Fiber from beans, fruits, and vegetables was associated with positive alterations in human gut microbiome



The human body contains over 10 times more microbial cells than human cells, although the entire microbiome only accounts for about for 1-3% total body mass,[6] with some weight-estimates ranging as high as 3 pounds (approximately 48 ounces or 1,400 grams). Research into the role that microbiota in the gut might play in the human immune system started in the late 1990s.[7] The microbiome of the gut has been characterised as a “forgotten organ”,[8] and the possibility has been raised that “the mammalian immune system, which seems to be designed to control microorganisms, is in fact controlled by microorganisms”.[9] The human microbiome may have a role in auto-immune diseases like diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, fibromyalgia, and perhaps some cancers.[10] A poor mix of microbes in the gut may also aggravate common obesity.[11][12][13] Since some of the microbes in the human body can modify the production of neurotransmitters known to occur in the brain, it may also relieve schizophrenia, depression, bipolar disorder and other neuro-chemical imbalances.[14]

The microbes being discussed are generally non-pathogenic (they do not cause disease unless they grow abnormally); they exist in harmony and symbiotically with their hosts.[15] Moreover, it has been stated that microbiome and host emerged as a unity along evolution by a process of integration.[16]

Effects on cognition

Microbes are also implicated in depression. The pathogenic bacteria Borrelia burgdorferi causes Lyme disease which causes depression in up to 2/3 of all cases.[39]Non-pathogenic bacteria are also implicated in depression in which bacterial populations are suppressed. One model of depression is periodic separation of infant mice from their mothers. These mice show reductions in Lactobacillus and Bifidobacterium species, functional gut abnormalities, increased corticosterone (stress hormone) levels, weight loss, and causes them to not swim as much in a forced swim test as control mice, indicating behavioural despair. Treating the mice with Lactobacillus lowered corticosterone levels and gut abnormalities.[40] Another experiment has replicated the effect that germ free mice have an exaggerated stress response and also found reduced expression of brain-derived neurotrophic factor in the cortex and hippocampus.[41] Another experiment showed that treating the maternally separated mice with a probiotic culture of Bifodobacterium infantis minimizes weight loss, causes mice to swim longer and causes an increase in the amount of the serotonin precursor tryptophan produced.[42] Increasing serotonin levels through selective serotonin reuptake inhibitors is the primary treatment of depression in humans. Human patients with depression are less able to properly digest fructose,[43] which is also associated with a reduction in tryptophan production.[44] Eliminating fructose from their diet improved their depression.[45]


Gut microbes are also implicated in anxiety disorders. In humans, anxiety disorders are common in patients with disturbed gut flora.[46] The bacteria Campylobacter jejuni has been shown to cause anxious behaviour in mice.[47] Germ free mice show less anxious behaviour and also less NR2B mRNA expression selectively in the central amygdala which might be responsible for the anxiolytic behaviour since NR2B antagonists have an anxiolytic effect on behaviour.[48] The behavioural change might also be caused by increased brain-derived neurotrophic factor (BDNF) mRNA expression possibly inducing plasticity in the dentate granular layer of the hippocampus.[49] BDNF and the hippocampus are implicated in memory. Increased gut bacterial diversity has been shown to improve both working and reference memory as well as reducing anxiety-like behaviour.[50]


Autistic populations have a unique microbiome consisting of more clostridial species.[51] Half of all autistic children with gastrointestinal dysfunction were found to have the bacteria Sutterella which was completely absent in non-autistic children with gastrointestinal dysfunction.[52] There is evidence that for some children with late-onset autism antibiotics can alleviate symptoms temporarily.[53]

Immune system

The symbiotic relationship between animal host and microbiota has a significant impact on shaping the immune system. The immune system is able to recognize the types of bacteria that are harmful to the host and combats them, while allowing the helpful bacteria to carry out their functions. After an infant is born completely sterile, their gut is quickly populated by commensal bacteria that affect the immune response, resulting in future tolerance to that bacteria. This early colonization helps to establish the symbiotic microbiome inside the host early in its life. The bacteria are also able to stimulate lymphoid tissue associated with the gut mucosa. This enables the tissue to produce antibodies for pathogens that may enter the gut. It has been found that bacteria may also play a role in the activation of TLRs (toll-like receptors) in the intestines. TLRs are a type of PRR (pattern recognition receptor) used by host cells to help repair damage and recognize dangers to the host. This could be important in immune tolerance and autoimmune diseases. Pathogens could influence this symbiotic coexistence leading to immune dysregulation and susceptibility to diseases. This could provide new direction for managing immunological and metabolic diseases.[54]

Human microbiome 

The human microbiome consists of about 100 trillion microbial cells, outnumbering human cells 10 to 1.[55] It can significantly affect human physiology. For example, in healthy individuals the microbiota provide a wide range of metabolic functions that humans lack.[56] In diseased individuals altered microbiota are associated with diseases such as neonatal necrotizing enterocolitis,[57] inflammatory bowel disease[58] and vaginosis.[59]

Fiber from beans, fruits, and vegetables was associated with positive alterations in human gut microbiome

Peer-Reviewed PLoS One. 2015; 10(4): e0124599. 
Published online 2015 Apr 15. doi:  10.1371/journal.pone.0124599

Increasing evidence suggests that the composition of the human gut microbiome is important in the etiology of human diseases; however, the personal factors that influence the gut microbiome composition are poorly characterized. Animal models point to sex hormone-related differentials in microbiome composition. In this study, we investigated the relationship of sex, body mass index (BMI) and dietary fiber intake with the gut microbiome in 82 humans. We sequenced fecal 16S rRNA genes by 454 FLX technology, then clustered and classified the reads to microbial genomes using the QIIME pipeline. Relationships of sex, BMI, and fiber intake with overall gut microbiome composition and specific taxon abundances were assessed by permutational MANOVA and multivariate logistic regression, respectively. We found that sex was associated with the gut microbiome composition overall (p=0.001). The gut microbiome in women was characterized by a lower abundance of Bacteroidetes (p=0.03). BMI (>25 kg/m2 vs. <25 kg/m2) was associated with the gut microbiome composition overall (p=0.05), and this relationship was strong in women (p=0.03) but not in men (p=0.29). Fiber from beans and from fruits and vegetables were associated, respectively, with greater abundance of Actinobacteria (p=0.006 and false discovery rate adjusted q=0.05) and Clostridia (p=0.009 and false discovery rate adjusted q=0.09). Our findings suggest that sex, BMI, and dietary fiber contribute to shaping the gut microbiome in humans. Better understanding of these relationships may have significant implications for gastrointestinal health and disease prevention.

Full Research Article >>>


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