@adreno i hope you don't mind posting me here. I felt that the microbiome is a key feature of this thread so i decided to run an Text Analysis to 8553 PubMed Entries.
These are the most frequent terms found :
['microbiota', 'study', 'disease', 'gut', 'human', 'intestinal', 'bacterial', 'patient', 'bacteria', 'microbial', 'result', 'species', 'increase', 'association', '
inflammation', 'samples', 'effect', 'infection', 'treatment', '
immune', 'microbiome', 'gene', 'host', 'composition', 'health', 'role', 'cells', 'level', 'healthy', 'response', 'group', 'different', 'show', 'analysis', 'oral', 'methods', 'clinical', 'development', 'suggest', 'subjects', 'siginificant', 'reduction', 'data', 'therapy', 'fecal', 'changes', 'compared', 'including', 'function', 'mechanism', 'significant', 'found', 'factors', 'strains', 'system', 'important', 'review', '
probiotics', 'potential', 'metabolic', 'gastrointestinal', 'groups', 'recent', 'diversity', 'observation', 'investigate', 'present', 'activity', 'specific', 'community', 'new', '16s', 'risk', 'bowel', 'higher', 'use', 'identified', 'control', 'infants', 'humans', 'tract', 'pathogens', 'probiotic', 'decrease', 'high', 'communities', 'total', 'complex', 'diet', 'differences', 'mice', 'individuals', 'acid', 'microorganisms', 'evidence', 'understanding', 'lactobacillus', '
periodontal', 'among', 'number', 'chronic', 'demonstrate', 'finding', '
mucosal', 'cause', 'dietary', 'cell', 'resistance', 'several', 'children', 'prevention', '
ibd',...........SNIP]
So Inflammation is a topic commonly found within these entries. We then move to frequent phrases :
[('vice', 'versa'), ('lamina', 'propria'), ("peyer's", 'patches'), ('enzymelinked', 'immunosorbent'), ('magnetic', 'resonance'), ('gel', 'electrophoresis'),
('lymph', 'nodes'), ('gradient', 'gel'), ('polymerase', 'chain'),
('cystic', 'fibrosis'), ('checkerboard', 'dnadna'), ('16s', 'rrna'), ('eikenella', 'corrodens'), ('necrotizing', 'enterocolitis'), ('95%', 'ci'), ('proton', 'pump'),
('ulcerative', 'colitis'), ('bronchoalveolar', 'lavage'), ('ribotype', '027'), ('denaturing', 'gradient'), ('flow', 'cytometry'), ('terminal', 'restriction'), ('tannerella', 'forsythia'), ('parvimonas', 'micra'), ('confidence', 'interval'), ('akkermansia', 'muciniphila'), ('cross', 'talk'), ('national', 'institutes'), ('inulintype', 'fructans'), ('logistic', 'regression'), ('chain', 'reaction'), ('et', 'al'), ('mycobacterium', 'avium'), ('restriction', 'fragment'), ('sexually', 'transmitted'), ('fragment', 'length'), ('escherichia', 'coli'), ('faecalibacterium', 'prausnitzii'), ('tight', 'junction'), ('truncated', '250'), ('necrosis', 'factoralpha'), ('dnadna', 'hybridization'), ('treponema', 'denticola'), ('peptic', 'ulcer'),
('mesenteric', 'lymph'), ('enterica', 'serovar'), ('fatty', 'acids'), ('subspecies', 'paratuberculosis'), ('ribosomal', 'rna'), ('crevicular', 'fluid'), ('caesarean', 'section'), ('250', 'words'), ('shortchain', 'fatty'), ('matrixassisted', 'laser'), ('fluorescent', 'situ'), ('double', 'blind'),
('atopic', 'dermatitis'), ('operational', 'taxonomic'), ('porphyromonas', 'gingivalis'), ('avium', 'subspecies'), ('actinobacillus', 'actinomycetemcomitans'), ('saccharomyces', 'cerevisiae'), ('north', 'america'), ('tolllike', 'receptor'), ('root', 'canal'), ('twin', 'pairs'), ('fluorescence', 'situ'), ('mass', 'spectrometry'), ('situ', 'hybridization'), ('haemophilus', 'influenzae'), ('morbidity', 'mortality'), ('critically', 'ill'), ('listeria', 'monocytogenes'), ('middle', 'ear'), ('electron', 'microscopy'), ('pocket', 'depth'), ('hepatocellular', 'carcinoma'), ('peptostreptococcus', 'micros'), ('saccharomyces', 'boulardii'), ('root', 'planing'), ('pseudomonas', 'aeruginosa'), ('hydrogen', 'peroxide'), ('reactive', 'oxygen'), ('length', 'polymorphism'), ('serovar', 'typhimurium'),
('nonalcoholic', 'steatohepatitis'), ('gardnerella', 'vaginalis'), ('methanogenic', 'archaea'), ('african', 'americans'),
('immune', 'system'), ('mesial', 'aspect'), ('methanobrevibacter', 'smithii'), ('obstructive', 'pulmonary'), ('cesarean', 'section'), ('highperformance', 'liquid'), ('colony', 'forming'), ('poorly', 'understood'),
('tumor', 'necrosis'),
('irritable', 'bowel'), ('helicobacter', 'pylori')]
Notice the fact that Lymph Nodes, ulcerative colitis, nonalcoholic steatohepatitis, irritable bowel, immune system are comonly found.
Most associated diseases :
**********************************************************************************
Enter term : disease
window size : 3
min freq : 5
19:11:11.373298
**********************************************************************************
('ulcerative', 1793.2532328635089)
('recent', 541.6996459716866)
('pulmonary', 520.3166727424668)
('obstructive', 517.8851252919544)
('activity', 483.4073468684177)
('nafld', 449.2590420439453)
('pathogenesis', 448.1122419356345)
('ibds', 441.33259937056266)
('coeliac', 424.8747658827942)
('destructive', 377.28625706512855)
('kidney', 373.0662154483366)
('endstage', 340.16627623035345)
('bowel', 317.1739177825322)
('irritable', 301.6142328282185)
('alcoholic', 300.1386502180286)
('chronic', 299.06108612353796)
('risk', 297.5353802518765)
('association', 295.8244513368049)
('inflammation', 287.73398985419226)
('development', 286.120285382312)
('diarrheal', 268.85011756371637)
('neurodegeneration', 256.0447598350479)
('remains', 245.96393294777633)
('advanced', 226.37606574651807)
('ulcer', 218.1957736362355)
("crohn's", 212.41280075605965)
('coronary', 211.6791516837664)
('aim', 208.442548759162)
('peptic', 202.88257048272612)
('susceptibility', 202.83349944659295)
In case you see anything worth pursuing further please let me know