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Table 1 Factors, types of dysbiosis caused in the gut, consequences and alternative therapeutic approaches

From: Extrinsic factors influencing gut microbes, the immediate consequences and restoring eubiosis

Extrinsic Factors Observations in the gut Alteration in the gut Alternative remedies
Dietary
 High-fat/high-sugar aAdherent-invasive Escherichia coli (AIEC) Permeability in the intestinal mucosal and reduced expression of tight junction proteins zo-1 and occluding. Compromising selective absorption and triggers the onset of metabolic endotoxemia (Martinez-Medina et al. 2014) PUFA and conjugated linoleic acid (CLA), phytochemicals, Mediterranean diet
 A high-protein diet aPotentially toxic substances such as sulfide, indole, ammonia and N-nitroso compounds) Deleterious and toxic for the intestine (Martínez et al. 2010) PUFA and conjugated linoleic acid (CLA), phytochemicals, Mediterranean diet
 Excess dietary intake of protein and amino acids aSynthesis of nitric oxide (NO) Development of an obesity-associated microbiota, ulcerative colitis (Martinez-Medina et al. 2014), lead to DNA damage (Martinez-Medina et al. 2014; Irrazábal et al. 2014) PUFA and conjugated linoleic acid (CLA) due to anti-inflammatory characteristic
 Excess nutrient intake aFirmicutes Obesity related to inflammatory metabolic disorders culminating from dysbiosis (Frank et al. 2007) Probiotic (Lactobacillus paracasei) acirculating levels of ANGPTL4 and reduces body fat
 Vitamin D deficiency Induced dysbiosis in the gut microbiota Play a role in the pathogenesis of IBD and arisk of colitis (Ananthakrishnan 2015) Vitamin D supplementation had an anti-inflammation due to the inhibition of pro inflammatory genes such as TNF genes
 Red meat (thiol-containing amino acids) aSulfate-reducing bacteria (e.g. Desulfovibrio spp., in the intestine bMucus formation, inhibits methylation of DNA and a the generation of reactive oxygen species (Ananthakrishnan 2015) Stress such as exercise under sun or heat exposure) is recommended
 Saturated fatty acids and low in polyunsaturated fatty acids (vegetable oil) mouse model aBilophilawadsworthia Inflammatory reaction mediated by Th1 cells and colitis, high bad low-density lipoprotein (LDL) cholesterol level (Ananthakrishnan 2015; Liu et al. 2020) Feeding on mono-saturated fats and polyunsaturated fatty acids (vegetable oil)
 Sucralose (aspartame and saccharin) in mouse model aClostridia, Bacteroides and total aerobic bacteria, rise in pH (Schultz et al. 2009) Pro-inflammatory genes and unpredictable faecal metabolites (Zhang et al. 2012) FMT, PUFA and conjugated linoleic acid (CLA), mediterranean diet
 Gluten Dysbiosis in microbiota, apathogenic bacteria a Risk of coeliac diseases or even proven gluten
intolerance, constipation and diarrhea (Schroeder et al. 2018)
Gluten-free diet and hydration
 Fasting and hibernation aBacteroidetes and Verrucomicrobia
bFirmicutes (more polysaccharides)
Capable of degrading mucin, suppress the immune system thus aFirmicutes (more polysaccharides) the tolerance of the host to its microbes (Secor and Carey 2016) PUFA and conjugated linoleic acid (CLA), phytochemicals, Mediterranean diet and hydrating
 Starvation aProteobacteria in the gut Risk of inflammation at the mucosal layers that leads to the breaking down of epithelial barrier called ‘leaking gut’ (Couteau et al. 2001) PUFA and conjugated linoleic acid (CLA), phytochemicals, Mediterranean diet
 Antibiotic (dextran sulfate sodium) aLiberation of sialic acid 2, 3-linked sialylatedglycans from the intestine (mouse model), Huang et al. 2015)
aSalmonellaenterica serovar Typhimurium and C. dificile (Ng et al. 2013)
Intestinal inflammation, IBD and persisting diarrhoea Butyrate is anti-inflammatory effect (expressed by reducing the production of pro-inflammatory factors such as Nf-kb) making it a valuable ally in the treatment of IBD symptoms (Longo and Mattson 2014)
Non-steroidal anti-inflammatory drugs
 Metformin (hepatic gluconeogenesis inhibitor) a in E. coli Although used as the standard medication for type 2 diabetes, it cause gut microbiota dysbiosis(Chassaing et al. 2015) Probiotics (Lactobacillus rhamnosus)
 Proton-pump inhibitors aC. difficile C. difficile associated diarrhoea (Freedberg et al. 2015) and hepatic encephalopathy in cirrhotic patients (Tralongo et al. 2017) Probiotics (L. rhamnosus)ensure eubiosis (Tralongo et al. 2017), Fecalmicrobial transplantation (Garza and Dutilh 2015)
 Aspirin, ibuprofen and naproxen (a month long intake) aBacteroidaceae and Enterobacteriaceae (Rogers and Aronoff 2016) Risk of stomach ulcers Proton-pump inhibitors are often prescribed in combination
 Emulsifiers (polysorbate-80 and arboxymethylcellulose) mice aProteobacteria in the mucus was enriched, bVerrucomicrobia and Bacteriodetes  Low grade inflammation, a risk if obesity and metabolic disorders (Chassaing et al. 2015) While avoiding processed foods as much possible, avoid eating late at night
Artificial cleansing for
colonoscopy
Microbial load in the gut is bby about 30-fold bBacterial diversity in the short term but restored after approximately 14 days (Parnell and Reimer 2012) Prebiotics (inulin fibre) gives SCFAs including butyric acid
 Prebiotics (oligofructose) aBacteroidetesbFirmicutes in ob/ob mice and in rats Genetically prone to develop obesity and insulin resistance (Parnell and Reimer 2012) A. muciniphila thickens the mucus layer, thereby b gut permeability, endotoxemia, obesity and preventing inflammation
 Probiotics (A. muciniphila) Mucin degrading bacteria aSeverity in colitis models (Kang et al. 2013) Administer only when relevant
Other factors
 Oxidative stress aEnterobacteriaceae Secretion of lipopolysaccharide (LPS) intensifies response to inflammation (Lupp et al. 2007) PUFA and conjugated linoleic acid (CLA), phytochemicals, Mediterranean diet
 Temperature of 6 °C (mouse model) aFirmicutes and bBacteroidetes Thus activating non thermopile groups of bacteria (Chevalier et al. 2015) Maintaining normal body temperature is highly recommended
 Mode of delivery (caesarian section) aepithelial bacteria bBifidobacteria spp. lactobacillus spp. High rate of asthma and allergies (Bäckhed et al. 2015) Delivery through virginal canal and Probiotics supplementation of missing taxa
 Feeding method (formula fed) Profound influence on microbiota composition Overweight and risk of childhood obesity (Bäckhed et al. 2015) Breast feeding supply Bifidobacterium longum subspp. infantis, Lactobacillus
  1. aDenotes increased in abundance, expansion etc
  2. bDenotes decreased in abundance, reduced etc