[6], A study by the National Human Genome Research Institute in Bethesda, Maryland, researched the DNA of human skin fungi at 14 different locations on the body. Schroeder FA, Lin CL, Crusio WE, Akbarian S. Antidepressant-like effects of the histone deacetylase inhibitor, sodium butyrate, in the mouse, Principles and clinical implications of the brain-gut-enteric microbiota axis, Diversity of the human intestinal microbial flora. However, animal and plant-proteins influence the gut microbiota in different ways. Anammox bacteria can also use a variety of inorganic metal oxides as an alternative to nitrite (Shaw et al., 2020). Velagapudi VR, Hezaveh R, Reigstad CS, Gopalacharyulu P, Yetukuri L, Islam S, Felin J, Perkins R, Born J, Oresic M, et al. The Approved List of biological agents Page 7 of 39 Health and Safety Executive how likely it is that the infection would spread to the community; the availability of any prophylaxis1 or treatment. For example, the IECs secrete an isoform of alkaline phosphatase (intestinal alkaline phosphatase) that dephosphorylates the LPS endotoxin[107]. The gut microbiota maintains a symbiotic relationship with the gut mucosa and imparts substantial metabolic, immunological and gut protective functions in the healthy individual. Furthermore, butyrate can prevent the accumulation of toxic metabolic by-products such as D-lactate[38]. However, TNF-a administered to healthy subjects resulted in no depressive symptoms,38 suggesting that toxin induced inflammation caused the mood disturbance. Conflict of interest: the authors declare no potential conflict of interest. Lorenzi, A.S.; Bonatelli, M.L. Breast milk contains indigestible glycans termed as human milk oligosaccharides (HMO) which are easily broken down by these bacteria. [59], Hand washing can damage skin because the stratum corneum top layer of skin consists of 15 to 20 layers of keratin disks, corneocytes, each of which is each surrounded by a thin film of skin lipids which can be removed by alcohols and detergents. Fermentation is a metabolic process that produces chemical changes in organic substrates through the action of enzymes.In biochemistry, it is narrowly defined as the extraction of energy from carbohydrates in the absence of oxygen. It has been speculated since long that the gut microbiota bear significant functional role in maintaining the gut in the normal individual and human health as a whole. The existence of the gut-brain axis was proposed in the landmark study by Sudo and colleagues that discovered the impaired stress response in germ-free mice. Studies have shown that several strains of Bifidobacterium, especially the Bifidobacterium longus subs infantis contain unique gene cluster (HMO-related gene cluster 1) that codes for difference glycosidases (sialidase, fucosidase, hexosaminidase and galactosidase) and carbohydrate transporters that are capable of importing and metabolizing HMOs[134]. Of all locations in our homes, kitchens are among the most heavily colonized by bacteria, and are likely where we are exposed to the broadest diversity of microbes (Scott et al., 1982; Ojima et al., 2002a; Ojima et al., 2002b; Sinclair and Gerba, 2011).Microbial exposures arise both directly, from handling, preparing, and eating food, and indirectly, from contact with [10], The researchers at North Carolina State University discovered that while it was difficult to predict every strain of bacteria in the microbiome of the navel that they could predict which strains would be prevalent and which strains of bacteria would be quite rare in the microbiome. 1. The microbiota is defined as all microorganisms in a particular location, such as the GI tract or skin.10,11 This distinction is relevant as this review will focus on the microbiota of the gut in the context of the gut-brain axis, though there will be discussion of the human microbiome where appropriate. Hooper LV. Before Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, et al. The gut microbiota, which derives its nutrient from host dietary components and shed epithelial cells, is an organ by itself with an extensive metabolic capability and substantial functional plasticity[34]. Regardless of the species inhabiting the gut, as long as their symbiotic role is the same, the human host will be able to function as normal.20 Symbiotic bacteria assist with immune tolerance, intestinal homeostasis, amino acid and vitamin synthesis of the host, leading to a healthy metabolism.13, As infants consume increasing amounts of solid food, the microbiome is exposed to diverse energy substrates, developing its carbon metabolism.22,23 The adult microbiome becomes dominated by the Bacteroidetes and Firmicutes phyla, rather than the Lactobacillus and Bifidobacterium genera.24 Relatively smaller quantities of the Proteobacteria, Verrucomicrobia, Actinobacteria, and Cyanobactera phyla, and Fusobacteria genus can also be found.13 However, due to many factors including diet, environment, season, health status, it is almost impossible to define a normal microbiome for the average human population. Ochman H, Lawrence JG, Groisman EA. Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J, Nitisinprasert S. Microbial community of healthy thai vegetarians and non-vegetarians, their core gut microbiota, and pathogen risk, Diet-microbiota interactions and their implications for healthy living. Likewise, comparison of bacterial phyla did not show a significant difference in the Bacteroidetes to Firmicutes ratio between obese and lean volunteers (n = 20) (45). PMC legacy view observed that carotid-femoral pulse wave velocity, a measure of arterial stiffness, was negatively associated with microbiome diversity (p = 0.001) in women (n = 617) (33). The interaction between host and microbes along with the functional capacity of the microbiota can be studied. Another set of innate immune cells, namely the innate lymphoid cells (ILCs) are capable of responding rapidly to epithelium-derived cytokine signals[100]. On average, twenty five percent of plasma metabolites are different between omnivores and vegans, suggesting a significant direct effect of diet on the host metabolome. The HGC individuals have a functionally much robust gut microbiome and lower prevalence of metabolic disorders and obesity. Intestinal goblet cells and mucins in health and disease: recent insights and progress. Kim M, Yu Z. The oxalate that is synthesized in the intestine as a result of carbohydrate fermentation and bacterial metabolism is countered by organisms such as Oxalobacter formigenes, Lactobacillus species, and Bifidobacterium species thereby reducing the risk of formation of oxalate stone in the kidney[40,41]. There was also an increase in the production of the SCFAs[144]. Changes in microbiota composition might be due to differences in bacteria directly consumed through food, differences in substrates consumed, variations in transit time through the gastrointestinal system, pH, host secretion influenced by dietary patterns, and regulation of gene expression of the host himself and/or his/her microbiota (24). The gut microbiota can also modulate mucosal glycosylation patterns that are microbial attachment sites both at the cell surface and subcellular levels. Microbial ecology: human gut microbes associated with obesity. On the contrary, the abundance of anaerobic organisms like Bacteroides sp. Liu, X.; Yang, G.; Que, Q.; Wang, Q.; Zhang, Z.; Huang, L. How Do Landscape Heterogeneity, Community Structure, and Topographical Factors Contribute to the Plant Diversity of Urban Remnant Vegetation at Different Scales? In the previously mentioned study by De Filippo et al., Prevotella was exclusively present in the children of Burkina Faso consuming a diet low in fat and animal protein and rich in starch, fiber, and plant protein when compared to children living in Italy consuming a Western diet, high in animal protein, sugar, starch, and fat, and low in fiber (40). Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook. The major drawback in using these techniques is the difficulty in studying the culture characteristics of various colonies on a petri plate. Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, et al.. The findings above, coupled with the recent surge of interest of gut health in the media, underscore the importance of future research in understanding the gut flora. Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, et al.. However, several weaknesses are identified in the course of this selected review. Other studies have shown vegan/vegetarian diets, high in plant-based foods, to be associated with high abundances of Prevotella (48, 49). Papers are submitted upon individual invitation or recommendation by the scientific editors and undergo peer review progress in the field that systematically reviews the most exciting advances in scientific literature. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. These principles were initially controversial. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al.. A human gut microbial gene catalogue established by metagenomic sequencing. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Although most of these studies have focused on bacterial species in the gut microbiome, other studies have elucidated the importance of other microorganisms, such as yeast. The major concern that stems out of use of broad-spectrum antibiotics, besides alteration of the normal gut microbial diversity, is the phenomenon of propagating the resistance strain via horizontal gene transfer[154,155]. The sIgA can in turn coat the gut microbiota. For example, polyphenol extracts from tea generate an increase in Bifidobacterium and LactobacillusEnterococcus spp., which then yields an increased SCFA production on human microbiota in vitro (69). This review aims to discuss the development of the gut microbiota, the linkage of dysbiosis to anxiety and depression, and possible applications of probiotics to reduce symptoms. The mechanism of communication among these organs stems from the microbial products and microbial metabolites of ingested nutrients. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. Spits H, Cupedo T. Innate lymphoid cells: emerging insights in development, lineage relationships, and function. Inflammation switches the differentiation program of Ly6Chi monocytes from antiinflammatory macrophages to inflammatory dendritic cells in the colon. The new PMC design is here! SCFAs act as a substrate to maintain colonic epithelium, and are correlated with plant based food consumption (56). Additionally, vegans and vegetarians have significantly higher counts of certain Bacteroidetes-related operational taxonomic units compared to omnivores. Feature The sIgA that coats the microbiota are predominantly of sIgA2 subclass, which is more resistant to degradation by bacterial proteases. Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. [@F @B#g$"Fj} 0 pW Members of genus Bacteroides have been shown to synthesize conjugated linoleic acid (CLA) that is known to be antidiabetic, antiatherogenic, antiobesogenic, hypolipidemic and have immunomodulatory properties[45-47]. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. While both populations ate diets centered around carbohydrates and vegetables, the Chinese diet was heavier in animal fat and protein than the Indian diet of whole grains and plant-based vegetarian foods. Goblet cell-specific expression of a peptide targeted for apical secretion. These are all factors that have been shown to possibly modify our microbiota. Combined with the community structure and topographical factors, the impact factors of plant diversity under different buffer radii were analyzed by multiple regression analysis. This change was not seen after the mice underwent vagatomies, suggesting that the parasympathetic nervous system was imperative for the bacterias effects on their stress response.24. [1], A study of the area between toes in 100 young adults found 14 different genera of fungi. When participants were given formulas with FOS and fiber, their Bifidobacteria increased from 5.1 to 26.6% (P = 0.003) after 14 days. [46] Current research on the skin microbiota's role in psoriasis is inconsistent therefore there are no potential probiotic treatments. The other issue of concern in 16S rRNA based sequencing is the variability of results across different sequencing centers, both for predominant and minor taxa. Furthermore, as shown in a recent study on the association of gut microbiome with atherosclerosis, there may not be significant changes in the enterotype observed in disease conditions[32]. cluster XIVa species (38). Kida Y, Shimizu T, Kuwano K. Sodium butyrate up-regulates cathelicidin gene expression via activator protein-1 and histone acetylation at the promoter region in a human lung epithelial cell line, EBC-1. Thus, the abundance of Ruminococcus is influenced by both animal and plant based diets. Contributions: MC initialized the concept of this literature review; MC, NA, LH, MB, EW all contributed to research, drafting, and editing of the review. Devillard E, McIntosh FM, Duncan SH, Wallace RJ. [38] Atopic dermatitis flares are associated with low bacterial diversity due to colonisation by S. aureus and following standard treatment, bacterial diversity has been seen to increase. Clayton TA, Baker D, Lindon JC, Everett JR, Nicholson JK. Zelante T, Iannitti RG, Cunha C, De Luca A, Giovannini G, Pieraccini G, Zecchi R, DAngelo C, Massi-Benedetti C, Fallarino F, et al. The other mechanism that the gut microbiota has evolved is to keep a check on the overgrowth of pathogenic strains by inducing local immunoglobulins. Current research is focusing on the establishment of causal relationships in people and the development of therapeutic interventions such as personalized nutrition (18). Bacteroides have anti-inflammatory properties which are essential against dermatitis. Research has shown that the balance of Bacteroidetes and Firmicutes is an important marker for obesity and higher BMI. OHara AM, Shanahan F. The gut flora as a forgotten organ. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al.. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Conversion of cholic acid and chenodeoxycholic acid into their 7-oxo derivatives by Bacteroides intestinalis AM-1 isolated from human feces. This is likely due to their ability to tolerate bile, which is common in gut environments of those who consume animal products. The gut microbiota is represented by more than 1,000 microbial species, belonging primary to just two phyla: Bacteroidetes and Firmicutes (21). Individuals consuming pea protein exhibit increases in beneficial Bifidobacterium and Lactobacillus and decreases in pathogenic Bacteroides fragilis and Clostridium perfringens and, consequently increases in intestinal SCFA levels (54). can also digest HMO, the abundance of Bifidobacterium is higher in breast-fed infants, thus pointing towards competitive relationship between these two organisms in favor of Bifidobacterium in breast-fed infants. For example, it was demonstrated that rural African children had a higher abundance of Prevotella, while children from Europe had higher proportions of Bacteroides[140]. [13], The Belly Button Biodiversity Project began at North Carolina State University in early 2011 with two initial groups of 35 and 25 volunteers. These patients rated an overall happier mood on daily analogue scales using six dimensions of mood including energetic/tired, composed/anxious, elated/depressed, clearheaded/muddled, confident/unsure, and agreeable/angry.51, In a 30-day study, healthy volunteers with no previous depressive symptoms were given either probiotics or antidepressants. [38] High populations of P. acnes are linked to acne vulgaris although only certain strains are strongly associated with acne while others with healthy skin. A possible explanation for this correlation may be found in the observation that a 20% increase in Firmicutes and a corresponding decrease in Bacteroidetes abundance is associated with a 150 kcal/day increase in energy harvest, resulting in weight gain overtime. Visit our dedicated information section to learn more about MDPI. [30], If activated, the immune system in the skin produces cell-mediated immunity against microbes such as dermatophytes (skin fungi). S. epidermidis produces succinic acid which has been shown to inhibit P. acnes growth. A human gut microbial gene catalogue established by metagenomic sequencing. The Bacteroidetes:Firmicutes ratio was three times higher in the US children consuming the Western diet (43). Different buffer radius settings can affect the relative importance of these factors to plant diversity. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. You seem to have javascript disabled. At a 500 m buffer radius, community structure combined with road disturbance indices was strongly related to diversity indices in herb and shrub layers. Sherman MP, Zaghouani H, Niklas V. Gut microbiota, the immune system, and diet influence the neonatal gut-brain axis. In pre-term infants, bacteria that colonize the gut include Bifidobacterium and Lactobacillus and basically, these differ depending on the type of feeding habits. SCFAs, especially butyrate have also been implicated in the development and function of Tregs. Furthermore, Bacteroides thetaiotaomicron is demonstrated to augment the efficiency of lipid hydrolysis by up regulating expression of a colipase that is required by pancreatic lipase for lipid digestion[42]. Studies note changes in central neural chemistry, inflammatory lung conditions, and non-alcoholic fatty liver disease pathogenesis with changes to microbial composition (7072). The abundance of Bacteroidetes in the Italian children was less than half of that seen than in the Burkina Faso children (22.4 vs. 57.7%, respectively). Some studies report that this change activates inflammation (induces pro-inflammatory cytokines such as IL-1, IL-6, and TNF-) and leads to metabolic disorders (66). 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