Diet and the Human Gut Microbiome: An International Review

Jares E, Jarvis D, Jassem E, Jenko K, Jiméneracruz Uscanga RD, Johnston SL, Joos G, Jošt M, Julge K, Jung K, Just J, Jutel M, Kaidashev I, Kalayci O, Kalyoncu F, Kapsali J, Kardas P, Karjalainen J, Kasala CA, Katotomichelakis M, Kavaliukaite L, Kazi BS, Keil T, Keith P, Khaitov M, Khaltaev N, Kim Y, Kirenga B, Kleine‐Tebbe J, Klimek L, Koffi N’Goran B, Kompoti E, Kopač P, Koppelman G, KorenJeverica A, Koskinen S, Košnik M, Kostov KV, Kowalski ML, Kralimarkova T, Kramer Vrščaj K, Kraxner H, Kreft S, Kritikos V, Kudlay D, Kuitunen M, Kull I, Kuna P, Kupczyk M, Kvedariene V, Kyriakakou M, Lalek N, Landi M, Lane S, Larenas‐Linnemann D, Lau S, Laune D, Lavrut J, Le L, Lenzenhuber M, Lessa M, Levin M, Li J, Lieberman P, Liotta G, Lipworth B, Liu X, Lobo R, Lodrup Carlsen KC, Lombardi C, Louis R, Loukidis S, Lourenço O, Luna Pech JA, Madjar B, Maggi E, Magnan A, Mahboub B, Mair A, Mais Y, Maitland van der Zee A, Makela M, Makris M, Malling H, Mandajieva M, Manning P, Manousakis M, Maragoudakis P, Marseglia G, Marshall G, Reza Masjedi M, Máspero JF, Matta Campos JJ, Maurer M, Mavale‐Manuel S, Meço C, Melén E, Melioli G, Melo‐Gomes E, Meltzer EO, Menditto E, Menzies‐Gow A, Merk H, Michel J, Micheli Y, Miculinic N, Midão L, Mihaltan F, Mikos N, Milanese M, Milenkovic B, Mitsias D, Moalla B, Moda G, Mogica Martínez MD, Mohammad Y, Moin M, Molimard M, Momas I, Mommers M, Monaco A, Montefort S, Mora D, Morais‐Almeida M, Mösges R, Mostafa B, Mullol J, Münter L, Muraro A, Murray R, Musarra A, Mustakov T, Naclerio R, Nadeau KC, Nadif R, Nakonechna A, Namazova‐Baranova L, Navarro‐Locsin G, Neffen H, Nekam K, Neou A, Nettis E, Neuberger D, Nicod L, Nicola S, Niederberger‐Leppin V, Niedoszytko M, Nieto A, Novellino E, Nunes E, Nyembue D, O’Hehir R, Odjakova C, Ohta K, Okamoto Y, Okubo K, Oliver B, Onorato GL, Pia Orru M, Ouédraogo S, Ouoba K, Paggiaro PL, Pagkalos A, Pajno G, Pala G, Palaniappan S, Pali‐Schöll I, Palkonen S, Palmer S, Panaitescu Bunu C, Panzner P, Papadopoulos NG, Papanikolaou V, Papi A, Paralchev B, Paraskevopoulos G, Park H, Passalacqua G, Patella V, Pavord I, Pawankar R, Pedersen S, Peleve S, Pellegino S, Pereira A, Pérez T, Perna A, Peroni D, Pfaar O, Pham‐Thi N, Pigearias B, Pin I, Piskou K, Pitsios C, Plavec D, Poethig D, Pohl W, Poplas Susic A, Popov TA, Portejoie F, Potter P, Poulsen L, Prados‐Torres A, Prarros F, Price D, Prokopakis E, Puggioni F, Puig‐Domenech E, Puy R, Rabe K, Raciborski F, Ramos J, Recto MT, Reda SM, Regateiro FS, Reider N, Reitsma S, Repka‐Ramirez S, Ridolo E, Rimmer J, Rivero Yeverino D, Angelo Rizzo J, Robalo‐Cordeiro C, Roberts G, Roche N, Rodríguez González M, Rodríguez Zagal E, Rolla G, Rolland C, Roller‐Wirnsberger R, Roman Rodriguez M, Romano A, Romantowski J, Rombaux P, Romualdez J, Rosado‐Pinto J, Rosario N, Rosenwasser L, Rossi O, Rottem M, Rouadi P, Rovina N, Rozman Sinur I, Ruiz M, Ruiz Segura LT, Ryan D, Sagara H, Sakai D, Sakurai D, Saleh W, Salimaki J, Samitas K, Samolinski B, Sánchez Coronel MG, Sanchez‐Borges M, Sanchez‐Lopez J, Sarafoleanu C, Sarquis Serpa F, Sastre‐Dominguez J, Savi E, Sawaf B, Scadding GK, Scheire S, Schmid‐Grendelmeier P, Schuhl JF, Schunemann H, Schvalbová M, Schwarze J, Scichilone N, Senna G, Sepúlveda C, Serrano E, Shields M, Shishkov V, Siafakas N, Simeonov A, FER Simons E, Carlos Sisul J, Sitkauskiene B, Skrindo I, SokličKošak T, Solé D, Sooronbaev T, Soto‐Martinez M, Soto‐Quiros M, Sousa Pinto B, Sova M, Soyka M, Specjalski K, Spranger O, Stamataki S, Stefanaki L, Stellato C, Stelmach R, Strandberg T, Stute P, Subramaniam A, Suppli Ulrik C, Sutherland M, Sylvestre S, Syrigou A, Taborda Barata L, Takovska N, Tan R, Tan F, Tan V, Ping Tang I, Taniguchi M, Tannert L, Tantilipikorn P, Tattersall J, Tesi F, Thijs C, Thomas M, To T, Todo‐Bom A, Togias A, Tomazic P, Tomic‐Spiric V, Toppila‐Salmi S, Toskala E, Triggiani M, Triller N, Triller K, Tsiligianni I, Uberti M, Ulmeanu R, Urbancic J, Urrutia Pereira M, Vachova M, Valdés F, Valenta R, Valentin Rostan M, Valero A, Valiulis A, Vallianatou M, Valovirta E, Van Eerd M, Van Ganse E, Hage M, Vandenplas O, Vasankari T, Vassileva D, Velasco Munoz C, Ventura MT, Vera‐Munoz C, Vicheva D, Vichyanond P, Vidgren P, Viegi G, Vogelmeier C, Von Hertzen L, Vontetsianos T, Vourdas D, Tran Thien Quan V, Wagenmann M, Walker S, Wallace D, Wang DY, Waserman S, Wickman M, Williams S, Williams D, Wilson N, Wong G, Woo K, Wright J, Wroczynski P, Xepapadaki P, Yakovliev P, Yamaguchi M, Yan K, Yeow Yap Y, Yawn B, Yiallouros P, Yorgancioglu A, Yoshihara S, Young I, Yusuf OB, Zaidi A, Zaitoun F, Zar H, Zedda M, Zernotti ME, Zhang L, Zhong N, Zidarn M, Zubrinich C. Cabbage and fermented vegetables: From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID-19

Large differences in COVID‐19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS‐CoV‐2 binds to its receptor, the angiotensin‐converting enzyme 2 (ACE2). As a result of SARS‐CoV‐2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT₁R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID‐19. The nuclear factor (erythroid‐derived 2)‐like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT₁R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof‐of‐concept of dietary manipulations that may enhance Nrf2‐associated antioxidant effects, helpful in mitigating COVID‐19 severity.

Association between physical activity and changes in intestinal microbiota composition: A systematic review

INTRODUCTION

The intestinal microbiota comprises bacteria, fungi, archaea, protists, helminths and viruses that symbiotically inhabit the digestive system. To date, research has provided limited data on the possible association between an active lifestyle and a healthy composition of human microbiota. This review was aimed to summarize the results of human studies comparing the microbiome of healthy individuals with different physical activity amounts.

METHODS

We searched Medline/Ovid, NIH/PubMed, and Academic Search Complete between August-October 2020. Inclusion criteria comprised: (a) cross-sectional studies focused on comparing gut microbiome among subjects with different physical activity levels; (b) studies describing human gut microbiome responses to any type of exercise stimulus; (c) studies containing healthy adult women and men. We excluded studies containing diet modifications, probiotic or prebiotic consumption, as well as studies focused on diabetes, hypertension, cancer, hormonal dysfunction. Methodological quality and risk of bias for each study were assessed using the Risk Of Bias In Non-randomized Studies-of Interventions tool. The results from cross-sectional and longitudinal studies are shown independently.

RESULTS

A total of 17 articles were eligible for inclusion: ten cross-sectional and seven longitudinal studies. Main outcomes vary significantly according to physical activity amounts in longitudinal studies. We identified discrete changes in diversity indexes and relative abundance of certain bacteria in active people.

CONCLUSION

As literature in this field is rapidly growing, it is important that studies incorporate diverse methods to evaluate other aspects related to active lifestyles such as sleep and dietary patterns. Exploration of other groups such as viruses, archaea and parasites may lead to a better understanding of gut microbiota adaptation to physical activity and sports and its potentially beneficial effects on host metabolism and endurance.

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

BACKGROUND

Gastric adenocarcinoma is associated with H. pylori infection and inflammation that can result in the dysbiosis of gastric microbiota. The association of intestinal microbiota with gastric adenocarcinoma subtypes or with gastric gastrointestinal stromal tumors (GIST) is however not well known. Therefore, we performed 16S rRNA gene sequencing on DNA isolated from stool samples of Finnish patients and controls to study differences in microbiota among different histological subtypes of gastric adenocarcinoma, gastric GIST and healthy controls.

RESULTS

We found that gut microbiota alpha diversity was lowest in diffuse adenocarcinoma patients, followed by intestinal type and GIST patients, although the differences were not significant compared to controls. Beta-diversity analysis however showed significant differences in microbiota composition for all subtypes compared to controls. Significantly higher abundance of Enterobacteriaceae was observed in both adenocarcinoma subtypes, whereas lower abundance of Bifidobacteriaceae was seen only in diffuse adenocarcinoma and of Oscillibacter in intestinal adenocarcinoma. Both GIST and adenocarcinoma patients had higher abundance of Enterobacteriaceae and lower abundance of Lactobacillaceae and Oscillibacter while lower abundance of Lachnoclostridium, Bifidobacterium, Parabacteroides and Barnesiella was seen only in the adenocarcinoma patients.

CONCLUSIONS

Our analysis shows association of higher Enterobacteriaceae abundance with all types of gastric tumors. Therefore it could be potentially useful as a marker of gastric malignancies. Lower gut microbiota diversity might be indicative of poorly differentiated, invasive, advanced or aggressive tumors and could possibly be a prognostic marker for gastric tumors.

The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome

The COVID-19 pandemic has the potential to affect the human microbiome in infected and uninfected individuals, having a substantial impact on human health over the long term. This pandemic intersects with a decades-long decline in microbial diversity and ancestral microbes due to hygiene, antibiotics, and urban living (the hygiene hypothesis). High-risk groups succumbing to COVID-19 include those with preexisting conditions, such as diabetes and obesity, which are also associated with microbiome abnormalities. Current pandemic control measures and practices will have broad, uneven, and potentially long-term effects for the human microbiome across the planet, given the implementation of physical separation, extensive hygiene, travel barriers, and other measures that influence overall microbial loss and inability for reinoculation. Although much remains uncertain or unknown about the virus and its consequences, implementing pandemic control practices could significantly affect the microbiome. In this Perspective, we explore many facets of COVID-19-induced societal changes and their possible effects on the microbiome, and discuss current and future challenges regarding the interplay between this pandemic and the microbiome. Recent recognition of the microbiome's influence on human health makes it critical to consider both how the microbiome, shaped by biosocial processes, affects susceptibility to the coronavirus and, conversely, how COVID-19 disease and prevention measures may affect the microbiome. This knowledge may prove key in prevention and treatment, and long-term biological and social outcomes of this pandemic.

Impact of Appendectomy on Gut Microbiota

Background: Considered vestigial from the classic point of view, the vermiform appendix has long been the subject of intensive studies. The recent understanding of appendix function in the context of unique architecture and bacterial complexity and density allows considering it as a safehouse for intestinal biodiversity. Methods: This review analyzes and assesses the current state of scientific knowledge regarding the role of the vermiform appendix in normal gut microbiota maintenance as a crucial factor of host homeostasis. It also highlights the difference in microbial composition between the large bowel and the appendix, as well as the association between the surgical excision, appendectomy, and dysbiosis-induced diseases. In addition, the review discusses the results of epidemiologic studies on appendectomy as a risk factor for the initiation of gastrointestinal carcinogenesis. It also highlights the association between appendectomy and a series of chronic inflammatory and neurologic disorders, including inflammatory bowel disease.

The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns

Background

Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifestyles. These understudied populations are arguably better subjects in answering human-gut microbiome evolution because of their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have exhibited high biodiversity and seasonal patterns in their gut microbiome composition at the family level, where some taxa disappear in one season and reappear later. Such seasonal changes have been profiled, but the nucleotide changes remain unexplored at the genome level. Thus, it is still elusive how microbial communities change with seasonal changes at the genome level.

Results

In this study, we performed a strain-level single nucleotide polymorphism (SNP) analysis on 40 Hadza fecal metagenome samples spanning three seasons. With more SNP presented in the wet season, eight prevalent species have significant SNP enrichment with the increasing number of SNP calling by VarScan2, among which only three species have relatively high abundances. Eighty-three genes have the most SNP distributions between the wet season and dry season. Many of these genes are derived from Ruminococcus obeum, and mainly participated in metabolic pathways including carbon metabolism, pyruvate metabolism, and glycolysis.

Conclusions

Eight prevalent species have significant SNP enrichments with the increasing number of SNP, among which only Eubacterium biforme, Eubacterium hallii and Ruminococcus obeum have relatively high species abundances. Many genes in the microbiomes also presented characteristic SNP distributions between the wet season and the dry season. This implies that the seasonal changes might indirectly impact the mutation patterns for specific species and functions for the gut microbiome of the population that lives in traditional lifestyles through changing the diet in wet and dry seasons, indicating the role of these variants in these species’ adaptation to the changing environment and diets.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07372-0.

Climate Change, Food Supply, and Dietary Guidelines

Food production is affected by climate change, and, in turn, food production is responsible for 20-30% of greenhouse gases. The food system must increase output as the population increases and must meet nutrition and health needs while simultaneously assisting in achieving the Sustainable Development Goals. Good nutrition is important for combatting infection, reducing child mortality, and controlling obesity and chronic disease throughout the life course. Dietary guidelines provide advice for a healthy diet, and the main principles are now well established and compatible with sustainable development. Climate change will have a significant effect on food supply; however, with political commitment and substantial investment, projected improvements will be sufficient to provide food for the healthy diets needed to achieve the Sustainable Development Goals. Some changes will need to be made to food production, nutrient content will need monitoring, and more equitable distribution is required to meet the dietary guidelines. Increased breastfeeding rates will improve infant and adult health while helping to reduce greenhouse gases.

Microbiota-Mediated Immune Regulation in Atherosclerosis

There is a high level of interest in identifying metabolites of endogenously produced or dietary compounds generated by the gastrointestinal (GI) tract microbiota, and determining the functions of these metabolites in health and disease. There is a wealth of compelling evidence that the microbiota is linked with many complex chronic inflammatory diseases, including atherosclerosis. Macrophages are key target immune cells in atherosclerosis. A hallmark of atherosclerosis is the accumulation of pro-inflammatory macrophages in coronary arteries that respond to pro-atherogenic stimuli and failure of digesting lipids that contribute to foam cell formation in atherosclerotic plaques. This review illustrates the role of tryptophan-derived microbiota metabolites as an aryl hydrocarbon receptor (AhR) ligand that has immunomodulatory properties. Also, microbiota-dependent trimethylamine-N-oxide (TMAO) metabolite production is associated with a deleterious effect that promotes atherosclerosis, and metabolite indoxyl sulfate has been shown to exacerbate atherosclerosis. Our objective in this review is to discuss the role of microbiota-derived metabolites in atherosclerosis, specifically the consequences of microbiota-induced effects of innate immunity in response to atherogenic stimuli, and how specific beneficial/detrimental metabolites impact the development of atherosclerosis by regulating chronic endotoxemic and lipotoxic inflammation.

Nutritional combinatorial impact on the gut microbiota and plasma short-chain fatty acids levels in the prevention of mammary cancer in Her2/neu estrogen receptor-negative transgenic mice

Breast cancer is the second leading cause of cancer-related mortality in women. Various nutritional compounds possess anti-carcinogenic properties which may be mediated through their effects on the gut microbiota and its production of short-chain fatty acids (SCFAs) for the prevention of breast cancer. We evaluated the impact of broccoli sprouts (BSp), green tea polyphenols (GTPs) and their combination on the gut microbiota and SCFAs metabolism from the microbiota in Her2/neu transgenic mice that spontaneously develop estrogen receptor-negative [ER(-)] mammary tumors. The mice were grouped based on the dietary treatment: control, BSp, GTPs or their combination from beginning in early life (BE) or life-long from conception (LC). We found that the combination group showed the strongest inhibiting effect on tumor growth volume and a significant increase in tumor latency. BSp treatment was integrally more efficacious than the GTPs group when compared to the control group. There was similar clustering of microbiota of BSp-fed mice with combination-fed mice, and GTPs-fed mice with control-fed mice at pre-tumor in the BE group and at pre-tumor and post-tumor in the LC group. The mice on all dietary treatment groups incurred a significant increase of Adlercreutzia, Lactobacillus genus and Lachnospiraceae, S24-7 family in the both BE and LC groups. We found no change in SCFAs levels in the plasma of BSp-fed, GTPs-fed and combination-fed mice of the BE group. Marked changes were observed in the mice of the LC group consisting of significant increases in propionate and isobutyrate in GTPs-fed and combination-fed mice. These studies indicate that nutrients such as BSp and GTPs differentially affect the gut microbial composition in both the BE and LC groups and the key metabolites (SCFAs) levels in the LC group. The findings also suggest that temporal factors related to different time windows of consumption during the life-span can have a promising influence on the gut microbial composition, SCFAs profiles and ER(-) breast cancer prevention.

Different effects of high-fat diets rich in different oils on lipids metabolism, oxidative stress and gut microbiota

The study aimed to investigate the different effects of high-fat (HF) diets rich in different oils on lipid metabolism, oxidative stress, and gut mirobiota. C57BL/6 mice were divided into 4 groups: (1) control group (CG) was fed with normal diet, (2) olive oil (OO) group was fed with high-fat diet containing OO, (3) lard oil (LO) group was fed with high-fat diet containing LO, (4) soybean oil (SO) group was fed with high-fat diet containing SO. After 12 weeks, serum lipids, and oxidative stress indices were analyzed. Gut microbiota analysis was carried out based on the sequencing results of 16S rRNA. High fat diet can increase serum and liver lipids and upregulate sterol regulatory element-binding protein-1c related genes expression. Serum and liver malondialdehyde (MDA) levels in LO group were significantly higher than those in CG and OO groups. In CG, the family Muribaculaceae, Lactobacillaceae, Lachnospiraceae and Desulfovibrionaceae had the large effect sizes. HF diets resulted in the increase of Actinobacteria and Enterococcaceae abundance, and the decrease of Bacteroidetes, Proteobacteria Lactobacillales and microbiota diversity. The abundance of Actinobacteria and Lactobacillales is the link to the serum TC and MDA levels. HF diets have the harmful influence on the serum lipids, oxidative stress and endothelial function. They can also cause gut microbiota dysbiosis.

Probiotics in the Management of Atopic Dermatitis for Children: A Case-Based Review

Background

Atopic dermatitis or eczema is one of the most common dermatologic problems, especially in children. Several studies have hypothesized that alteration of gut-colonizing microbes might have induced and conditioned the development of the disease. Thus, modulation of microbial diversity and abundance might help alleviate symptoms and conditions for patients. Given the ability of commensal and symbiotic microorganisms in modulating the immune system, probiotics administration has been studied in previous research in the management of eczema. However, until today, there are conflicting results between studies making inconclusive recommendations towards probiotics supplementation in the management of atopic dermatitis. This case-based review was done to assess and evaluate the therapeutic efficacy of probiotics supplementation in the management of eczema in children.

Method

An electronic database search was conducted in PubMed-NCBI, Cochrane, EBSCO, ProQuest, and SCOPUS in March 2020. Individual studies and reviews were then gathered for screening using predetermined inclusion and exclusion criteria. The included studies were then critically appraised for their validity and importance.

Result

A total of 5 studies, all of which were RCTs, were included in this review. Out of all the studies included, 4 showed no clinically significant improvements in using probiotics in the management of eczema in children as they did not pass the minimal clinically important difference (MCID) of eczema severity as determined by SCORAD (SCORing Atopic Dermatitis).

Conclusion

Supplementation of probiotics in the management of eczema in children does not show a clinically relevant difference vs. standard treatment in reducing eczema severity.

Microbiota, diet and the generation of reactive nitrogen compounds

It is becoming increasingly clear that commensal bacteria inhabiting our body surfaces interact closely with the host to modulate a vast number of physiological functions. Metabolism of dietary components by gut microbiota can result in formation of a variety of reactive compounds associated with both favorable and unfavorable health effects. N-nitrosamines and trimethylamine-N-oxide (TMAO) have been associated with detrimental health effects, including increased risk of cardiovascular and metabolic disease. Contrary, bacteria-dependent formation of nitric oxide and related bioactive nitrogen oxides from dietary nitrate have been associated with salutary effects on cardiovascular function, metabolic control and more. Here we briefly discuss how the microbiota interacts with dietary factors to regulate host functions in health and disease, focusing on formation of reactive nitrogen compounds.

Western Diet: Implications for Brain Function and Behavior

The Western diet (WD) pattern characterized by high daily intake of saturated fats and refined carbohydrates often leads to obesity and overweight, and it has been linked to cognitive impairment and emotional disorders in both animal models and humans. This dietary pattern alters the composition of gut microbiota, influencing brain function by different mechanisms involving the gut-brain axis. In addition, long-term exposure to highly palatable foods typical of WD could induce addictive-like eating behaviors and hypothalamic-pituitary-adrenal (HPA) axis dysregulation associated with chronic stress, anxiety, and depression. In turn, chronic stress modulates eating behavior, and it could have detrimental effects on different brain regions such as the hippocampus, hypothalamus, amygdala, and several cortical regions. Moreover, obesity and overweight induce neuroinflammation, causing neuronal dysfunction. In this review, we summarize the current scientific evidence about the mechanisms and factors relating WD consumption with altered brain function and behavior. Possible therapeutic interventions and limitations are also discussed, aiming to tackle and prevent this current pandemic.

Roadmap to functional characterization of the human intestinal microbiota in its interaction with the host

It is known for more than 100 years that the intestinal microbes are important for the host's health and the last decade this is being intensely studied with a focus on the mechanistic aspects. Among the fundamental functions of the intestinal microbiome are the priming of the immune system, the production of essential vitamins and the energy harvest from foods. By now, several dozens of diseases, both intestinal and non-intestinal related, have been associated with the intestinal microbiome. Initially, this was based on the description of the composition between groups of different health status or treatment arms based on phylogenetic approaches based on the 16S rRNA gene sequences. This way of analysis has mostly moved to the analysis of all the genes or transcripts of the microbiome i.e. metagenomics and meta-transcriptomics. Differences are regularly found but these have to be taken with caution as we still do not know what the majority of genes of the intestinal microbiome are capable of doing. To circumvent this caveat researchers are studying the proteins and the metabolites of the microbiome and the host via metaproteomics and metabolomics approaches. However, also here the complexity is high and only a fraction of signals obtained with high throughput instruments can be identified and assigned to a known protein or molecule. Therefore, modern microbiome research needs advancement of existing and development of new analytical techniques. The usage of model systems like intestinal organoids where samples can be taken and processed rapidly as well as microfluidics systems may help. This review aims to elucidate what we know about the functionality of the human intestinal microbiome, what technologies are advancing this knowledge, and what innovations are still required to further evolve this actively developing field.

Dysbiosis is one of the risk factor for stroke and cognitive impairment and potential target for treatment

More than 50 million people have various forms of cognitive impairment basically caused by neurodegenerative diseases, such as Alzheimer's, Parkinson's, and cerebrovascular diseases as well as stroke. Often these conditions coexist and exacerbate one another. The damaged area in post-stroke dementia may lead to neurodegenerative lesions. Gut microbiome functions like an endocrine organ by generating bioactive metabolites that can directly or indirectly impact human physiology. An alteration in the composition and function of intestinal flora, i.e. gut dysbiosis, is implicated in neurodegenerative and cerebrovascular diseases. Additionally, gut dysbiosis may accelerate the progression of cognitive impairment. Dysbiosis may result from obesity; metabolic disorders, cardiovascular disease, and sleep disorders, Lack of physical activity is associated with dysbiosis as well. These may coexist in various patterns in older people, enhancing the risk, incidence, and progression of cerebrovascular lesions, neurodegenerative disorders, and cognitive impairment, creating a vicious circle. Recently, it has been reported that several metabolites produced by gut microbiota (e.g., trimethylamine/trimethylamine N-oxide, short-chain fatty acids, secondary bile acids) may be linked to neurodegenerative and cerebrovascular diseases. New treatment modalities, including prebiotic and probiotics, may normalize the gut microbiota composition, change the brain-gut barrier, and decrease the risk of the pathology development. Fecal microbiota transplantation, sometimes in combination with other methods, is used for remodeling and replenishing the symbiotic gut microbiome. This promising field of research is associated with basic findings of bidirectional communication between body organs and gut microbiota that creates new possibilities of pharmacological treatments of many clinical conditions. The authors present the role of gut microbiota in physiology, and the novel therapeutic targets in modulation of intestinal microbiota Personalized therapies based on their personal genome make up could offer benefits by modulating microbiota cross-talk with brain and cardiovascular system. A healthy lifestyle, including pre and probiotic nutrition is generally recommended. Prevention may also be enhanced by correcting gut dysbiosis resulting a reduced risk of post-stroke cognitive impairment including dementia.

Gut Bacteria have a novel sweet tooth: ribose sensing and scavenging from fiber

Dietary fiber is known to influence symbiotic gut microbiota community structure and physiology; however, how and if dietary fiber can induce further exogenous nutrient uptake within gut microbes is ill-defined. Recent findings highlight how during periods of high-fiber consumption, a prevalent gut bacteria senses and scavenges the ubiquitous sugar ribose. This molecular adaptation exemplifies how particular gut microbes have developed a sophisticated system to scavenge nutrients in a diet-dependent manner.

The role of the gut microbiome on radiation therapy efficacy and gastrointestinal complications: A systematic review

Radiation therapy (RT) is an essential component of therapy either curative or palliative armamentarium in oncology, but its efficacy varies considerably among patients through many extrinsic and intrinsic mechanisms of the tumour, which are beginning to be better understood. Recent studies have shown that the gut microbiome represents a key factor in the modulation of the systemic immune response and consequently on patients' outcome. Moreover, the emergence of biomarkers that are derived from the gut microbiota has fuelled the development of adjuvant strategies for patients treated with immunotherapy in combination or not with RT. Despite progress in development of more precise radiotherapy techniques, almost all patients undergoing RT to the abdomen, pelvis, or rectum develop acute adverse events as a consequence of several dose-limiting parameters such as the location of irradiation that may subsequently damage normal tissue including the intestinal epithelium. Several lines of evidence in preclinical models identified that vancomycin improves RT-induced gastrointestinal toxicities such as diarrhea and oral mucositis. In order to gain further insight into this rapidly evolving field, we have systematically reviewed the studies that have described how the gut microbiome may directly or indirectly modulate RT efficacy and its gastro-intestinal toxicities. Lastly, we outline current knowledge gaps and discuss potentially more satisfactory therapeutic options to restore the functionality of the gut microbiome of patients treated with RT.

Healthy dietary patterns to reduce obesity-related metabolic disease: polyphenol-microbiome interactions unifying health effects across geography

PURPOSE OF REVIEW

The spread of the Western lifestyle across the globe has led to a pandemic in obesity-related metabolic disease. The Mediterranean diet (MedDiet), Okinawa diet (OkD) and Nordic diet, derived from very different regions of the world and culinary traditions, have a large whole plant food component and are associated with reduced disease risk. This review focuses on polyphenol : microbiome interactions as one possible common mechanistic driver linking the protective effects whole plant foods against metabolic disease across healthy dietary patterns irrespective of geography.

RECENT FINDINGS

Although mechanistic evidence in humans is still scarce, animal studies suggest that polyphenol or polyphenol rich foods induce changes within the gut microbiota and its metabolic output of trimethylamine N-oxide, short-chain fatty acids, bile acids and small phenolic acids. These cross-kingdom signaling molecules regulate mammalian lipid and glucose homeostasis, inflammation and energy storage or thermogenesis, physiological processes determining obesity-related metabolic and cardiovascular disease risk. However, it appears that where in the intestine metabolites are produced, the microbiota communities involved, and interactions between the metabolites themselves, can all influence physiological responses, highlighting the need for a greater understanding of the kinetics and site of production of microbial metabolites within the gut.

SUMMARY

Interactions between polyphenols and metabolites produced by the gut microbiota are emerging as a possible unifying protective mechanism underpinning diverse healthy dietary patterns signaling across culinary traditions, across geography and across domains of life.

Gut Microbiome Alters the Activity of Liver Cytochromes P450 in Mice With Sex-Dependent Differences

Sexual differences and the composition/function of the gut microbiome are not considered the most important players in the drug metabolism field; however, from the recent data it is obvious that they may significantly affect the response of the patient to therapy. Here, we evaluated the effect of microbial colonization and sex differences on mRNA expression and the enzymatic activity of hepatic cytochromes P450 (CYPs) in germ-free (GF) mice, lacking the intestinal flora, and control specific-pathogen-free (SPF) mice. We observed a significant increase in the expression of Cyp3a11 in female SPF mice compared to the male group. However, the sex differences were erased in GF mice, and the expression of Cyp3a11 was about the same in both sexes. We have also found higher Cyp2c38 gene expression in female mice compared to male mice in both the SPF and GF groups. Moreover, these changes were confirmed at the level of enzymatic activity, where the female mice exhibit higher levels of functional CYP2C than males in both groups. Interestingly, we observed the same trend as with CYP3A enzymes: a diminished difference between the sexes in GF mice. The presented data indicate that the mouse gut microbiome plays an important role in sustaining sexual dimorphism in terms of hepatic gene expression and metabolism.

Gut Microbiota and Intestinal Trans-Epithelial Permeability

Constant remodeling of tight junctions to regulate trans-epithelial permeability is essential in maintaining intestinal barrier functions and thus preventing diffusion of small molecules and bacteria to host systemic circulation. Gut microbiota dysbiosis and dysfunctional gut barrier have been correlated to a large number of diseases such as obesity, type 2 diabetes and inflammatory bowel disease. This led to the hypothesis that gut bacteria-epithelial cell interactions are key regulators of epithelial permeability through the modulation of tight junctions. Nevertheless, the molecular basis of host-pathogen interactions remains unclear mostly due to the inability of most in vitro models to recreate the differentiated tissue structure and components observed in the normal intestinal epithelium. Recent advances have led to the development of a novel cellular model derived from intestinal epithelial stem cells, the so-called organoids, encompassing all epithelial cell types and reproducing physiological properties of the intestinal tissue. We summarize herein knowledge on molecular aspects of intestinal barrier functions and the involvement of gut bacteria-epithelial cell interactions. This review also focuses on epithelial organoids as a promising model for epithelial barrier functions to study molecular aspects of gut microbiota-host interaction.

Targeting the gut microbiota by Asian and Western dietary constituents: a new avenue for diabetes

Increasing numerous diabetes annually is a great concern in public health globally. Gut microbiota recently has been suggested to be an emerging organ acting as a critical regulator in diabetes. Notably, gut microbiota is closely affected through an individual's nutrient intake and dietary pattern. Moreover, the metabolites of diets through gut microbiota are closely associated with the development of diabetes. Increasing evidence has established the association of different dietary pattern with alterations of the gut microbiota profile, in particular, the Asian diet and Western diet are typically as essential components linked to the interactions between gut microbiota and induction of obesity which is a significant risk factor for diabetes. In addition, some bacteria-related therapeutic methods including probiotics, dietary short-chain fatty acids immunotherapy, and gut microbiome transfer would be applied in the clinical prevention and control diabetes. Taken together, based on current published observations, the gut microbiota may serve as regulator or targets by the Asian diet and Western diet, contributing to the prevention or induction of diabetes eventually. In general, in the upcoming future, one of the emerging strategies for the prevention and control of diabetes may modulate gut microbiota through precise dietary strategies.

Iron Supplementation Influence on the Gut Microbiota and Probiotic Intake Effect in Iron Deficiency-A Literature-Based Review

Iron deficiency in the human body is a global issue with an impact on more than two billion individuals worldwide. The most important functions ensured by adequate amounts of iron in the body are related to transport and storage of oxygen, electron transfer, mediation of oxidation-reduction reactions, synthesis of hormones, the replication of DNA, cell cycle restoration and control, fixation of nitrogen, and antioxidant effects. In the case of iron deficiency, even marginal insufficiencies may impair the proper functionality of the human body. On the other hand, an excess in iron concentration has a major impact on the gut microbiota composition. There are several non-genetic causes that lead to iron deficiencies, and thus, several approaches in their treatment. The most common methods are related to food fortifications and supplements. In this review, following a summary of iron metabolism and its health implications, we analyzed the scientific literature for the influence of iron fortification and supplementation on the gut microbiome and the effect of probiotics, prebiotics, and/or synbiotics in iron absorption and availability for the organism.

Identification of the HT-29 cell line as a model for investigating MCT1 transporters in sigmoid colon adenocarcinoma

MCT1 transporters play a crucial role in the symbiotic relationship between humans and their colonic microbiome by facilitating the transport of bacteria-derived short chain fatty acids. Expression of colonic MCT1 transporters, localized in surface epithelial cells, is regulated by luminal butyrate levels. However, MCT1 also transports lactate and can be used by cancer cells to facilitate anaerobic glycolysis. Using immunolocalization techniques, this study investigated whether changes in MCT1 during cancer varied between different colonic regions. Whilst MCT1 abundance did not significantly change in transverse colon adenocarcinoma (P = 0.363, N = 6, paired T-Test), there was an increase in MCT1 in sigmoid colon adenocarcinoma (P = 0.010, N = 21, paired T-test). Using RT-PCR and western blotting, three human intestinal cell lines were tested for their suitability as a MCT1 cancer cell model. Experiments with Caco-2 cells confirmed that they modelled normal cells, with MCT1 only expressed after exposure to butyrate. In contrast, MCT1 was expressed in the absence of butyrate in both HCT-8 and HT-29 cell lines, with consistently high levels of MCT1 protein being present in HT-29 cells. Furthermore, butyrate treatment of HT-29 cells significantly decreased both MCT1 protein abundance (P < 0.001, N = 4, unpaired T-test) and glycosylation of its' chaperone protein, CD147 (P < 0.001, N = 4, unpaired T-test). These data suggest that (i) MCT1 transporter abundance increases in sigmoid colon adenocarcinoma, and (ii) HT-29 cells are an appropriate cell model with which to investigate MCT1 function in this disease.

Host glycan utilization within the Bacteroidetes Sus-like paradigm

The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these are adept at scavenging host glycans within this environment, including mucin O-linked glycans, N-linked glycoproteins and highly sulfated glycosaminoglycans (GAGs) such as heparin (Hep) and chondroitin sulfate (CS). Several recent biochemical studies have revealed the specific polysaccharide utilization loci (PULs) within the model symbiont Bacteroides thetaiotaomicron for the deconstruction of these host glycans. Here we discuss the Sus-like paradigm that defines glycan uptake by the Bacteroidetes and the salient details of the PULs that target heparin/heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (DS)/hyaluronic acid (HA), respectively, in B. thetaiotaomicron. The ability of the Bacteroidetes to target highly sulfated host glycans is key to their success in the gut environment but can lead to inflammation in susceptible hosts. Therefore, our continued understanding of the molecular strategies employed by these bacteria to scavenge carbohydrate nutrition is likely to lead to novel ways to alter their metabolism to promote host health.

Strengthening the Immune System and Reducing Inflammation and Oxidative Stress through Diet and Nutrition: Considerations during the COVID-19 Crisis

The coronavirus-disease 2019 (COVID-19) was announced as a global pandemic by the World Health Organization. Challenges arise concerning how to optimally support the immune system in the general population, especially under self-confinement. An optimal immune response depends on an adequate diet and nutrition in order to keep infection at bay. For example, sufficient protein intake is crucial for optimal antibody production. Low micronutrient status, such as of vitamin A or zinc, has been associated with increased infection risk. Frequently, poor nutrient status is associated with inflammation and oxidative stress, which in turn can impact the immune system. Dietary constituents with especially high anti-inflammatory and antioxidant capacity include vitamin C, vitamin E, and phytochemicals such as carotenoids and polyphenols. Several of these can interact with transcription factors such as NF-kB and Nrf-2, related to anti-inflammatory and antioxidant effects, respectively. Vitamin D in particular may perturb viral cellular infection via interacting with cell entry receptors (angiotensin converting enzyme 2), ACE2. Dietary fiber, fermented by the gut microbiota into short-chain fatty acids, has also been shown to produce anti-inflammatory effects. In this review, we highlight the importance of an optimal status of relevant nutrients to effectively reduce inflammation and oxidative stress, thereby strengthening the immune system during the COVID-19 crisis.

Evidence Supporting a Phased Immuno-physiological Approach to COVID-19 From Prevention Through Recovery

This paper presents an evidence-based strategy for improving clinical outcomes in COVID-19. Recommendations are based on the phases of the disease, because optimal interventions for one phase may not be appropriate for a different phase. The four phases addressed are: Prevention, Infection, Inflammation and Recovery. Underlying this phased approach is recognition of emerging evidence for two different components of pathophysiology, early infection and late stage severe complications. These two aspects of the disease suggest two different patterns of clinical emphasis that seem on the surface to be not entirely concordant. We describe the application of therapeutic strategies and appropriate tactics that address four main stages of disease progression for COVID-19. Emerging evidence in COVID-19 suggests that the SARS-CoV-2 virus may both evade the innate immune response and kill macrophages. Delayed innate immune response and a depleted population of macrophages can theoretically result in a blunted antigen presentation, delaying and diminishing activation of the adaptive immune response. Thus, one clinical strategy involves supporting patient innate and adaptive immune responses early in the time course of illness, with the goal of improving the timeliness, readiness, and robustness of both the innate and adaptive immune responses. At the other end of the disease pathology spectrum, risk of fatality in COVID-19 is driven by excessive and persistent upregulation of inflammatory mechanisms associated with cytokine storm. Thus, the second clinical strategy is to prevent or mitigate excessive inflammatory response to prevent the cytokine storm associated with high mortality risk. Clinical support for immune system pathogen clearance mechanisms involves obligate activation of immune response components that are inherently inflammatory. This puts the goals of the first clinical strategy (immune activation) potentially at odds with the goals of the second strategy(mitigation of proinflammatory effects). This creates a need for discernment about the time course of the illness and with that, understanding of which components of an overall strategy to apply at each phase of the time course of the illness. We review evidence from early observational studies and the existing literature on both outcomes and mechanisms of disease, to inform a phased approach to support the patient at risk for infection, with infection, with escalating inflammation during infection, and at risk of negative sequelae as they move into recovery.