Table 5 Characteristics of the morphology, habitat and beneficial/adverse effects on the host organism of selected intestinal bacteria, determined based on 16s sequence

Acutalibacter muris

Anaerobic, no-spore-forming, no-motile but motility-associated proteins are encoded in the genome, rod-shaped, long rods with tapered ends, mesophilic, Gram (+)

Gastrointestinal tract (GIT) of animals. Plant, soil and aquatic samples

Catalase (-)

(https://bacdive.dsmz.de)

Agathobaculum butyriciproducens

Anaerobic, no spore-forming, no-motile, plump rods, mesophilic, Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (-), oxydase (-), butyric acid (+), acetic acid (+), ethanol (+), butanol (+)

A.b. phylogenetically, belongs to the family Ruminococcaceae [3]. As a result of the ability to produce short-chain fatty acids (SCFAs), A.b. induces cognitive improvement, reduces Alzheimer’s disease pathologies in a mouse model, and plays a key role in the activation of microglia. AB is considered as a therapeutic strategy in Parkinson’s disease [51]

Anaerobutyricum hallii, A. soehngenii

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (+)

GIT of human (A.h.) as well as GIT of human and pig (A.s.)

Catalase (-), oxydase (-), butyric acid (+), formic acid (+)

People with type 2 diabetes lack A.h. in the gut. Due to the ability of A.h. to utilise glucose and form butyrate, is an important microorganism for the metabolic balance of the gut. Trophic interactions between bifidobacteria and A.h. lead to the formation of acetate, butyrate, propionate, and formate [87]. As used, D- and L-lactate in the presence of acetate and probably affects host bile acid metabolism [110]. A.s. improves insulin sensitivity [48]

Anaerostipes butyraticus

Anaerobic, spore-forming, nonmotile, long rods that occur in filaments, mesophilic, Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Butyric acid (+), acetic acid (+), propionic acid (+)

Ab depends on host health – one study reported reduced abundance in the faeces of patients with multiple system atrophy [28]

Blautia coccoides,

B. glucerasea,

B. producta,

B. pseudococcoides

Anaerobic, most strains being sporeless (B.c.), no-spore-forming (B.g., B.p.), spore-forming (B.p.),

no-motile or motile (B.p.), spherical/oval, appear in pairs or strands (B.c.), mesophilic, Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (-), lactic acid (+), acetic acid (+) (B.c., B.g., B.p.), additionally formic acid (+) (B.g.), succinic acid (+) and ethanol (+) (B.p.)

B.c. degrades glycosylceramides to ceramides and then metabolises the ceramides to fatty acids and sphingoid bases, which are absorbed by the intestine and produced a beneficial effect [52]. B.g. produces a specific extracellular glucosylceramide enzyme that hydrolyses glucosylceramide into functional substances with a specific preventive effect against colon cancer [52]. B.pr inhibits the growth of vancomycin resistant enterococci by secreting a lantibiotic. Because the lanthipeptide does not affect other commensal bacteria, B.pr. may be a potential probiotic to prevent the transmission of conditional antibiotic-resistant pathogens. B.pr inhibits the proliferation of C. perfringens [52]

Butyricicoccus pullicaecorum

Anaerobic, without spore formation, no motile, coccus shaped, usually arranged in pairs (occasionally in short chains), mesophilic/ thermophilic, Gram (+)

GIT of human and chicken. Plant, soil and aquatic samples

Butyric acid (+)

B.p. decreases intestinal myeloperoxidase (MPO), tumour necrosis factor α (TNFα) and interleukin (IL)−12 levels [105]. B.p. reduces feed conversion and protects from potentially harmful intestinal microorganisms and necrotic enteritis in broilers [27, 29]

Faecalibacterium butyricigenerans,

F. duncaniae,

F. gallinarum,

F. hattorii,

F. longum,

F. prausnitzii

Anaerobic or extremely oxygen sensitive (Fp), no spore-forming, no motile, rod-shaped (F.b., F.p.), straight rods (Fd, Fg, Fh) or long rods (F.l.), mesophilic, Gram (-)

GIT of human (Fb, Fg, Fl) as well as GIT of human and animals; plant, soil, and aquatic samples (F.d., F.h., F. p.)

Catalase (-), butyric acid (+) (Fg), additionally formic acid (+), lactic acid (+) (Fd, Fh, Fp) and acetic acid (+) (F.b., F.l.)

F.b. produces SCFAs and has the function of treating ulcerative colitis [116] as well as F.d., F.g. and F.h. are described as the main producers of SCFAs [82, 116]. The f.p. has an important role in providing energy to colonocytes and maintaining intestinal health. A decrease in the count of Fp is frequently observed in various diseases with associated intestinal inflammatory processes, such as inflammatory bowel disease, type 2 diabetes, colorectal cancer, and Crohn’s disease

[59, 62, 76]. F.p. modulates inflammatory signals by releasing immune-suppressing molecules [53]

Fournierella massiliensis

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (-)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (-), oxydase (-), butyric acid (+), isobutyric acid (+), acetic acid (+), propionic acid (+)

[100]

Fusicatenibacter saccharivorans

Anaerobic, without spores, without germs, rod or spindle-shaped, arranged in pairs and short chains, Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Lactic acid (+), formic acid (+), succinic acid (+), acetic acid (+)

[95, 96]

Gemmiger formicilis, G. gallinarum

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (+), oxydase (-), butyric acid (+) (G.f.), additionally lactic acid (+) (G.g.)

The activity of Gf results in the release of specific volatile odour compounds (exhaled metabolites in the breath) indicating the state of health and assess recent or long-term exposure to various contaminants [11]. G.g. produces SCFA [114] and has a protective role via the reduction of inflammatory cytokines [101]

Gorbachella massiliensis

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (-), halophilic

GIT of human

Catalase (-), oxydase (-), butyric acid (+)

SCFA G.M. produces of SCFAs [25, 26]

Gordonibacter pamelaeae

Anaerobic, without spore formation, motile with subpolar flagellum, coccobacillus or ovoid shaped, in pairs or in short chains, mesophilic,

Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (+), urolithins (+)

G.p. have been implicated as a cause of ulcerative colitis, liver and anal abscesses [112] and systemic bacteraemia [109]. Urolithins are relevant for the development of novel probiotics, functional foods, and food complements, especially for people with metabotype 0 who are unable to produce bioactive urolithins [85, 86]

Helicobacter pullorum

Microaerophile, nospore-forming, motile, slightly curved rod with a single polar flagellum that is non-sheathe, mesophilic or thermophilic, Gram (-)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (+)

Hp is associated with hepatobiliary and gastrointestinal diseases in chickens and humans [15]. H.p. is able to tolerate high bile stress, variation in expression of certain bile stress response proteins, and oxidative. Its DNA was detected in livers from patients with primary sclerosing cholangitis, cirrhosis, and hepatocellular carcinoma. Few data are currently available on the incidence of antibiotic resistance of H.p. [45]

Intestinimonas timonensis

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (-)

GIT of human

Catalase (-), oxydase (-), acetic acid (+), butyric acid (+), propionic acid (+)

Genome analysis indicates the ability to utilise starch, sulphur and l-serine and to produce l-cysteine and riboflavin (vit B2) [2, 26]

Lactobacillus crispatus,

L. gallinarum,

L. helveticus

Aerotolerant anaerobe or microaerophil; no-spore-forming, no-motile, rod-shaped, mesophilic

or thermophilic (L.h.), Gram (+)

Vaginal discharge (L.c.), GIT of human and animals. Plant, soil and aquatic samples

Catalase (-), lactic acid (+), additionally hydrogen peroxide (+) (L.c.), indole-3-lactic acid (+) (L.g.) and butyric acid (+) (L.h.)

L.c. effectively treats bacterial vaginosis if used alone or alongside antibiotic treatment if an infection had already arisen [9, 92, 94]. L.c. is a major component of the chicken GIT microbiota [9]. Lg modulates the gut microbiota and produces anticancer metabolites to protect against colorectal tumorigenesis (Sugimura et al. 2021). Their presence reduces the count of E. coli O157 excreted in faeces. Indole-3-lactic acid has anti-inflammatory properties. Lg is most persistent in the ileum and ceca due to its sensitivity to bile [33, 92]. Lg effectively adheres to chicken LMH epithelial cell lines in vitro and can strongly colonise the gastrointestinal tract of broiler chickens in vivo [55, 92]. L.g. can reduce colonization of the cecum by C. jejuni [5]. L.h. has higher proteolytic activity than most other lactobacilli [22, 35, 97], reduces blood pressure without adverse effects, improves sleep in patients aged 60–81 years, reduces the length of upper respiratory tract illnesses, has a positive effect on calcium metabolism in women between the ages of 50–78, decreases parathyroid hormone, associated with bone loss and with Bifidobacterium longum, taken in combination, reduces symptoms of anxiety and depression [21, 61]

Ligilactobacillus salivarius

GIT of human and animals, oral cavity of human, porcine and avian. Plant, soil and aquatic samples

Catalase (-), ferment hexoses to lactic acid on EMP pathway, or to lactic acid, acetic acid, ethanol on pentose phosphate pathway, some strains can produce L(+) lactic acid and D(−) isomer

L.s. relieves flatulence in individuals suffering from irritable bowel syndrome [69], inhibits pathogens, helps treat inflammatory diseases hereby demonstrating therapeutic benefit in the management of pancreatic necrosis [21, 24]. Symptoms of atopic dermatitis disappear in some children in the presence of L.s. [66]

Limosilactobacillus urinaemulieris

Microaerobic, mesophilic/ or thermophilic, Gram (+)

GIT of animals, human urinary tract. Plant, soil and aquatic samples

Lactic acid (+), acetic acid (+), ethanol (+)

[48, 49, [50]

Mediterraneibacter glycyrrhizinilyticus

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (-)

 [84, 99]

Megamonas funiformis,

M. hypermegale,

M. rupellensis

Anaerobic, nonspore-forming, nonmotile, large rods with or without a central, subterminal or terminal swelling, in young plate cultures, cells consist of fairly homogeneous-sized, mesophilic, Gramme (-) or Gram (-) or variable (M. hypermegale, M. rupellensis)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (-), oxydase (-), acetic acid (+), propionic acid (+) (M.f., M.r.), lactic acid (+) (M.f., M.h.), succinic acid (+) (M.f.), butyric acid (+) (M.h.)

The amount of M.f. [83, 102] h. [88] i r. [18] affects the concentration of SCFAs in the intestine, especially M.h. which leads to skewed immune function in Behcet’s disease patients [88]

Mucispirillum schaedleri

Anaerobic, no-spore-forming, curved to spiral rods with single, unsheathed, bipolar flagella, mesophilic,

Gram (-)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (+), oxydase (+), halophile

M.s. is causally linked to the development of Crohn’s disease-like colitis in immunodeficient mice [79]. SM is resistant on oxidative stress and can modify gene expression in host mucosal tissue and participate in inflammation [54]

Neglectibacter timonensis

Anaerobic, no-spore-forming, no-motile, rod-shaped, occur in pairs, mesophilic, Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (+)/(-), oxydase (-), halophile

[115]

Oscillibacter massiliensis

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (-)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (-), oxydase (-)

[64, 103]

Phascolarctobacterium faecium

Anaerobic, no-spore-forming, no-motile, mesophilic, Gram (-)

GIT of human and animal. Plant, soil and aquatic samples

Acetic acid (+), propionic acid (+)

Pf count are changed by adding cruciferous vegetables to the diet. The level of intestinal P.f. may be different during human life. The colonisation rate in infants is significantly low for those aged 10–30 years old, 30–60 years old adults, and elders [111]

Phocaeicola coprocola, P. dorei,

P. massiliensis,

P. plebeius

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (-)

GIT of human and animal. Several reported cases of human blood contamination (P.c.), one asymptomatic case found in blood (P.m.). Common in indigenous Japanese (P.p.). Plant, soil and aquatic samples

Catalase (-)

The 16 S rRNA gene sequence analysis allowed to prepare a description of: P.c. [34] P.d. [8, 34] d m. [30, 34]. P.p. digests porphyran, a polysaccharide derived from Porphyra seaweed (nori), which humans are unable to digest on their own [38]

Ruthenibacterium lactatiformans

Anaerobic, no-spore-forming, no-motile, rod-shaped, occur singly and in pairs, mesophilic, Gram (-)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (-), lactic acid (+), succinic acid (+), acetic acid (+)

R.l. reduces inflammation and stimulates CTL (cytotoxic T-lymphocyte associated protein) [89]. The result may point to a noninvasive method of increasing the therapeutic index of immunotherapy with diet or probiotics [32]

Subdoligranulum variabile

Anaerobic, no-spore-forming, no-motile,

rod-shaped, mesophilic, Gram (+)

GIT of human and animal. Plant, soil and aquatic samples

Catalase (-), oxydase (-), butyric acid (+), formic acid (+)

S.v. forms a consortium of bacterial species commonly present in the intestine and participates in the hydrolysis of dietary fiber [16]. S.v. correlates positively with fecal microbiota richness, HDL-cholesterol and adiponectin levels as negative correlates with fat mass, adipocyte diameter and leptin, insulin, CRP and IL-6 levels [104]