The diversity of factors influencing human digestive microbiota in healthy adults and their interaction: A scoping review

doi:10.21203/rs.3.rs-4663650/v1

Download PDF

Research Article

The diversity of factors influencing human digestive microbiota in healthy adults and their interaction: A scoping review

https://doi.org/10.21203/rs.3.rs-4663650/v1

This work is licensed under a CC BY 4.0 License

You are reading this latest preprint version

Background / objectives

Human digestive microbiota is affected by a wide variety of different factors. The objective of this study was to perform a scoping review that gathers and updates the information available about factors that affect human digestive microbiota in healthy adults. It is also reviewed if other factors are considered and if some type of interaction between them is studied. We searched in MEDLINE, Web of Science, Scielo, PROSPERO, and Cochrane databases. Two authors independently reviewed study eligibility and data extraction. Articles were classified based on the main factor studied upon one of the following categories: diet, habits, environment, or chemical exposure.

Results

The literature search provided a total of 73 studies that met the inclusion criteria. The presence of data about the influence of diet, habits, environment, and exposition to chemicals on digestive microbiota were registered. Analysis of the studies indicates that the assessment of risk factors is often focused on a specific aspect (diet, habits, environment, and chemicals) and the study of the interaction between factors is up to now not sufficiently investigated. In addition, there are some situations probably relevant to the human digestive microbiota that are not being assessed (snacking, intermittent fasting, type of sport practiced, living with pets or working with animals, type of transportation daily used, home cleaning habits, treatments with radiotherapy, immune suppressants, corticosteroids).

Conclusions

Little is known about the impact of the combined interaction of possible risk factors (diet, habits, environment, and chemical exposure) of dysbiosis in human digestive microbiota. Further studies are encouraged to evaluate more broadly the interactions between the risk factors that may influence the diversity of the human digestive microbiota. All of them are factors that act together every day on our health.

gut microbiota dysbiosis

diet

lifestyle

environment

chemicals

Knowledge about human microbiota has taken a growing interest in studies due to its impact on health. It has also been described that some factors, such as diet, consumption of prebiotics and probiotics, medication, living places, physical activity, socioeconomic status, alcohol and tobacco consumption, and stress, have an impact on the digestive microbiota. ^{1, 2, 3, 4, 5, 6, 7, 8} In these studies, the data collection consists of microbiological and genetic analyses on feces or saliva. Several of them also use a questionnaire about habits and other circumstances of the participants that may impact the microbiota composition and diversity. ^{8, 9}

Up to now, there are some details that have been investigated that could be relevant to investigate. Some factors described affecting human microbiota are familiar environment and dental care.^7,9 Working activity and place, living with pets and frequent contact with animals such as fish, chickens, or cows with their specific microbiota, are sources of microorganisms. ^{10, 11} To the best of our knowledge, these factors have not been included yet in research to study the human digestive microbiota.

We conducted a scoping review to compile the factors described in the literature that influence the human digestive microbiota. Our objective was to review these factors that have an impact and may lead to dysbiosis in healthy adults. Due to the influence of the digestive microbiota on health, a profound knowledge of the factors that influence the human microbiota and its interactions would pave the way for preventive health care.

This scoping review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and meta-analyses (PRISMA) guidelines for Scoping Review (PRISMA-ScR). ¹²

Eligibility criteria

Inclusion criteria

Original research articles included in the scoping review were studies involving healthy human adults older than 19 years describing factors that influence in digestive microbiota (including oral, gastric, or intestinal microbiota) leading to dysbiosis. We have classified these factors into four categories:

-DIET: characteristics of the diet, type of food consumed, nutritional supplements, pro and prebiotics, specific diets.

-CHEMICALS: commonly used drugs, antibiotics, vitamins, herbal products, herbicides, pesticides.

-ENVIRONMENT: rural or urban, type of accommodation, cohabiting family, work activity, workplace, pets, household cleaning, means of transportation frequently used.

-HABITS: sleep, physical activity, tobacco, alcohol, drugs.

We selected papers published from 1 January 1950 to 30 September 2023 in English or Spanish. We included any research articles (no design restriction), systematic reviews, or meta-analysis, with or without questionnaires. We did not include conference abstracts.

Exclusion criteria

Studies about humans younger than 19 years, menopause, gestation, and digestive diseases and their pathogeny, diagnosis, or treatment (intestinal inflammatory diseases, celiac disease, gastric or oral diseases, eating disorders, parasitic diseases, fecal transplant). We also excluded studies about any other diseases such as mental, nervous system, kidney, skin, eyes, respiratory system, liver, pancreas, blood, obesity, metabolic syndrome, diabetes, COVID, HIV, or cancer.

Literature search strategy

Bibliographic search was made in five scientific databases: Web of Science (WoS), PubMed, Scielo, Cochrane, and PROSPERO.

After considering synonyms, keywords selected were: “Gastrointestinal microbiome”, “Gastrointestinal or gut or enteric or intestine or stomach or oral or mouth”, “Microbiome or microbiota or flora or microflora or bacteria”, “Dysbiosis or dysymbiosis or dysbacteriosis”. The final search strategy used was: ((Gastrointestinal OR gut OR intestine OR enteric OR stomach OR oral OR mouth) AND (microbiome OR microflora OR flora OR microbiota OR bacteria)) AND ((intestinal OR gut OR enteric) AND (dysbiosis OR dys-symbiosis OR dysbacteriosis)).

Eligibility assessment and data extraction

Literature search results were uploaded to the bibliography management tool Mendeley, and duplicates were removed. Screening by title and abstract was done by two trained review authors (BPL, CM) based on the inclusion and exclusion criteria. The full text of the selected references was retrieved, and BPL and CM screened them according to the selection criteria. The entire process was carried out independently and by blinding the reviewers. Disagreements were resolved by discussion and consensus.

Additional studies found by non-systematic search and relevant to the researchers have been included.

Data extraction included the following: First author, year of publication, number of participants, age, diet, habit, environment, chemical-related factors, and questionnaire item-descriptions.

We retrieved a total of 2864 references. After eliminating duplicates (996) with the bibliographic tool Mendeley it remained 1868 references. 73 studies fulfilled the criteria for inclusion. The search strategy and selection of publications are shown in Figure 1.

[Here Figure 1]

Of the total of 73 studies, 50 are research studies, and 22 are reviews or meta-analysis papers. Every research study found was classified into one of the following four categories of factors:

-DIET: 22 papers addressing probiotics, prebiotics, sweeteners, type of foods, ultra-processed food, specific diets (Mediterranean diet, vegan diet), fermented foods, plant-based food polyphenols, or protein supplements (Table 1)

-HABITS: 7 studies about sleep, physical activity, tobacco, alcohol, or drugs (Table 2).

-ENVIRONMENT: 11 articles regarding rural/urban environment, living near a mine, nursing homes, cohabiting family (partner, children, parents, grandparents), short hospitalization periods, long ocean voyages, or exposure to high altitudes (Table 3).

-CHEMICALS: 10 papers about antibiotics, methamphetamine, opioids, metformin, vitamin D, proton-pump inhibitors, herbicides, fungicides, titanium oxide nanoparticles, or herbal treatments (, Table 4).

One study addressed two or more of these categories and was included in the discussion.⁷⁰

First, a review was made of the results related to the factors studied in every paper. In 41 of these research studies questionnaires were used. In Tables 1 to 4, questions of the questionnaires used in every study are split into the four categories mentioned (diet, habits, environment, and chemicals) and data of these four categories retrieved in every study were recorded.

Diet

Overall, diet was the most studied factor about its influence on digestive microbiota (43% of the papers included in the scoping review) (Table 1). In the literature reviewed, probiotics have been shown to influence digestive microbiota to prevent or treat some diseases, decrease dysbiosis due to age, or help to maintain a normal microbiota in a meat-based diet. ^{13, 14. 15} Besides, the effect of commercial probiotics in healthy subjects was proven to increase the diversity of the oral cavity.¹⁶ Fermented food has taken greater importance due to its relationship with positive microbiota changes and other effects such as reduction of academic stress and inflammatory markers. ^{17, 18, 19}

The intake of dietary fibre with different prebiotics also influences digestive microbiota. A diet rich in fiber increases the levels of beneficial bacteria and short-chain fatty acids (SCFA). ^{20, 21, 22} Supplementing with milk oligosaccharides, a prebiotic based on resistant starch, induces the growth of beneficial bifidobacteria. ^{23, 24} It has also been described that a greater intake of dietary fiber from cereals, fruits, and vegetables is associated with shifts in gut microbiome composition and a reduction of C-reactive protein. ²⁵ Inulin consumption modified the microbiota composition with higher microbial diversity ²⁶. Dietary addition of L. casei, B. breve and a prebiotic product, results in an improvement of intestinal physiologic traits and an increase of total fecal bifidobacteria ²⁷.

Polyphenols also have been shown to affect the gut microbiota. Some of them have protective effects of the goblet cells of the intestinal mucosa. Other polyphenols have been shown to increase the counts of Lactobacillus and Bifidobacterium and improve gut and host health. ^{28, 29} The type of diet has also been related to gut microbiota status. High adherence to Southern European Atlantic Diet produces a greater number of total bacteria, Actinobacteria, Lactobacillus, and Bifidobacterium genus.³⁰ Significant correlations between bacterial taxa and Mediterranean Diet adherence were observed in centenarians, nonagenarians, and younger subjects.³¹ Microbiota associated to Mediterranean diet was enriched with beneficial bacteria that induces anti-inflammatory status and reduces the risk of developing gut diseases. ³² Individual foods have also been shown to influence digestive microbiota. Green tea liquid consumed daily decreased Bacteroidetes in feces and pathogenic bacteria in saliva. ³³ A diet heavily based on beans and dairy products reduced gut diversity with less beneficial bacteria.³⁴ A long-term protein supplementation may have a negative effect on gut microbiota and increase the risk of intestinal diseases.^{35, 36} Nevertheless, natural plant extracts with polyphenols, prebiotics, probiotics, and regular physical exercise improved gut microbiota, reducing dysbiosis produced by High Protein Diet (HPD). ³⁶

Consumption of more than five servings per day of ultra-processed food produced a decrease in microbiota diversity ³⁷. Sesame seed snacks and plant-based smoothies produced a notable increase in endogenous antioxidants in plasma and an improvement in gut microbiota. ³⁸

Pure saccharin supplementation did not alter gut microbial diversity, while Vitamin D supplementation increased the overall diversity of gut microbiota in healthy females with vitamin D deficiency. ^{39, 40} Food additives also affect gut microbiota composition. Some sweeteners and some emulsifiers may alter microbiota. Food preservatives increase the growth of proinflammatory bacteria, while anti-inflammatory bacteria decrease. Acidifiers can reduce coliform presence and increase lactic acid bacteria, and colorants can reduce microbiota diversity in vitro. Nevertheless, the long-term impact of food additives on gut microbiota needs to be examined ⁴¹.

[Here Table 1]

Habits

As shown in Table 2, there are different types of habits that influence digestive microbiota, such as physical activity, which has been shown to increase microbial diversity. ⁴² The quality of sleep also influences the microbiota, although not in all the circumstances. The microbiome is resistant to changes after consecutive days of sleeping restriction. ⁴³ However, an acute sleep-wake cycle shift of 2 to 4 hours (subjects postpone their regular sleeping time for 2 to 4 hours) affects the functional profiles of gut microbes and interactions among them ⁴⁴. Alcohol consumption or smoking or the combination of both cause gut microbiota dysbiosis in healthy men. Noteworthy, smoking alone causes more severe dysbiosis than drinking alone. ⁴⁵ Furthermore, smoking habits also modified oral microbiota diversity and heavy episodic drinking is associated with a specific stool type phenotype (Bristol stool scale). ⁴⁶ Consumption of heroin, ephedrine, and methamphetamine produced changes in the microbiota. Bacterial diversity was higher in SUD (substance use disorders) and this increases with the length of substance abuse.⁴⁷ Intestinal colonization by oral bacteria has been demonstrated; therefore, oral hygiene becomes more important ^46,48. In fact, the salivary microbiome was affected by denture use ⁴⁶.

[Here Table 2]

Environment

The environment is also an important factor to study in this context (Table 3). References retrieved have shown different sources of influence on gut microbiota. Blastocystis, a component of gut microbiota, has a higher prevalence in non-westernized individuals ⁴⁹. Differences in gut microbiota composition were found in individuals with the same ethnicity but coming from different Italian regions. ⁵⁰ Medication and time spent in the nursing home contributed to microbiota dysbiosis more than age and frailty. The microbiota of residents who had lived in the nursing home for more than 1 year were enriched in inflammatory and pathogenic species and reduced in anti-inflammatory and symbiotic species. ⁵¹

Nevertheless, it has been described that short-term hospitalization did not impact the richness or structure of the salivary microbiome.⁵²

Indoor spaces often harbor unique microbial communities. Indoor air in residences contained a greater number of culturable bacteria than outdoor air. Differences in bacterial flora in settled dust in two buildings were greater than differences between seasons. Bacterial communities on surfaces in offices were different between cities, and the microbiota in a home were identifiable by family. Humans are also major sources of bacteria in indoor air. ⁵³

As for the quality of the environment, long-term exposure to metals in residents near a mining and smelting area produced different profiles of gut microbiota. These effects were higher in men because of mining and smelting activity.⁵⁴ Currently, it is under discussion whether air pollution due to emissions from factories, chimneys, or livestock also affects gut microbiota since it may be trapped in the food. Some studies showed that gut microbiota metabolized the inorganic arsenic into toxic metabolites. Currently, there are some chemicals and pesticides that are considered microbiota-disrupting chemicals. ⁵⁵ The living altitude also influences the microbiota composition, which was enriched in Prevotella and Bacteroidetes in subjects living in high altitudes (>1500m) while Faecalibacterium and Blautia were increased in the low altitude group (<1500m). ⁵⁶

Microbiota diversity can also change due to traveling. Sun et al., (2022) reported that a 135-day sea expedition produced “seafaring syndrome” (SS) with abnormal defecation, frequent insomnia, poor sleeping quality, and overeating. Noteworthy, a significant correlation between the gut microbiome perturbation and this syndrome was found. ⁵⁷

Cohabitation with other people also influences digestive microbiota. Microbial dysbiosis might be caused in healthy partners cohabiting with Ulcerous Colitis patients and anxiety and stress are related to reduced diversity. ^{58, 59} People with larger social networks tend to have a more diverse microbiome. Cohabiting time affected strain sharing more than age or genetics. ⁶⁰ A high similarity in the oral microbiota composition was found between members of the same family, higher between twins, parents, or brothers, and less or none between grandparents and grandchildren. There was also a similarity between classmates. ⁹

[Here Table 3]

Chemicals

Chemicals have proven to be important factors that influence digestive microbiota (Table 4). Non steroidal anti-inflammatory drugs (NSAID) provoke changes in gut microbiota. Bacterial population in the gastrointestinal tract reflects the combination of medications and varied with the type of NSAID that people take ⁶¹. Proton Pump Inhibitors (PPI) have been associated with a decrease in microbiota diversity and an increase of Lactobacilus, Steptococcus, Staphylococcus and E.coli. ⁶²^{, 63} Antibiotics are clearly an important factor that changes gut microbiota characteristics. Azithromycin alters the diversity of the salivary microbiome and delays the recovery of the diversity of gut microbiota after a treatment. ⁶⁴ Moxifloxacin reduced bacterial diversity, which is not recovered until 16 to 21 days ⁶⁵. S. boulardii treatment can mitigate some antibiotic-induced microbiota changes (dysbiosis).⁶⁶ Metformine has an effect of reduction of gut microbiome diversity already after 24 hours of administration.⁶⁷ Decreased diversity of Shanon and Chao indices was observed in methadone-treated subjects. ⁶⁸ Also, essential oils may be considered as a factor that influences the gut microbiome. Notably, a component of these oils, geraniol, has proven to increase butyrate-producer bacteria and improve intestinal dysbiosis.⁶⁹

[Here Table 4]

Diet, chemicals, environment, and/or habits interaction

Summing up, diet, chemicals, environment, and habits have been described as influencing the digestive microbiota. These factors are typically considered individually without considering the interactions between them. Diet, sleep quality, medications, supplements, physical activity, and psychological status are considered possible causes of dysbiosis. ^{70, 71, 72} However, it is also very important to study the interactions between factors on the microbiota quality. Boisseau et al. (2022) found that the microbiota of athletes is different from the rest of the population. Diets and treatments could be the origin of these differences. However, it is also known that exercise improves microbiota in sedentary people, but excessive practice does not improve microbiota and even worsens health. Nevertheless, there are no studies on humans that search for the interaction between diet and physical activity. ⁶ Also, a positive interaction was found between diet, physical exercise, and HPD. Natural plant extracts with polyphenols, prebiotics, probiotics, and regular physical exercise improved gut microbiota, reducing dysbiosis produced by HPD ³⁶.

Of the 73 articles that meet the inclusion criteria, the majority described the influence of diet, habits, chemicals, or environment independently affecting the gut microbiota. All the factors reviewed act together in people´s daily lives. Therefore, the existence of an interaction between them is something that should be considered. In fact, in almost all the studies analyzed, the questionnaires given to the participants contain questions about all or some of these factors in order to exclude their influence from the results.

In the group of 19 papers about diet influence (Table 1) data were collected about diet (16/19), habits (12/19), environment (3/19), and chemicals (7/19)

In addition to checking the consumption of foods whose influence on the diet is proven, such as fermented foods, ^{17, 18, 19} it would be interesting to investigate more about whether there is a difference between homemade and commercial fermentation meals since there are already many elaborate fermentation products on the market whose microorganism content is probably different from the homemade ones. Information in this regard can be collected in the questionnaire (homemade or commercial). The positive effects of some types of diet rich in vegetables have been proven. ^{30, 31, 32, 33} Therefore, it is also necessary to ask about the frequency of consumption since we can eat vegetables, but not in an appropriate frequency to notice positive effects.³⁴

It would be also interesting to investigate about the consumption of diets high in proteins or protein supplements and their duration, given that, in some cases, it can negatively influence the digestive microbiota.³⁵ UP foods should also be checked since high consumption has been seen to affect the diversity of the digestive microbiota. ³⁷ Treatments with vitamin D are becoming more common in the population. Since this also influences the digestive microbiota, ⁴⁰ should be considered.

Furthermore, the influence of some nutritional habits, such as snacking, intermittent fasting, and the number of daily intakes were not included in any of the questionnaires. Herein, we suggest including snacking as another factor to be considered. Snacking behavior is a practice that can be done with different types of foods and therefore can contribute to improving diet but also to worsening it.⁷² Other factors that may be suitable to include were intermittent fasting and the number of daily intakes. These are habits that may influence the function of the digestive tract at different rhythms and frequencies, and this may affect the environment of microbiota.

The 6 papers that analyze habits influence (Table 2) data were retrieved about diet (5/6), habits (5/6), environment (1/6), and chemicals (2/6). Furthermore, these questionnaires do not consider the type of sport practiced. This is important to consider since team sports and sports in contact with water must be possible sources of different microbiota. Furthermore, none of these questionnaires considers body and hair hygiene, analyzing both frequency and time spent washing it. This may affect skin microbiota and, consequently, the digestive microbiota too.

In the 7 papers addressing the environmental factors (Table 3), data were recorded about diet (7/7), habits (7/7), environment (3/7), and chemicals (1/7). However, there were not retrieved other circumstances related to the environment. Living with pets may influence the human microbiota due to the interaction with their own specific microbiota. Domestic dogs share the house with the owners. Its microbiota has a taxonomic similarity with humans, much larger than mice or pig.^{73, 74} Living or working with another type of animals may influence the human microbiota, too, due to their different specific microbiota. The microbiome of teleost fish, broiler chicken, and clam (Agropecten ventricosus) is different from the microbiome of mammals.^{10, 75, 76} Cows that consume more pastures have a higher amount of Firmicutes and Bacteroidetes, while cows that consume more concentrated food have the inverse proportion.¹¹ Not only microorganisms from pets but also parasites may alter gut conditions and contribute to intestinal dysbiosis. ^{77, 78}

There are many professions developed in contact with animals and or with people with different microbiota composition, such as livestock, veterinary, fishing, agriculture, slaughterhouse, medicine, nursing, physiotherapy, nursing homes, public transport driver, police, prisons, schools, nurseries, masseuse, aesthetic centers (manicures, pedicures, tattoo artists, hairdressers), research laboratories with animal or biological material, zoos. We have not found any research about the influence of these kinds of environments on digestive microbiota, but they probably have some role in its variation. Moreover, the type of transportation daily used (individual, public) may also be an important source of variation of the microbiota taken from the environment.

Place of work may also be an influencing factor since different environments can harbor different microbiota: home, office, industry, field, ship, plane, educational center, and transports such as trucks and taxis. Home cleaning is a daily action that can also modify the home microbiome, and coexistence with domestic animals or working with them are also important data to collect in a questionnaire for microbiota research.

Pesticides also modify the microbiota of the animals. It has been described that long-term (lifelong) exposure to a low dose of a glyphosate herbicide (GBH-RUp) in drinking water led to significant changes in the intestinal microbiome composition in mice.⁷⁹ Daily contact with pesticides may be important for people working in aquaculture, poultry farming, and livestock farming.

Another possible source of variation in the human microbiota environment may be home cleaning habits. Cleaning of chicken sponges significantly affected its microbiome structure. The authors of this study visualize the role of kitchen sponges as microbial hot spot in building the environment with the capability to collect and spread bacteria. ⁸⁰ The environment has a high microbial diversity. Sites like home, offices, industry, and transport have very different physicochemical conditions. The role of the ambient microbiome in the skin and digestive microbiota is evident but not well understood nowadays. ⁸¹

The 8 papers regarding the chemical factors (Table 4) collected data about diet (5/8), habits (2/8), environment (1/8), and chemicals (7/8). Noteworthy, none of these questionnaires consider some type of therapy that could also affect the digestive microbiome, such as radiotherapy.⁸² There are also other treatments widely used as opioids,⁸³ immune suppressants, corticosteroids, and anovulatory that should be considered.

Almost all the studies included in this review investigated one of these factors and have provided evidence about their impact on our inner microbiota. However, further studies are necessary to obtain more data about the interaction between these aforementioned factors to shed light on their implications for the quality of the digestive microbiota.

Of all the articles reviewed, only one considers studying the interaction between factors. Boisseau et al. (6) reviewed the relationship between diet and physical activity. In humans, short-term changes in diet affect microbiota but in a transient way. A high fat content causes a decrease in Bifidobacteria, while protein increase bifidobacteria and lactobacillus, and carbohydrates increase Bifidobacteria and reduce Bacteroides. On the other hand, the microbiota of athletes is different of the rest of the population. Diets and treatments could be the origin of these differences. However, it is also known that exercise improves microbiota in sedentary people, but an excessive practice does not improve microbiota and even worsen health. Nevertheless, there are no studies on humans that search about the interaction between diet and physical activity. This can be extensive to the other factors. For example, it is possible that different changes in the microbiota of different individuals due to probiotic consumption could be due to differences in some other factor studied in this review.

Summing up, diet, chemicals, environment, and habits have been described to influence in the digestive microbiota. These factors are typically considered individually without considering the interactions between them. Furthermore, as shown in this review some cases that could influence human digestive microbiota are not yet studied. However, further studies are necessary to obtain more data about the influence on digestive microbiota of these aforementioned factors and about the interaction between all of them to shed light on their implications for the quality of the digestive microbiota. There is a great variety of questionnaires used in research about human digestive microbiota. It would be helpful to use a standardized tool that help to collect data about these factors.

Ethics approval and consent to participate

Not applicable

Consent for publication

Not applicable

Availability of data and materials

Not applicable

Competing interests

The authors declare that they have no competing interests

Funding

The financial support for the publication of this paper is made by Universidad Internacional de La Rioja. The role of the sponsor of this review was restricted to providing economic support, and it were not involved in the study process, manuscript preparation, or submission.

Authors´contributions

BPLL: Conceptualization, data curation, formal analysis, investigation, methodology, writing original draft and edition.

CMR: Data curation, formal analysis, investigation, methodology, writing review and edition, validation.

EGF: Formal analysis, methodology, supervision, validation, writing review.

Acknowledgements

Not applicable

McBurney MI, Davis C, Fraser CM, et al. Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions. Journal of Nutrition. 2019;149(11):1882-1895. doi:10.1093/jn/nxz154
Collins SM, Bercik P. The Relationship Between Intestinal Microbiota and the Central Nervous System in Normal Gastrointestinal Function and Disease. Gastroenterology. 2009;136(6):2003-2014. doi:10.1053/j.gastro.2009.01.075
Macfarlane GT, Steed H, Macfarlane S. Bacterial metabolism and health-related effects of galacto-oligosaccharides and other prebiotics. J Appl Microbiol. 2008;104(2):305-344. doi:10.1111/j.1365-2672.2007.03520.x
Robinson CJ, Bohannan BJM, Young VB. From Structure to Function: the Ecology of Host-Associated Microbial Communities. Microbiology and Molecular Biology Reviews. 2010;74(3):453-476. doi:10.1128/mmbr.00014-10
Rinninella E, Tohumcu E, Raoul P, et al. The role of diet in shaping human gut microbiota. Best Pract Res Clin Gastroenterol. 2023;62-63. doi:10.1016/j.bpg.2023.101828
Boisseau N, Barnich N, Koechlin-Ramonatxo C. The Nutrition-Microbiota-Physical Activity Triad: An Inspiring New Concept for Health and Sports Performance. Nutrients. 2022;14(5). doi:10.3390/nu14050924
Willis JR, González-Torres P, Pittis AA, et al. Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition. Microbiome. 2018;6(1). doi:10.1186/s40168-018-0592-3
Segovia-Rodríguez L, Echeverry-Alzate V, Rincón-Pérez I, et al. Gut microbiota and voluntary alcohol consumption. Transl Psychiatry. 2022;12(1). doi:10.1038/s41398-022-01920-2
Willis JR, Saus E, Iraola-Guzmán S, et al. Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors. NPJ Biofilms Microbiomes. 2022;8(1). doi:10.1038/s41522-022-00279-y
Llewellyn MS, Boutin S, Hoseinifar SH, Derome N. Teleost microbiomes: The state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol. 2014;5(JUN):1-1. doi:10.3389/fmicb.2014.00207
Fraga Cotelo M. Microbiota Ruminal: Estrategias de Modulación Con Microorganismos Fibrolíticos. Tesis de Maestría. Uruguay; 2010.
Tricco A, Lillie E, Zarin W, O’Brien KK. PRISMA Extension for Scoping Reviews (PRISMA-SCR): Checklist and Explanation. Ann Intern Med. 2018.
Butel M. Probiotics, gut microbiota and health. Med Mal Infect. 2014;44(1):1-8. doi:10.1016/j.medmal.2013.10.002
Rampelli S, Candela M, Severgnini M, et al. A probiotics-containing biscuit modulates modulates the intestinal microbiota in the elderly. J Nutr Health Aging. 2013;17(2).
Odamaki T, Kato K, Sugahara H, Xiao JZ, Abe F, Benno Y. Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: An open, randomised, parallel-group study. Benef Microbes. 2016;7(4):473-484. doi:10.3920/BM2015.0173
Dassi E, Ferretti P, Covello G, et al. The short-term impact of probiotic consumption on the oral cavity microbiome. Sci Rep. 2018;8(1). doi:10.1038/s41598-018-28491-x
Márquez-Morales L, El-Kassis EG, Cavazos-Arroyo J, Rocha-Rocha V, Martínez-Gutiérrez F, Pérez-Armendáriz B. Effect of the intake of a traditional mexican beverage fermented with lactic acid bacteria on academic stress in medical students. Nutrients. 2021;13(5). doi:10.3390/nu13051551
Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137-4153.e14. doi:10.1016/j.cell.2021.06.019
Galena AE, Chai J, Zhang J, et al. The effects of fermented vegetable consumption on the composition of the intestinal microbiota and levels of inflammatory markers in women: A pilot and feasibility study. PLoS One. 2022;17(10 October). doi:10.1371/journal.pone.0275275
Reyes LM, Vázquez RG, Arroyo SMC, et al. Correlation between diet and gut bacteria in a population of young adults. Int J Food Sci Nutr. 2016;67(4):470-478. doi:10.3109/09637486.2016.1162770
De Filippis F, Pellegrini N, Vannini L, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2016;65(11). doi:10.1136/gutjnl-2015-309957
Losno EA, Sieferle K, Perez-Cueto FJA, Ritz C. Vegan diet and the gut microbiota composition in healthy adults. Nutrients. 2021;13(7). doi:10.3390/nu13072402
Elison E, Vigsnaes LK, Rindom Krogsgaard L, et al. Oral supplementation of healthy adults with 2′-O-fucosyllactose and lacto-N-neotetraose is well tolerated and shifts the intestinal microbiota. British Journal of Nutrition. 2016;116(8):1356-1368. doi:10.1017/S0007114516003354
Alfa MJ, Strang D, Tappia PS, et al. A randomized trial to determine the impact of a digestion resistant starch composition on the gut microbiome in older and mid-age adults. Clinical Nutrition. 2018;37(3):797-807. doi:10.1016/j.clnu.2017.03.025
Ma W, Nguyen LH, Song M, et al. Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. Genome Med. 2021;13(1). doi:10.1186/s13073-021-00921-y
Kiewiet MBG, Elderman ME, El Aidy S, et al. Flexibility of Gut Microbiota in Ageing Individuals during Dietary Fiber Long-Chain Inulin Intake. Mol Nutr Food Res. 2021;65(4). doi:10.1002/mnfr.202000390
De Preter V, Vanhoutte T, Huys G, et al. First published Sep-tember 21. Am J Physiol Gas-trointest Liver Physiol. 2007;292:358-368. doi:10.1152/ajpgi.00052.2006.-Pre-and/or
Wan MLY, Co VA, El-Nezami H. Dietary polyphenol impact on gut health and microbiota. Crit Rev Food Sci Nutr. 2020. doi:10.1080/10408398.2020.1744512
Davinelli S, Scapagnini G. Interactions between dietary polyphenols and aging gut microbiota: A review. BioFactors. 2022;48(2):274-284. doi:10.1002/biof.1785
Castro-Penalonga M, Roca-Saavedra P, Miranda JM, et al. Influence of food consumption patterns and Galician lifestyle on human gut microbiota. J Physiol Biochem. 2018;74(1):85-92. doi:10.1007/s13105-017-0570-4
Palmas V, Pisanu S, Madau V, et al. Gut Microbiota Markers and Dietary Habits Associated with Extreme Longevity in Healthy Sardinian Centenarians. Nutrients. 2022;14(12). doi:10.3390/nu14122436
Illescas O, Rodríguez-Sosa M, Gariboldi M. Mediterranean diet to prevent the development of colon diseases: A meta-analysis of gut microbiota studies. Nutrients. 2021;13(7). doi:10.3390/nu13072234
Yuan X, Long Y, Ji Z, et al. Green Tea Liquid Consumption Alters the Human Intestinal and Oral Microbiome. Mol Nutr Food Res. 2018;62(12). doi:10.1002/mnfr.201800178
Lacourt-Ventura MY, Vilanova-Cuevas B, Rivera-Rodríguez D, et al. Soy and frequent dairy consumption with subsequent equol production reveals decreased gut health in a cohort of healthy puerto rican women. Int J Environ Res Public Health. 2021;18(16). doi:10.3390/ijerph18168254
Moreno-Pérez D, Bressa C, Bailén M, et al. Effect of a protein supplement on the gut microbiota of endurance athletes: A randomized, controlled, double-blind pilot study. Nutrients. 2018;10(3). doi:10.3390/nu10030337
Cai J, Chen Z, Wu W, Lin Q, Liang Y. High animal protein diet and gut microbiota in human health. Crit Rev Food Sci Nutr. 2022;62(22):6225-6237. doi:10.1080/10408398.2021.1898336
Cuevas-Sierra A, Milagro FI, Aranaz P, Martínez JA, Riezu-Boj JI. Gut microbiota differences according to ultra-processed food consumption in a spanish population. Nutrients. 2021;13(8). doi:10.3390/nu13082710
Zhang JY, Lo HC, Yang F Lo, Liu YF, Wu WM, Chou CC. Plant-based, antioxidant-rich snacks elevate plasma antioxidant ability and alter gut bacterial composition in older adults. Nutrients. 2021;13(11). doi:10.3390/nu13113872
Serrano J, Smith KR, Crouch AL, et al. High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice. Microbiome. 2021;9(1). doi:10.1186/s40168-020-00976-w
Singh P, Rawat A, Alwakeel M, Sharif E, Al Khodor S. The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals. Sci Rep. 2020;10(1). doi:10.1038/s41598-020-77806-4
Cao Y, Liu H, Qin N, Ren X, Zhu B, Xia X. Impact of food additives on the composition and function of gut microbiota: A review. Trends Food Sci Technol. 2020;99:295-310. doi:10.1016/j.tifs.2020.03.006
Estaki M, Pither J, Baumeister P, et al. Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions. Microbiome. 2016;4. doi:10.1186/s40168-016-0189-7
Zhang SL, Bai L, Goel N, et al. Human and rat gut microbiome composition is maintained following sleep restriction. Proc Natl Acad Sci U S A. 2017;114(8):E1564-E1571. doi:10.1073/pnas.1620673114
Liu Z, Wei ZY, Chen J, et al. Acute Sleep-Wake Cycle Shift Results in Community Alteration of Human Gut Microbiome. mSphere. 2020;5(1). doi:10.1128/msphere.00914-19
Lin R, Zhang Y, Chen L, et al. The effects of cigarettes and alcohol on intestinal microbiota in healthy men. Journal of Microbiology. 2020;58(11):926-937. doi:10.1007/s12275-020-0006-7
Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M, Al Khodor S. Profiling the Salivary microbiome of the Qatari population. J Transl Med. 2020;18(1). doi:10.1186/s12967-020-02291-2
Xu Y, Xie Z, Wang H, et al. Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing. Sci Rep. 2017;7(1). doi:10.1038/s41598-017-03706-9
Castañeda C, Pacheco Y, Cuesta RE. Implicaciones de la microbiota oral en la salud del sistema digestivo. Revista Dilemas Contemporáneos: Educación, Política y Valores. 2021.
Beghini F, Pasolli E, Truong TD, Putignani L, Cacciò SM, Segata N. Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. ISME Journal. 2017;11(12):2848-2863. doi:10.1038/ismej.2017.139
Fontana A, Panebianco C, Picchianti-Diamanti A, et al. Gut microbiota profiles differ among individuals depending on their region of origin: An Italian pilot study. Int J Environ Res Public Health. 2019;16(21). doi:10.3390/ijerph16214065
Haran JP, Zeamer A, Ward D V., Dutta P, Bucci V, McCormick BA. The Nursing Home Older Adult Gut Microbiome Composition Shows Time-dependent Dysbiosis and Is Influenced by Medication Exposures, Age, Environment, and Frailty. Journals of Gerontology - Series A Biological Sciences and Medical Sciences. 2021;76(11):1930-1938. doi:10.1093/gerona/glab167
Cabral DJ, Wurster JI, Flokas ME, et al. The salivary microbiome is consistent between subjects and resistant to impacts of short-Term hospitalization. Sci Rep. 2017;7(1). doi:10.1038/s41598-017-11427-2
Stephens B. What Have We Learned about the Microbiomes of Indoor Environments? mSystems. 2016;1(4). doi:10.6084/m9.figshare.3459257.v1
Shao M, Zhu Y. Long-term metal exposure changes gut microbiota of residents surrounding a mining and smelting area. Sci Rep. 2020;10(1). doi:10.1038/s41598-020-61143-7
Anwar H, Iftikhar A, Muzaffar H, et al. Biodiversity of Gut Microbiota: Impact of Various Host and Environmental Factors. Biomed Res Int. 2021;2021. doi:10.1155/2021/5575245
Zuo H, Zheng T, Wu K, et al. High-altitude exposure decreases bone mineral density and its relationship with gut microbiota: Results from the China multi-ethnic cohort (CMEC) study. Environ Res. 2022;215. doi:10.1016/j.envres.2022.114206
Sun Z, Zhang M, Li M, et al. Interactions between Human Gut Microbiome Dynamics and Sub-Optimal Health Symptoms during Seafaring Expeditions.; 2022. https://journals.asm.org/journal/spectrum.
Chen GL, Zhang Y, Wang WY, et al. Partners of patients with ulcerative colitis exhibit a biologically relevant dysbiosis in fecal microbial metacommunities. World J Gastroenterol. 2017;23(25):4624-4631. doi:10.3748/wjg.v23.i25.4624
Johnson KVA. Gut microbiome composition and diversity are related to human personality traits. Hum Microb J. 2020;15. doi:10.1016/j.humic.2019.100069
Valles-Colomer M, Blanco-Míguez A, Manghi P, et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature. February 2023. doi:10.1038/s41586-022-05620-1
Rogers MAM, Aronoff DM. The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clinical Microbiology and Infection. 2016;22(2):178.e1-178.e9. doi:10.1016/j.cmi.2015.10.003
Imhann F, Jan Bonder M, Vich Vila A, et al. Proton pump inhibitors affect the gut microbiome. Gut. 2016;65:740-748. doi:10.1136/gutjnl
Hojo M, Asahara T, Nagahara A, et al. Gut Microbiota Composition Before and After Use of Proton Pump Inhibitors. Dig Dis Sci. 2018;63(11):2940-2949. doi:10.1007/s10620-018-5122-4
Anthony WE, Wang B, Sukhum K V., et al. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell Rep. 2022;39(2). doi:10.1016/j.celrep.2022.110649
Burdet C, Nguyen TT, Duval X, et al. Impact of antibiotic gut exposure on the temporal changes in microbiome diversity. Antimicrob Agents Chemother. 2019;63(10). doi:10.1128/AAC.00820-19
Kabbani TA, Pallav K, Dowd SE, et al. Prospective randomized controlled study on the effects of Saccharomyces boulardii CNCM I-745 and amoxicillin-clavulanate or the combination on the gut microbiota of healthy volunteers. Gut Microbes. 2017;8(1):17-32. doi:10.1080/19490976.2016.1267890
Elbere I, Kalnina I, Silamikelis I, et al. Association of metformin administration with gut microbiome dysbiosis in healthy volunteers. PLoS One. 2018;13(9). doi:10.1371/journal.pone.0204317
Cruz-Lebrón A, Johnson R, Mazahery C, et al. Chronic opioid use modulates human enteric microbiota and intestinal barrier integrity. Gut Microbes. 2021;13(1). doi:10.1080/19490976.2021.1946368
Rizzello F, Ricci C, Scandella M, et al. Dietary geraniol ameliorates intestinal dysbiosis and relieves symptoms in irritable bowel syndrome patients: A pilot study. BMC Complement Altern Med. 2018;18(1). doi:10.1186/s12906-018-2403-6
Brenner LA, Hoisington AJ, Stearns-Yoder KA, et al. Military-Related Exposures, Social Determinants of Health, and Dysbiosis: The United States-Veteran Microbiome Project (US-VMP). Front Cell Infect Microbiol. 2018;8. doi:10.3389/fcimb.2018.00400
Coman V, Vodnar DC. Gut microbiota and old age: Modulating factors and interventions for healthy longevity. Exp Gerontol. 2020;141.
Redondo-Useros N, Nova E, González-Zancada N, Díaz LE, Gómez-Martínez S, Marcos A. Microbiota and lifestyle: A special focus on diet. Nutrients. 2020;12(6):1-54. doi:10.3390/nu12061776
Hernandez J, Rhimi S, Kriaa A, et al. Domestic Environment and Gut Microbiota: Lessons from Pet Dogs. Microorganisms. 2022;10(5). doi:10.3390/microorganisms10050949
Soriano Ferrer C. La Microbiota Intestinal En Perros y Gatos y Su Relación Con El Sistema Inmunitario Asociado. Trabajo Fin de Grado. Zaragoza; 2021.
Peinado Martínez MJ. Efectos de Nuevos Aditivos Alimentarios Sobre La Composición de La Microbiota Digestiva En Pollos Broiler. Tesis Doctoral. Tesis Doctoral. (Universidad de Granada, ed.). Granada, España; 2015. http://hdl.handle.net/10481/42252.
Mazón-Suástegui JM, Tovar-Ramírez D, Ortiz-Cornejo NL, et al. Efecto de medicamentos homeopáticos sobre crecimiento, supervivencia y microbiota gastrointestinal, en juveniles del pectínido Argopecten ventricosus. Rev MVZ Cordoba. 2019;24(3):7328-7338. doi:10.21897/rmvz.1536
Piazzesi A, Putignani L. Impact of helminth–microbiome interactions on childhood health and development—A clinical perspective. Parasite Immunol. 2023;45(4). doi:10.1111/pim.12949
Garcia-Bonete MJ, Rajan A, Suriano F, Layunta E. The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea. Life. 2023;13(8). doi:10.3390/life13081765
Del Castilo I, Neumann AS, Lemos FS, et al. Lifelong Exposure to a Low-Dose of the Glyphosate-Based Herbicide RoundUp® Causes Intestinal Damage, Gut Dysbiosis, and Behavioral Changes in Mice. Int J Mol Sci. 2022;23(10). doi:10.3390/ijms23105583
Cardinale M, Kaiser D, Lueders T, Schnell S, Egert M. Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species. Sci Rep. 2017;7(1). doi:10.1038/s41598-017-06055-9
Gebrayel P, Nicco C, Al Khodor S, et al. Microbiota medicine: towards clinical revolution. J Transl Med. 2022;20(1). doi:10.1186/s12967-022-03296-9
Ren H, Wu Q, Sun Z, Fang M, Liu J, Luo J. Research progress and treatment of radiation enteritis and gut microbiota. Radiat Oncol J. 2023;41(2):61-68. doi:10.3857/roj.2023.00346
Satish S, Abu Y, Gomez D, Kumar Dutta R, Roy S. HIV, opioid use, and alterations to the gut microbiome: elucidating independent and synergistic effects. Front Immunol. 2023;14. doi:10.3389/fimmu.2023.1156862

Tables 1 to 4 are available in the Supplementary Files section

No competing interests reported.

Download PDF

Editor assigned by journal
02 Jul, 2024
Submission checks completed at journal
02 Jul, 2024
First submitted to journal
30 Jun, 2024

You are reading this latest preprint version

The diversity of factors influencing human digestive microbiota in healthy adults and their interaction: A scoping review

Status:

Version 1

Abstract

Figures

INTRODUCTION

MATERIALS AND METHODS

RESULTS

DISCUSSION

CONCLUSIONS

Declarations

References

Tables

Additional Declarations

Supplementary Files

Status:

Version 1