Microbiome
Microbiome
The microbiome consists of microbes that are both helpful and potentially harmful. Most are symbiotic (where both the human body and microbiota benefit) and some, in smaller numbers, are pathogenic (promoting disease). In a healthy body, pathogenic and symbiotic microbiota coexist without problems. But if there is a disturbance in that balance—brought on by infectious illnesses, certain diets, or the prolonged use of antibiotics or other bacteria-destroying medications—dysbiosis occurs, stopping these normal interactions. As a result, the body may become more susceptible to disease.
https://www.hsph.harvard.edu/nutritionsource/microbiome/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7043356/
Human Microbiome Project:
If humans are thought of as a composite of microbial and human cells, the human genetic landscape as an aggregate of the genes in the human genome and the microbiome, and human metabolic features as a blend of human and microbial traits, then the picture that emerges is one of a human 'supra-organism'.
The microorganisms that live inside and on humans (known as the microbiota) are estimated to outnumber human somatic and germ cells by a factor of ten.
If humans are thought of as a composite of microbial and human cells, the human genetic landscape as an aggregate of the genes in the human genome and the microbiome, and human metabolic features as a blend of human and microbial traits, then the picture that emerges is one of a human 'supra-organism'.
it is hoped that the HMP will not only identify new ways to determine health and predisposition to diseases but also define the parameters needed to design, implement and monitor strategies for intentionally manipulating the human microbiota, to optimize its performance in the context of an individual's physiology.
https://www.nature.com/articles/nature06244
Gut Brain Axis
The gut microbiota is the set of microorganisms present in the gut, and it is connected to the central nervous system via the gut-brain axisnumerous studies have demonstrated its involvement in human behaviour and its relationship with several pathologiesThe results showed that gut dysbiosis predicts the development of these pathologies and influences their pathogenesisit was found that different psychobiotics, mainly dietary fibers and probiotics of the Lactobacillus family, improved different cognitive functions such as cognitive performance and induce a reduced cortisol response
https://doi.org/10.1016/j.psyneuen.2021.105640
Psychobiotics are probiotics strains with potential benefits for host physical health and is widely used for mental disease therapy.The gut-brain axis is bidirectional association between the gastrointestinal system and the CNS that coordinates the functions of the ENS and CNSThe term “Psychobiotics†refers to probiotics, prebiotics, and all microbiota-targeted interventions that can manipu-late microbiota-gut-brain signals and have positive effects on neurological functions such as mood, cognition, and anxietyFermented foods including yogurt, kefir, tempeh, and kimchi are rich sources of probiotics
GABA is an amino acid with a non-protein conformation and one of the secretory metabolites of pro-biotics, especially lactic acid bacteria (LAB)Remarkably, the food industry has a critical role in reducing depression and anxiety in the society by producing functional foods con-taining probiotic species with the ability to produce GABAIt is defined that Psychobiotics are a subclass of probiotics that bring mental health benefits to the host by interacting with gut bacteria as well as oncobiotics, pharmabiotics, and metabioticsIn addition to their positive psychological effects, Psycho-biotics could induce the production of neuro-transmitters and neuro-hormones that exhibit psychotropic effects in the studied models.confirmed that kefir grains contain species such as Acetobacter aceti, L. fructivorans, Acetobacter sp., Enterococcus faecium, Leu-conostoc spp., L. delbrueckii delbrueckii, L. fermentum, L. kefiranofaciens, Candida famata, and Candida krusei|Note|Water Kefir and Milk Kefirthey reported positive effects of these strains in improving memory, visual-spatial and abstraction proper-ties, as well as executive and language functions in Alz-heimer|Note|Kefir GrainsÂLikewise, the probiotic strain L. helveticus was isolated from fermented milk which can improve cognitive function in elderly and middle-aged adultsSaccharomyces cerevisiaethat fermented milk with L. casei Shirota can improve mood, increase fecal serotonin, and reduce stress level in the investigated students
Cogito Ergo Sum Bacterium
Are we humans really the individual, bounded selves we take ourselves to be?
Microbiome science is also confounding a long tradition in anatomy and physiology that defines our individual identity in terms of the higher functions of the human brain mediating self-awareness, personality traits, and emotional stateIn addition, short chain fatty acids, which are metabolic waste products of gut microorganisms, promote the differentiation of B cells into plasma cells that secrete protective immunoglobulin A molecules (IgAs) [12], and there is evidence that the gut microbiome has an important systemic effect of inhibiting the IgEs that mediate many allergic diseases (asthma, eczema, etc.), severe systemic reactions to allergens, and some autoimmune diseasesTherefore, the experimental evidence for microbiome effects on behavioral traits that we consider to define our sense of self––who and what we are––has profound implications beyond their biomedical significance and especially for our philosophical comprehension of the human selfhis fluidity in host–microbial relations has two profound consequences. The first––specific––one is that the scope of genome-based precision medicine [27] needs to be reassessed in the light of the evidence that many medically important traits are not shaped exclusively by the human genetic makeup but depend to a significant degree on the genetic capabilities of the microbiome [28]. The second––more far-reaching––consequence is that the growing realization that much of the genetic constitution of every human body is microbial [8] radically undermines any definition of “self†in terms of our individual human genomeWe want to stress that the discovery of the foundational importance of the microbiome for the genetic constitution of the human is qualitatively different from the much older argument that the environment has an influence over our genome. It is qualitatively different, first, insofar as the older distinction left untouched the assumption that it is our nuclear genome that is alone constitutive of the human individual self and merely granted the environment some “influence†over the genome. It is qualitatively different, second, because what is at stake is not actually influence: The microbiome is not “influencing†the genome; it is coconstituting the metaorganisms we humans are.growing realization that the composition and activities of our microbial partners are directly involved in the key biological processes that define traditional concepts of the selfTextbooks are being revised and lecture courses redrafted to accommodate the new biology of the microbiome.the finding that microorganisms are a constitutive part of ourselves calls for a new configuration of the effort to understand what it means to be humanAs we see it, it is important but not enough to argue that “we have never been individuals†[3]––or to suggest that human and microbial worlds are inseparably “entangled†[30–32].What is needed, in addition, is a whole new configuration of research, one where arts and science are combined.what it means to be a living human being at home in a microbial world, one on which we depend and with which we are inseparably interwovenafter the illusion of the bounded, individual self. The human is more than the human
How the microbiome challenges our concept of self
The key question about biological individuality raised by microbiome research is the extent to which our identity as an evolutionary or physiological individual depends on the microbes living in and on uWe agree that causal relationships between individual microbes or small groups of microbes and the host are very likely to impact how the host survives and thrives in daily life.Many microbiome participants are known empirically and theoretically to be transient, opportunistic, or even inactiveFor instance, we might establish the “identity†of a criminal through genetic material left at the scene and then excuse the crime on the basis of the criminal’s state of mind during the crime (she was not “herselfâ€).We are challenging the authors’ suggestion that the humanities and arts need to be fundamentally overhauled in light of microbiome research (their call for a “whole new configuration of research†resulting in “microbial humanitiesâ€).We wholeheartedly agree with Rees and colleagues that the humanities and the natural sciences should not operate in isolation from one another
Three claims might be taken as implicit in this language:that many of themicrobial and macrobial taxa associated in such multi-species assemblages aremetabolically (or developmentally or structurally) interdependentthat suchinterdependence has co-evolved as a consequence of their association, andthatholobionts can be considered units of selectionMaking the case that interaction patternsfulfill the criteria associated with units of selection does require a relativelyW. F. Doolittle, A. Booth123substantial rethinking of various evolutionarily relevant concepts, especially that of‘‘reproduction.’we have known for many decades that major biogeochemicalcycles in the ocean or on land are driven by microbes and that microbes affectanimal, human, and plant health directly in many ways, not all negative,Advances will come from empirical studies thatstart with rigorous assumptions and a clear framework for detectingcoevolution and teasing apart levels of selectionthe microbial taxa that partner with any given hostmacrobe or with each other can be highly variable taxonomically—not the sameIt’s the song, not the singer: an exploration of...123strains, the same species, or even, sometimes, the same phyla. Many holobiontsnevertheless maintain relative functional stability by recruitment of microbial taxa,physiologically or biochemically equivalent but not necessarily of the same geneticlineages, from the environmentThese authors suggest that an appropriately ecological microbial classification wouldrecognize functional ‘‘guilds,’’ phylogenetically heterogeneous groups defined onlyby their possession of one or more biochemical capacities
And functional gastrointestinal disorders such as irritable bowel syndrome represent a disorder of the axis, rather than an isolated problem either of psychology or of gastrointestinal function
We are living in a microbial world
|Note|MAterial World MAdonna
the brain–gut–microbiome axis has become a major research area at the interface of neuroscience and microbiology
he study of how microbes within the body can interact with human brain and behaviour can offer a more complete understanding of human psychology
Freud and others within the psychoanalytical school of thought placed a great emphasis on unconscious processes in human psychology
|Note|the microbes made me do it
the brain–gut–microbiota axis represents a further, physiological means through which unconscious processes may impact on our behaviour
but also leads to a subjective appraisal that is driven by an emotional response that is in turn tied up with a bodily response to the information
there has been little research integrating the study of the mind and brain with the microbiological study of the bacteria in the human body, especially the gut
have described it as nothing less than a paradigm shift in neuroscience; this is clearly an area in which the discipline of psychology could make a substantial contribution
highlighting the potential role of this axis in interpersonal social psychology
The gastrointestinal tract also contains an enteric nervous system comprising an interconnected network of neurons, similar in number to the neurons in the spinal cord (Sasselli, Pachnis, & Burns, 2012).
The brain sends signals to the gut, which impacts upon its sensory and secretory function, and in return receives visceral information from the gut
A great volume of interoceptive information is sent from the gut to the brain, and much of this will not be processed consciously (Mayer, 2011),
|Note|Interoceptive: relating to stimuli produced within an organism, especially in the gut and other internal organs."In our study, we used the five items of the Private Body Consciousness subscale as a measure of interoceptive awareness."
bacteria found within the gut can produce neurotransmitters that can also be found within the central nervous system
For example, evidence suggests that a strain of Lactobacillus brevis can produce GABA
Nonetheless, a propensity to heightened anxiety may also be transmitted biologically, not only through human genes, but also via the microbiota via vaginal delivery
The physiological impact of chronic stress can be contrasted with acute stress.
te stress is associated with release of cortisol via the HPA axis
In contrast, chronic stress is associated with dysregulation of the HPA axis
in irritable bowel syndrome (IBS), a disorder of the brain–gut–microbiome axis, HPA axis activation persists for longer than in healthy controls
It is perhaps not surprising that this question has not been well studied in humans, as researchers lack in vivo methods for studying the composition and function of the gut microbiota; assessment typically requires the collection of stool samples.
The gut microbiota has been shown to interact with host cognition in numerous laboratory animal model studies
A psychology of the human brain–gut–microbiome axis.