Table 3 Levels of associations between bacteria and markers
Bacteria (taxonomic affiliation) | Changea | RMC | LME | Bacteria properties | |
|---|---|---|---|---|---|
ZON | CALP | ||||
Class Alphaproteobacteria | Zon (−) | Exhibited numerous positive co-occurrences with other microbes [71]; enriched in vaginally delivered standard formula-fed infants three months post delivery [72]; high abundance in placentas of women with IBD, but not in stool [73]; high abundance in patients with Crohn's Disease [74]; third major constituent gut microbiome in infants with respiratory and gastrointestinal diseases [75] | |||
Class Clostridia | Zon (+) | Dominates in infants [76]; in the formula-fed infants colonization occurred consistently throughout the 1st year of life, whereas in some breast-fed infants it was inhibited until weaning [77]; anti-inflammatory activity [78,79,80] | |||
Order Clostridiales (class Clostridia) | Calp (−) Zon ( +) | Butyrate production [81, 82]; suppression of proinflammatory bacteria [83]; protective role of the taxa in IBD pathogenesis [84]; induction an immune response [67] | |||
Family Ruminococcaceae (class Clostridia) | Calp (−) Zon (+) | Ruminococcaceae is more abundant in women with low serum zonulin concentration and can enhance intestinal barrier integrity [85]; involved in modulation of gut barrier function[86]; SCFAs producer [87]; more abundant in people with diets high in carbohydrates [88, 89] | |||
Genus Ruminococcus (gnavus group) (family Ruminococcaceae, order Clostridiales, class Clostridia) | Same | Zon (+) | Increased in patients with IBS-D [90] and Crohn’s Disease [91] | ||
Genus Ruminococcus (torques group) (family Ruminococcaceae, order Clostridiales, class Clostridia) | Zon (+) | Calp (common slope model, positive β coeff.) | Butyrate production, important role in Crohn’s Disease [91]; mucin degradation [54] | ||
Family Lachnospiraceae (order Clostridiales, class Clostridia) | Same | Zon (+) | Butyrate producer [92] induces the expression of Treg—suppression of the colonic inflammatory response [62] | ||
Genus Lachnoclostridium (family Lachnospiraceae, order Clostridiales, class Clostridia) | Same | Zon (+) | Enhanced the utilization of carbohydrates [93] showed a positive association with secondary bile acids in mice [94]; SCFAs producer [95]; correlated with vitamin B6 metabolism and tryptophan metabolism in mice with colitis [96]; lower abundances was observed in neoplasms of gastrointestinal tract [97]; decreased in Autism Spectrum Disorders [98]; overdominant in population of native Alaska with high incidence of sporadic colorectal cancer [99]; positively correlated with body mass index, alanine aminotransferase, aspartate aminotransferase levels in patients with non-alcoholic fatty liver disease (NAFLD) [100] | ||
Genus Anaerostipes (family Lachnospiraceae, order Clostridiales, class Clostridia) | Oppo-site | Calp (−) | Butyrate producer [101] | ||
Family Peptostreptococcaceae (order Clostridiales, class Clostridia) | Same | Zon (+) | Overrepresented in gut microbiota of non-breastfed infants [102]; present in infants fed with standard cow’s milk formula [103]; overrepresented in infants living with pets and underrepresented in infants living with older siblings [104] | ||
Class Bacilli | Zon (−) | Dominant in duodenum and in the jejunum; producer of enzymes, bile acid hydrolases, ACE-like inhibitors, SCFAs, hydrogen peroxide, group B vitamins, beneficial for gut health [105]; participate in metabolism of dietary components, xenobiotics and drugs helping to maintain intestinal homeostasis and host health [106, 107] | |||
Order Bacillales (class Bacilli) | Zon (−) | Enriched in preterm infants fed with mom’s own milk [108]; overrepresented in cesarean section delivered neonates [109]; second major microbiome constituent of neonatal intensive care unit rooms [110] | |||
Family Staphylococcaceae (order Bacillales, class Bacilli) | Calp (+) Zon (−) | Present in human milk [111] | |||
Genus Staphylococcus (family Staphylococcaceae, order Bacillales, class Bacilli) | Calp (+) Zon (−) | One of the most prominent bacteria of human milk [112]; correlated with higher fecal calprotectin concentration in infants [113]; pathological bacteria decreased over time after delivery [114], super antigen function stimulates the systemic secretion of IgA in neonates, protecting against allergies [115]; promotes the modulation of the infant immune system without causing an adverse inflammatory response, induction of T-reg cells via butyric acid and propionic acid [116]; participate in the saccharolytic fermentation of carbohydrates, which end products that positively affect host cells and gut bacterial community [117] | |||
Family Enterococcaceae (class Bacilli) | Same | Calp (+) | Opportunistic pathogen [118]; potential biomarker for IBD [119] | ||
Genus Enterococcus (family Enterococcaceae, class Bacilli) | Calp (+) | Higher counts in premature infants with necrotizing enterocolitis (NEC) [120]; significant positive correlations between fecal calprotectin levels and intestinal colonization levels Enterococcus in Preterm Infants during the Neonatal Period [17]; more abundant in feces of formula fed infants [121]; a leading hospital-associated pathogen [122] | |||
Family Carnobacteriaceae (class Bacilli) | Same | potential biomarker of autoimmunological disease [123]; abundance in oral microbiome was associated with decreased risk of colorectal cancer [124] | |||
Class Coriobacteriia | Zon (+) | Greater prevalence in formula-fed babies [125]; significantly higher in coeliac infants [126]; lower relative abundances in atopic dermatitis children [127]; increased in Crohn’s Disese [128] | |||
Order Coriobacteriales (class Coriobacteria) | Same | Zon (+) | Negatively associated with fecal protease activity associated with various gastrointestinal tract diseases [129]; can be considered as pathobionts, because their occurrence has been associated with a range of pathologies such as bacteremia, periodontitis, and vaginosis [130]; belongs to class Actinobacteria which correlates with fecal calprotectin [25] | ||
Order Corynebacteriales | Oppo-site | Subset is pathogen [131]; belongs to class Actinobacteria which correlates with fecal calprotectin [25] | |||
Genus Corynebacterium 1 (order Corynebacteriales) | Zon (−) | Human skin bacteria, dominant in gut microbiome of Cesarean Section (CS) born infants [132]; counts in gut microbiome of CS born children negatively associated with maternal dairy intake [133]; present in Meconium of Preterm Neonates [134]; dominant in oral microbiome of CS born infants [135] | |||
Order Erysipelotrichales | Zon (+) | More abundant in infants at 4 weeks fed with cow-milk based formula, at 26 weeks in breast milk fed children and those receiving fructooligosaccharides (FOS) [103]; decreased in new-onset Crohn’s disease [56]; lower abundance in blood of patients with cirrhosis [136]; increased in HIV infection [137] | |||
Order Pseudomonadales | Zon (−) | Associated with normal calprotectin level in Gambian infants [138]; belongs to Gammaproteobacteria negatively correlates with calprotectin [25]; associated with neutrophilia and lower vaccine responses in infants [139]; pathogenic taxa [140] | |||
Family Moraxellaceae | Zon (−) | Dominant phylum in human breast milk [141]; overrepresented in Crohn’s disease closely associated with microaerobic energy metabolism, amino acid degradation, and energy deficiency characterized by low ATP levels [142]; lowered in colorectal cancer gut microbiome [143]; belongs to class Gammaproteobacteria which is negatively associated with calprotectin concentration [25] | |||