial differences in the gut microbiota and related covariates (e.g., stress) may yield new insight into unexplained colorectal cancer disparities.

METHODS

Healthy non-Hispanic black or white women (age ≥19 years) provided survey data, anthropometrics, and stool samples. Fecal DNA was collected and isolated from a wipe. Polymerase chain reaction was used to amplify the V4 region of the 16SrRNA gene and 250 bases were sequenced using the MiSeq platform. Microbiome data were analyzed using QIIME. Operational taxonomic unit data were log transformed and normalized. Analyses were conducted using linear models in R Package "limma."

RESULTS

Fecal samples were analyzed for 80 women (M (SD) age = 39.9 (14.0) years, 47 black, 33 white). Blacks had greater average body mass index (33.3 versus 27.5 kg/m, p < .01) and waist circumference (98.3 versus 86.6 cm, p = .003) than whites. Whites reported more stressful life events (p = .026) and greater distress (p = .052) than blacks. Final models accounted for these differences. There were no significant differences in dietary variables. Unadjusted comparisons revealed no racial differences in alpha diversity. Racial differences were observed in beta diversity and abundance of top 10 operational taxonomic units. Blacks had higher abundances than whites of Faecalibacterium (p = .034) and Bacteroides (p = .038). Stress was associated with abundances of Bifidobacterium. The association between race and Bacteroides (logFC = 1.72, 0 = 0.020) persisted in fully adjusted models.

CONCLUSIONS

Racial differences in the gut microbiota were observed including higher Bacteroides among blacks. Efforts to cultivate an "ideal" gut microbiota may help reduce colorectal cancer risk.

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance

The alpha diversity of ecologic communities is affected by many biotic and abiotic drivers and, in turn, affects ecosystem functioning. Yet, patterns of alpha diversity in host-associated microbial communities (microbiomes) are poorly studied and the appropriateness of general theory is untested. Expanding diversity theory to include microbiomes is essential as diversity is a frequently cited metric of their status. Here, we review and newly analyze reports of alpha diversity for animal gut microbiomes. We demonstrate that both diet and body size affect diversity in the gut but that gut physiology (fermenter versus simple) is the most important driver. We also assess the advantages of various diversity metrics. The importance of diversity in microbiomes is often assumed but has not been tested outright. Therefore, we close by discussing how to integrate microbiomes into the field of biodiversity-ecosystem functioning to more clearly understand when and why a host supports diverse microbial communities.

A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway

Muskoxen (Ovibos moschatus) are ruminants adapted to a high-fibre diet. There is increasing interest in the role that gut microbes play in the digestion and utilization of these specialized diets but only limited data available on the gut microbiome of high-Arctic animals. In this study, we metabarcoded the 16S rRNA region of faecal samples from muskoxen of Northeast Greenland, Northwest Greenland and Norway, and quantified the effects of physiological and temporal factors on bacterial composition. We found significant effects of body mass, year of sampling and location on the gut bacterial communities of North East Greenland muskoxen. These effects were however dwarfed by the effects of location, emphasizing the importance of the local ecology on the gut bacterial community. Habitat alterations and rising temperatures may therefore have a considerable impact on muskoxen health and reproductive success. Moreover, muskoxen are hunted and consumed in Greenland, Canada and Alaska; therefore, this study also screened for potential zoonoses of food safety interest. A total of 13 potentially zoonotic genera were identified, including the genera Erysipelothrix and Yersinia implicated in recent mass die-offs of the muskoxen themselves.

Impact of Edible Cricket Consumption on Gut Microbiota in Healthy Adults, a Double-blind, Randomized Crossover Trial

Edible insects are often considered a nutritious, protein-rich, environmentally sustainable alternative to traditional livestock with growing popularity among North American consumers. While the nutrient composition of several insects is characterized, all potential health impacts have not been evaluated. In addition to high protein levels, crickets contain chitin and other fibers that may influence gut health. In this study, we evaluated the effects of consuming 25 grams/day whole cricket powder on gut microbiota composition, while assessing safety and tolerability. Twenty healthy adults participated in this six-week, double-blind, crossover dietary intervention. Participants were randomized into two study arms and consumed either cricket-containing or control breakfast foods for 14 days, followed by a washout period and assignment to the opposite treatment. Blood and stool samples were collected at baseline and after each treatment period to assess liver function and microbiota changes. Results demonstrate cricket consumption is tolerable and non-toxic at the studied dose. Cricket powder supported growth of the probiotic bacterium, Bifidobacterium animalis, which increased 5.7-fold. Cricket consumption was also associated with reduced plasma TNF-α. These data suggest that eating crickets may improve gut health and reduce systemic inflammation; however, more research is needed to understand these effects and underlying mechanisms.

Gut microbial diversity is associated with lower arterial stiffness in women

Aims

The gut microbiome influences metabolic syndrome (MetS) and inflammation and is therapeutically modifiable. Arterial stiffness is poorly correlated with most traditional risk factors. Our aim was to examine whether gut microbial composition is associated with arterial stiffness.

Methods and results

We assessed the correlation between carotid-femoral pulse wave velocity (PWV), a measure of arterial stiffness, and gut microbiome composition in 617 middle-aged women from the TwinsUK cohort with concurrent serum metabolomics data. Pulse wave velocity was negatively correlated with gut microbiome alpha diversity (Shannon index, Beta(SE)= -0.25(0.07), P = 1 × 10-4) after adjustment for covariates. We identified seven operational taxonomic units associated with PWV after adjusting for covariates and multiple testing-two belonging to the Ruminococcaceae family. Associations between microbe abundances, microbe diversity, and PWV remained significant after adjustment for levels of gut-derived metabolites (indolepropionate, trimethylamine oxide, and phenylacetylglutamine). We linearly combined the PWV-associated gut microbiome-derived variables and found that microbiome factors explained 8.3% (95% confidence interval 4.3-12.4%) of the variance in PWV. A formal mediation analysis revealed that only a small proportion (5.51%) of the total effect of the gut microbiome on PWV was mediated by insulin resistance and visceral fat, c-reactive protein, and cardiovascular risk factors after adjusting for age, body mass index, and mean arterial pressure.

Conclusions

Gut microbiome diversity is inversely associated with arterial stiffness in women. The effect of gut microbiome composition on PWV is only minimally mediated by MetS. This first human observation linking the gut microbiome to arterial stiffness suggests that targeting the microbiome may be a way to treat arterial ageing.

Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota

Multiple sclerosis (MS) is more common in western countries with diet being a potential contributing factor. Here we show that intermittent fasting (IF) ameliorated clinical course and pathology of the MS model, experimental autoimmune encephalomyelitis (EAE). IF led to increased gut bacteria richness, enrichment of the Lactobacillaceae, Bacteroidaceae, and Prevotellaceae families and enhanced antioxidative microbial metabolic pathways. IF altered T cells in the gut with a reduction of IL-17 producing T cells and an increase in regulatory T cells. Fecal microbiome transplantation from mice on IF ameliorated EAE in immunized recipient mice on a normal diet, suggesting that IF effects are at least partially mediated by the gut flora. In a pilot clinical trial in MS patients, intermittent energy restriction altered blood adipokines and the gut flora resembling protective changes observed in mice. In conclusion, IF has potent immunomodulatory effects that are at least partially mediated by the gut microbiome.

Recognizing Depression from the Microbiota⁻Gut⁻Brain Axis

Major depression is one of the leading causes of disability, morbidity, and mortality worldwide. The brain⁻gut axis functions are disturbed, revealed by a dysfunction of the brain, immune system, endocrine system, and gut. Traditional depression treatments all target the brain, with different drugs and/or psychotherapy. Unfortunately, most of the patients have never received any treatment. Studies indicate that gut microbiota could be a direct cause for the disorder. Abnormal microbiota and the microbiota⁻gut⁻brain dysfunction may cause mental disorders, while correcting these disturbance could alleviate depression. Nowadays, the gut microbiota modulation has become a hot topic in treatment research of mental disorders. Depression is closely related with the health condition of the brain⁻gut axis, and maintaining/restoring the normal condition of gut microbiota helps in the prevention/therapy of mental disorders.

Gut Microbiota Composition in Mid-Pregnancy Is Associated with Gestational Weight Gain but Not Prepregnancy Body Mass Index

Background: Pregnancy is a time of numerous hormonal, metabolic, and immunological changes for both the mother and the fetus. Furthermore, maternal gut microbiota composition (GMC) is altered during pregnancy. One major factor affecting GMC in pregnant and nonpregnant populations is obesity. The aim was to analyze associations between maternal overweight/obesity, as well as gestational weight gain (GWG) and GMC. Moreover, the modifying effect of depression and anxiety symptom scores on weight and GMC were investigated.

Methods: Study included 46 women from the FinnBrain Birth Cohort study, of which 36 were normal weight, and 11 overweight or obese according to their prepregnancy body mass index (BMI). Stool samples were collected in gestational week 24, and the GMC was sequenced with Illumina MiSeq approach. Hierarchical clustering was executed to illuminate group formation according to the GMC. The population was divided according to Firmicutes and Bacteroidetes dominance. Symptoms of depression, general anxiety, and pregnancy-related anxiety were measured by using standardized questionnaires.

Results: Excessive GWG was associated with distinct GMC in mid-pregnancy as measured by hierarchical clustering and grouping according to Firmicutes or Bacteroidetes dominance, with Bacteroidetes being prominent and Firmicutes being less prominent in the GMC among those with increased GWG. Reduced alpha diversity was observed among the Bacteroidetes-dominated subjects. There were no zero-order effects between the abundances of bacterial genera or phyla, alpha or beta diversity, and prepregnancy BMI or GWG.

Conclusion:Bacteroidetes-dominated GMC in mid-pregnancy is associated with increased GWG and reduced alpha diversity.

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.

Shifts on Gut Microbiota Associated to Mediterranean Diet Adherence and Specific Dietary Intakes on General Adult Population

There is increasing evidence for the interaction between gut microbiome, diet, and health. It is known that dysbiosis is related to disease and that most of the times this imbalances in gut microbial populations can be promoted through diet. Western dietary habits, which are characterized by high intakes of calories, animal proteins, saturated fats, and simple sugars have been linked with higher risk of obesity, diabetes, cancer, and cardiovascular disease. However, little is known about the impact of dietary patterns, dietary components, and nutrients on gut microbiota in healthy people. The aim of our study is to determine the effect of nutrient compounds as well as adherence to a dietary pattern, as the Mediterranean diet (MD) on the gut microbiome of healthy adults. Consequently, gut microbiota composition in healthy individuals, may be used as a potential biomarker to identify nutritional habits as well as risk of disease related to these habits. Dietary information from healthy volunteers (n = 27) was recorded using the Food Frequency Questionnaire. Adherence to the MD was measured using the PREDIMED test. Microbiota composition and diversity were obtained by 16S rRNA gene sequencing and specific quantitative polymerase chain reaction. Microbial metabolic activity was determined by quantification of short chain fatty acids (SCFA) on high performance liquid chromatography (HPLC). The results indicated that a higher ratio of Firmicutes–Bacteroidetes was related to lower adherence to the MD, and greater presence of Bacteroidetes was associated with lower animal protein intake. High consumption of animal protein, saturated fats, and sugars affected gut microbiota diversity. A significant higher presence of Christensenellaceae was found in normal-weight individuals compared to those who were overweight. This was also the case in volunteers with greater adherence to the MD compared to those with lower adherence. Butyricimonas, Desulfovibrio, and Oscillospira genera were associated with a BMI <25 and the genus Catenibacterium with a higher PREDIMED score. Higher bifidobacterial counts, and higher total SCFA were related to greater consumption of plant-based nutrients, such as vegetable proteins and polysaccharides. Better adherence to the MD was associated with significantly higher levels of total SCFA. Consequently, diet and specific dietary components could affect microbiota composition, diversity, and activity, which may have an effect on host metabolism by increasing the risk of Western diseases.

Modulation of the Gastrointestinal Microbiome with Nondigestible Fermentable Carbohydrates To Improve Human Health

There is a clear association between the gastrointestinal (GI) microbiome and the development of chronic noncommunicable diseases, providing a rationale for the development of strategies that target the GI microbiota to improve human health. In this article, we discuss the potential of supplementing the human diet with nondigestible fermentable carbohydrates (NDFCs) to modulate the composition, structure, diversity, and metabolic potential of the GI microbiome in an attempt to prevent or treat human disease. The current concepts by which NDFCs can be administered to humans, including prebiotics, fermentable dietary fibers, and microbiota-accessible carbohydrates, as well as the mechanisms by which these carbohydrates exert their health benefits, are discussed. Epidemiological research presents compelling evidence for the health effects of NDFCs, with clinical studies providing further support for some of these benefits. However, rigorously designed human intervention studies with well-established clinical markers and microbial endpoints are still essential to establish (i) the clinical efficiency of specific NDFCs, (ii) the causal role of the GI microbiota in these effects, (iii) the underlying mechanisms involved, and (iv) the degree by which inter-individual differences between GI microbiomes influence these effects. Such studies would provide the mechanistic understanding needed for a systematic application of NDFCs to improve human health via GI microbiota modulation while also allowing the personalization of these dietary strategies.

Bacteriocins and bacteriophage; a narrow-minded approach to food and gut microbiology

Bacteriocins and bacteriophage (phage) are biological tools which exhibit targeted microbial killing, a phenomenon which until recently was seen as a major drawback for their use as antimicrobial agents. However, in an age when the deleterious consequences of broad-spectrum antibiotics on human health have become apparent, there is an urgent need to develop narrow-spectrum substitutes. Indeed, disruption of the microbial communities which exist on and in our bodies can generate immediate and long-term negative effects and this is particularly borne out in the gut microbiota community whose disruption has been linked to a number of disorders reaching as far as the brain. Moreover, the antibiotic resistance crisis has resulted in our inability to treat many bacterial infections and has triggered the search for damage-limiting alternatives. As bacteriocins and phage are natural entities they are relatively easy to isolate and characterise and are also ideal candidates for improving food safety and quality, forfeiting the need for largely unpopular chemical preservatives. This review highlights the efficacy of both antimicrobial agents in terms of gut health and food safety and explores the body of scientific evidence supporting their effectiveness in both environments.

Use of copper intrauterine device is not associated with higher bacterial vaginosis prevalence in Thai HIV-positive women

The study assessed and compared bacterial vaginosis (BV) prevalence in Thai women in reproductive age in four study groups - group 1, HIV-positive with copper intrauterine device (Cu-IUD); group 2, HIV-positive without Cu-IUD; group 3, HIV-negative with Cu-IUD; and group 4, HIV-negative without Cu-IUD. We conducted a cross-sectional study. BV prevalence was assessed by Nugent score and Amsel criteria. Descriptive statistics was used to present baseline characteristics; kwallis rank test - to compare variables between the four groups; logistic regression - to assess factors, related to BV prevalence. The analysis included 137 women in the four study groups with a median age of 39 years. Median BV prevalence by Nugent score was 45%, intermediate vaginal flora - 7% and normal vaginal flora - 48%. There was no statistically significant difference in the BV prevalence between the four study groups, p = 0.711. Threefold lower BV prevalence was found, assessed by Amsel criteria compared to Nugent score. Women with body mass index (BMI) < 20 had higher probability to have BV or intermediate vaginal flora, OR = 3.11, 95% CI (1.2-8.6), p = 0.025. The study found a high BV prevalence in the four study groups, related neither to HIV status, nor to Cu-IUD use. BV prevalence was associated only with low BMI. Thus, Cu-IUD could be a good contraceptive choice for HIV-positive women. Research in defining normal vaginal microbiota and improve diagnostic methods for BV should continue.

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China

In Hong Kong, cattle were traditionally raised by farmers as draft animals to plough rice fields. Due to urbanization in the 20th century, they were gradually abandoned and became wild cattle straying in suburban Hong Kong. Recently, these cattle were observed to have become omnivorous by eating leftover barbeque food waste in country parks. Microbiome analysis was performed on fecal samples of the omnivorous cattle using deep sequencing and the resulting microbiome was compared with that of traditional herbivorous cattle in Southern China. A more diverse gut microbiome was observed in the omnivorous cattle, suggesting that microbiota diversity increases as diet variation increases. At the genus level, the relative abundance of Anaeroplasma, Anaerovorax, Bacillus, Coprobacillus and Solibacillus significantly increased and those of Anaerofustis, Butyricimonas, Campylobacter, Coprococcus, Dehalobacterium, Phascolarctobacterium, rc4.4, RFN20, Succinivibrio and Turicibacter significantly decreased in the omnivorous group. The increase in microbial community levels of Bacillus and Anaerovorax likely attributes to the inclusion of meat in the diet; while the decrease in relative abundance of Coprococcus, Butyricimonas, Succinivibrio, Campylobacter and Phascolarctobacterium may reflect the reduction in grass intake. Furthermore, an increased consumption of resistant starch likely resulted in the increase in abundance of Anaeroplasma. In conclusion, a significant change in the gut microbial community was observed in the omnivorous cattle, suggesting that diet may be one of the factors that may signal an adaptation response by the cattle to maintain feed efficiency as a consequence of the change in environment.

Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth

BACKGROUND

In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated.

RESULTS

Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter "week 15"), and end-of-feeding test (hereafter "off-test"), were used to evaluate changes in the composition of the fecal microbiome of each animal over time. This study used 1205, 1295, and 1283 samples collected at weaning, week 15, and off-test, respectively. There were 1039 animals that had samples collected at all three time points and also had phenotypic records on back fat thickness (BF) and average daily body weight gain (ADG). Firmicutes and Bacteroidetes were the most abundant phyla at all three time points. The most abundant genera at all three time points included Clostridium, Escherichia, Bacteroides, Prevotella, Ruminococcus, Fusobacterium, Campylobacter, Eubacterium, and Lactobacillus. Two enterotypes were identified at each time point. However, only enterotypes at week 15 and off-test were significantly associated with BF. We report herein two novel findings: (i) alpha diversity and operational taxonomic unit (OTU) richness were moderately heritable at week 15, h2 of 0.15 ± 0.06 to 0.16 ± 0.07 and 0.23 ± 0.09 to 0.26 ± 0.08, respectively, as well as at off-test, h2 of 0.20 ± 0.09 to 0.33 ± 0.10 and 0.17 ± 0.08 to 0.24 ± 0.08, respectively, whereas very low heritability estimates for both measures were detected at weaning; and (ii) alpha diversity at week 15 had strong and negative genetic correlations with BF, - 0.53 ± 0.23 to - 0.45 ± 0.25, as well as with ADG, - 0.53 ± 0.32 to - 0.53 ± 0.29.

CONCLUSIONS

These results are important for efforts to genetically improve the domesticated pig because they suggest fecal microbiota diversity can be used as an indicator trait to improve traits that are expensive to measure.

Analysis of relationship between intestinal flora imbalance and ulcerative colitis based on 16S rRNA sequences

AIM

To detect the distribution of intestinal flora between ulcerative colitis (UC) patients and normal controls by high-throughput sequencing to discover the genus structures related to the formation and development of UC.

METHODS

Chromosomal DNA was extracted from each sample, and the length of DNA fragment was detected and quantified. Gene amplification and sequencing of the V3 region of 16S rRNA were then performed.

RESULTS

The structure of intestinal flora in UC patients exhibited a significant decrease in the numbers of Bacteroidetes, Proteobacteria, and Firmicute, compared with that of healthy controls. There were significant differences (P < 0.05) in the mean abundance of 11 metabolic pathways between the two groups.

CONCLUSION

There is a strong correlation between the abnormal changes of the intestinal flora structure and the occurrence and development of UC. Multiple metabolic pathways are involved in the formation and development of UC. It is helpful to understand the molecular pathological basis of UC by analyzing the key structures of bacterial flora, which will provide a theoretical basis for the reasonable design of new drugs.

Emerging Topics in Gastroenterology

The bacteria and fungi in the human gut make up a community of microorganisms that lives in symbiosis with humans, engaging in numerous diverse interactions that influence health. This article outlines the current knowledge on emerging topics in gastroenterology, including microbiome and probiotics, fecal microbiota transplantation, cyclic vomiting syndrome, eosinophilic esophagitis, and microscopic colitis.

Nutritional habits, risk, and progression of Parkinson disease

Parkinson disease (PD) is a multifactorial disease, where a genetic predisposition combines with putative environmental risk factors. Mounting evidence suggests that the initial PD pathological manifestations may be located in the gut to subsequently affect brain areas. Moreover, several lines of research demonstrated that there are bidirectional connections between the central nervous system and the gut, the "gut-brain axis" that influences both brain and gastrointestinal function. This opens a potential therapeutic window suggesting that specific dietary strategies may interact with the disease process and influence the risk of PD or modify its course. Dietary components can also theoretically modulate the chronic activation of the inflammatory response that is associated with aging, the strongest risk factor for PD, that has been suggested to hasten the underlying neurodegenerative process in PD. Here, we reviewed the evidence supporting an association between certain dietary compound and either the risk or progression of PD and have provided an overview of the possible pathomechanisms linking nutrition and neurodegeneration. The results of our review would not support a clear role for any dietary components in reducing the risk or progression of PD. However, the evidence favouring a connection between gut abnormalities, inflammation, and neurodegeneration in PD have become too compelling to be ignored, so that further research, also in the field of nutritional genomics, is highly warranted.

Microbial Interactions and Interventions in Colorectal Cancer

Recently, several lines of evidence that indicate a strong link between the development of colorectal cancer (CRC) and aspects of the gut microbiota have become apparent. However, it remains unclear how changes in the gut microbiota might influence carcinogenesis or how regional organization of the gut might influence the microbiota. In this review, we discuss several leading theories that connect gut microbial dysbiosis with CRC and set this against a backdrop of what is known about proximal-distal gut physiology and the pathways of CRC development and progression. Finally, we discuss the potential for gut microbial modulation therapies, for example, probiotics, antibiotics, and others, to target and improve gut microbial dysbiosis as a strategy for the prevention or treatment of CRC.

Microbiome symbionts and diet diversity incur costs on the immune system of insect larvae

Communities of symbiotic microorganisms that colonize the gastrointestinal tract play an important role in food digestion and protection against opportunistic microbes. Diet diversity increases the number of symbionts in the intestines, a benefit that is considered to impose no cost for the host organism. However, less is known about the possible immunological investments that hosts have to make in order to control the infections caused by symbiont populations that increase because of diet diversity. Using taxonomical composition analysis of the 16S rRNA V3 region, we show that enterococci are the dominating group of bacteria in the midgut of the larvae of the greater wax moth (Galleria mellonella). We found that the number of colony-forming units of enterococci and expressions of certain immunity-related antimicrobial peptide (AMP) genes such as Gallerimycin, Gloverin, 6-tox, Cecropin-D and Galiomicin increased in response to a more diverse diet, which in turn decreased the encapsulation response of the larvae. Treatment with antibiotics significantly lowered the expression of all AMP genes. Diet and antibiotic treatment interaction did not affect the expression of Gloverin and Galiomicin AMP genes, but significantly influenced the expression of Gallerimycin, 6-tox and Cecropin-D Taken together, our results suggest that diet diversity influences microbiome diversity and AMP gene expression, ultimately affecting an organism's capacity to mount an immune response. Elevated basal levels of immunity-related genes (Gloverin and Galiomicin) might act as a prophylactic against opportunistic infections and as a mechanism that controls the gut symbionts. This would indicate that a diverse diet imposes higher immunity costs on organisms.