Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies
Abstract
:1. Introduction
1.1. Microbiota Gut Dysbiosis
1.2. Traditional Probiotics vs. NGP in Obesity-Related Interventions and Treatments
Lactobacillus Strains [15] | Study Design, Target Species | Reference Study |
---|---|---|
L. bulgaricus Nutricion Medica® | ICT—Human | [16] |
L. casei Shirota | ICT—Human | [17] |
L. gasseri BNR17 | ICT—Human | [18] |
L. reuteri V3401 | ICT—Human | [19] |
L. rhamnosus CGMCC1.3724 | ICT—Human | [20] |
L. acidophilus NS1 | PCS—Mice | [21] |
L. johnsonii JNU3402 | PCS—Mice | [22] |
L. plantarum Ln4 | PCS—Mice | [23] |
L.curvatus HY7601 | PCS—Mice | [24] |
L. fermentum CQPC07 | PCS—Mice | [25] |
Bifidobacterium strains | Study design, Target Species, | Reference study |
B. animalis subsp. lactis 420 | ICT—Human | [26] |
B. breve B-3 | ICT—Human | [27] |
B. infantis DSM24737 (VSL#3) | ICT—Human | [28] |
B. lactis HN019 | ICT—Human | [29] |
B. longum APC1472 | ICT–Human/PCS–Mice | [30] |
B. adolescentis | PCS—Mice | [31] |
B. bifidum BGN4 | PCS—Mice | [32] |
Bacillus, Enterococcus, Streptococcus strains | Study design, Target Species, | Reference study |
Bacillus coagulans Unique IS2 | ICT—Human | [33] |
Bacillus amyloliquefaciens SC06 | PCS—Mice | [34] |
Bacillus spp. | PCS—Mice | [35] |
Enterococcus faecium R0026 | PCS—Mice | [36] |
Enterococcus faecalis AG5 | PCS—Rats | [37] |
Streptococcus thermophiles MN-ZLW-002 | PCS—Mice | [38] |
Saccharomyces strains | Study design, Target Species, | Reference study |
S. boulardii Biocodex | PCS–Mice | [39] |
S. cerevisiae SFBE | PCS–Rats | [40] |
2. Information and Criteria for Searching and Culturing Next-Generation Probiotics
2.1. Target Diseases, Microbiome Variability Composition, Biomarkers and Clinical Traits
2.1.1. Obesity, Metabolic, and Endocrine Diseases: Variability of Microbiota Composition
2.1.2. Nutrition and Diets, Dietary Exposure to Obesogens, and Microbiome Interactions
2.2. Culturing and Isolation of NGP through Combined Methodologies
2.3. Standardize Parameters When Using NGP in Clinical Studies
2.4. Whole Genome Sequencing, Next-Generation Sequencing, and Bioinformatics Analyses
2.5. Omics Data Integration: Big Data and Host Clinical Responses
2.6. Safety Assessment, Regulatory Frameworks, and Market Labeling
Country | Category | Regulatory Framework | Claims | Reference |
---|---|---|---|---|
USA | Drugs, nutraceuticals | FDA | Health claims Nutrient claims Structure claims GRAS | [145,146] |
Dietary supplements | DSHEA | Probiotics considered as foods | ||
Biological product | FDA (BLA) | Probiotics as a reference product, biosimilar product, or an interchangeable product; solely to be used for medical therapeutic purpose | ||
Life biotherapeutic agent | FDA | Probiotics as a biological product that contains live organisms and is applicable to the prevention, treatment, or cure of a disease or condition; recombinant life biotherapeutic agent | ||
Medical Food | FDA/DSHA | Probiotics specially formulated to be intended for dietary management under supervision; medical foods are exempt from the labeling requirements for nutrient content and health claims | ||
China | Functional foods | SFDA | Conventional foods mark (the presence of a specific ingredient in the label of regular foodstuffs) Healthy foods (the presence of health function) | [147] |
Europe | Functional Food and nutraceuticals | EFSA (FUFOSE) | Health claims, nutrition claims QPS | [143,144,148] |
Life biotherapeutic products | EMA | Probiotics as medicinal products containing live microorganisms for human use | ||
Japan | Functional foods and nutraceuticals | MHLW, FOSHU | Foods with functional claims Foods with nutrient functional claims | [149,150] |
Canada | Natural health products | FDA (CFIA) | Nutrient content claims Health claims | [151] |
3. Discussion
4. Conclusions
- Culturing of microorganisms from microbiota is the key activity to obtain NGP from healthy individuals, mainly through isolating those microorganisms identified as differentially decreased in the target disease or abundant in healthy microbiota, focusing on candidatus species from metagenomics studies.
- Screening and selection of the potential NGP in a target-disease population by using in vitro models before clinical interventions.
- Harmonization on performing exhaustive pre-analysis and post-intervention of individual microbiota composition through representative and validated methodologies (e.g., V3–V4 and Illumina MiSeq technology) is needed before administering NGP.
- There is a need to standardize bioinformatics and database tools for specifically designing analysis of large and universal microbiome datasets.
- NGP single strains or taxa consortium should have attributable documented benefits and their safety confirmation statements.
- Effective doses and well-defined patterns of administration of NGP should become factors for aligning intervention doses since the beginning of clinical translation.
- International guidelines on NGP and microbiota investigations for targeting obesity-related diseases prevention or treatments are needed. This will allow for more meaningful effect comparisons of harmonized and valuable studies, facilitating more robust meta-analysis.
- Data reuse and availability of open access interventional clinical trials data will contribute to obtaining significant association of clinical outcomes.
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
MDC | Microbiota-disrupting chemicals |
NGP | Next-generation probiotics |
GIT | Gastrointestinal tract |
PCOS | Polycystic ovary syndrome |
FAO | Food and Agriculture Organization of the United Nations |
WHO | World Health Organization |
ICT | Interventional clinical trials |
PCS | Preclinical studies |
DC | Dendritic cells |
IL | Interleukin |
LPS | Lipopolysaccharide |
TLR2 | Toll-like receptor 2 |
TNF | Tumor necrosis factor |
WGS | Whole genome sequencing |
NGS | New-generation sequencing |
AN | Anorexia nervosa |
HC | Healthy control |
HL | Hyperlipidemia |
HT | Hypertension |
LH | Lean healthy |
MetS | Metabolic syndrome |
MHNO | Metabolically healthy non-obese |
MHO | Metabolically healthy obese |
MUNO | Metabolically unhealthy non-obese |
MUO | Metabolically unhealthy obese |
NAFLD | Non-alcoholic fatty liver disease |
NASH | Non-alcoholic steatohepatitis |
OB | Obese |
OBH | Obese healthy |
OBT2D | Obese type 2 diabetes |
OW | Overweight |
RISK1 | Patients with only one disease |
RISK2 | Patients with two disease |
RISK3 | Patients with three disease |
SS | Simple steatosis |
T1D | Type 1 diabetes |
T2D | Type 2 diabetes |
TSNO | Tsumura Suzuki obese diabetes mice |
TSOD | Tsumura Suzuki non obesity mice |
BPA | Bisphenol A |
BPS | Bisphenol S |
YCFA | Yeast-extract-casein hydrolysate-fatty acids |
GAM | Gifu anaerobic medium |
BHI | Brain–heart infusion |
EMB | Eosin methylene blue |
LBS | Lactobacillus selection |
GMM | Gut microbiota medium |
MRS | Man, Rogosa, and Sharpe |
RNA | Ribonucleic acid |
rRNA | Ribosomal ribonucleic acid |
DNA | Deoxyribonucleic acid |
OTU | Operational taxonomic unit |
EU | European Union |
Ph. Eur. | European Pharmacopoeia |
US | United States |
GRAS | Generally recognized as safe |
FDA | Food and Drug Administration |
EFSA | European Food Safety Authority |
QPS | Qualified presumption of safety |
EMA | European Medicines Agency |
MHLW | Ministry of Health and Welfare |
FOSHU | Food for specified health use |
FUFOSE | Functional food science in Europe |
SFDA | State Food and Drug Administration |
DSHEA | Dietary Supplement Health and Education Act |
BLA | Biologic license application |
CFIA | The Canadian Food Inspection Agency |
GMP | Good manufacturing practice |
CFU | Colony-forming units |
OA | Open access |
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NGP Microbial Strains, Target Species, Study Reference | Study Design | Dietary Aspects | Clinical Effects and Functionality |
---|---|---|---|
Akkermansia muciniphila Muc [CIP 107961]—Human [41] [ClinicalTrials.gov Identifier: NCT02637115] | ICT: randomized, double-blind, placebo-controlled pilot study Live probiotics 1010/day vs. pasteurized probiotics 1010/day vs. placebo in patients with metabolic syndrome | Normal dietary intake and physical activity during the study period | ↑ Insulin sensitivity, ↓ insulinemia and ↓plasma total cholesterol |
Akkermansia muciniphila WST01—Human [42] [ClinicalTrials.gov Identifier: NCT04797442] | ICT: randomized, double-blind, placebo-controlled, multicenter clinical trial Probiotics vs. placebo in overweight or obese patients with type 2 diabetes | Intervention added onto lifestyle | Results will be available in June 2022 |
Christensenella minuta Xla1—Human [43] [ClinicalTrials.gov Identifier: NCT04663139] | ICT: randomized, partially placebo-controlled double-blind Probiotics vs. placebo in healthy volunteers, overweight, and obese adults | Agreement to keep food, drink, physical activities, and alcohol consumption habits unchanged throughout the study | Results will be available in October 2021 |
Eubacterium hallii—Human [44] [ClinicalTrials.gov Identifier: NCT04529473] | ICT:double-blind, randomized, placebo-controlled Probiotics vs. placebo | Maintenance of dietary habits and physical activity levels throughout the study period | Results will be available on January 2022 |
Hafnia alvei HA4597—Human [45] [ClinicalTrials.gov Identifier: NCT03657186] | ICT: multicenter, randomized, double-blind placebo-controlled study. Probiotics vs. placebo on weight reduction in overweight subjects | −20% hypocaloric diet and maintainance of the usual physical activity | ↑ Weight loss in overweight subjects, ↑ feeling of fullness, ↑ loss of hip circumference, ↓ fasting glycemia |
Lactococcus lactis NRRL-B50571—Human [46] [ClinicalTrials.gov Identifier: NCT02670811] | ICT: double-blind randomized controlled Probiotics vs. placebo on prehypertensive subjects | Participants were asked not to change their diet or lifestyle during the intervention | ↓ Systolic and diastolic blood pressure, ↓ Triglyceride, total cholesterol, and low-density lipoprotein |
Escherichia coli Nissle 1917—Human [47] [ClinicalTrials.gov Identifier: NCT02144948] | ICT: single group assignment. Patients with type 2 diabetes | - | Results not yet available or posted on ClinicalTrials.gov November 2021 |
Akkermansia muciniphila—Muc [CIP 107961]—Mice [48,49] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | ↓ Fat-mass gain, ↑ insulin sensitivity, restore gut barrier function by acting on TLR2, ↑ mucus later thickness; similar effects by a purified membrane protein alone (Amuc_1100) |
Clostridium butyricum CGMCC0313.1—Mice [50] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | ↓ Lipid accumulation in liver and serum, ↓ insulin levels, ↑ glucose tolerance, ↑ insulin sensitivity, ↓ TNF-α and ↑ IL-10 and IL-22 in colon |
Faecalibacterium prausnitzii VPI C13-20-A—Mice [51] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | ↑ Hepatic health, ↓ adipose tissue inflammation |
Bacteroides uniformis CECT 7771– Mice [52] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | ↓ Weight gain; ↓ dietary fat absorption; ↓ liver steatosis; ↓ serum cholesterol, triglyceride, glucose, insulin and leptin; ↑ glucose tolerance; ↑ TNF-α by DCs after LPS stimulation;↑ phagocytosis |
Parabacteroides goldsteinii JCM 13446—Mice [53] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | ↓ Obesity by ↑ adipose tissue thermogenesis, ↑ intestinal integrity ↓ inflammation, ↑ insulin sensitivity |
Christensenella minuta—Mice [54] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | ↓ Weight gain, ↓ adiposity. Highly heritable in a lean host phenotype |
Eubacterium hallii DSM 17630—Mice [55] | PCS: probiotics vs. control. Diabetes | High-fat diet/standard diet | ↑ Energy metabolism and ↑ insulin sensitivity through glycerol conversion 3hydroxypropionaldehyde |
Hafnia alvei HA4597—Mice [56] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | ↑ Beneficial anti-obesity and metabolic effects, ↓ food intake, ↓ body weight and ↓ fat mass gain |
Lactococcus lactis (GMM) LL-pCYT: HSP65-6P277 and LL-pHJ—Mice [57] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | ↓ Antigen-specific of cellular immunity |
Escherichia coli Nissle 1917 (EcN-GMM)– Mice [58] | PCS: probiotics vs. control. Obesity | High-fat diet/standard diet | Modulation of the neuropeptide expression of energy intake and expenditure in the hypothalamus |
Reference | Subjects and Disease | Dietary Aspects | Sample Size and Clinical Traits | Detection Technique | Microbial Taxa Modifications |
---|---|---|---|---|---|
Zhong et al. [66] | Human Obesity | NA | N = 382; MHNO n = 191; MUNO n = 61; MHO n = 66; MUO n = 64 | MiSeq platform (Illumina) V3–V4 region of the 16S rRNA gene | ↑ Lachnospiraceae, Bacteroidaceae, Methanobacteriaceae and Pasteurellaceae in MHNO and MUNO |
Jonduo et al. [67] | Human Obesity | Participant’s predominantly plant-based diet: vegetables (e.g., sweet potato, cassava, plantain, and beans) | n = 18; OB n = 9; Non-OB n = 9 | 454 GS FLX platform or 454 GS JUNIOR system (Roche) V1-V2 region of the 16S rRNA gene | ↑ Prevotella in almost all individuals |
Thingholm et al. [68] | Human Obesity | NA | n = 1280; LH n = 633; OBH n = 494; OBT2D n = 153 | MiSeq platform (Illumina) V1-V2 region of 16S rRNA gene | ↓ Akkermansia, Faecalibacterium, Oscillibacter, and Alistipes in obese individuals ↓ Faecalibacterium prausnitzii in obese individuals |
Schwiertz et al. [65] | Human Obesity | Western diet | n= 98; HC n = 30; OW n = 35; OB n = 33 | qPCR | ↑ Bacteroides in overweight vs. HC ↓ Ruminococcus flavefaciens in overweight and obese ↓ Bifidobacterium and Clostridium leptum in obese ↓ Methanobrevibacter in overweight and obese |
Gao et al. [69] | Human Obesity | NA | n = 192; HC n = 25; OW n = 22; OB n = 145 | MiSeq platform (Illumina) V4 region of the 16S rRNA gene | ↑ Lachnoclostridium, Fusobacterium, Escherichia-Shigella, Klebsiella, Bacillus, and Pseudomonas in OW and OB ↑ Clostridia, Faecalibacterium, Ruminococcus, Bifidobacterium, and Lachnospiraceae_UCG_008 in HC |
Armougom et al. [70] | Human Obesity Anorexia nervosa | NA | n= 49; HC n = 20; OB n = 20; AN n = 9 | qPCR | ↑ Lactobacillus in OB |
Horie et al. [71] | Mice Type 2 diabetes | NA | 5-week-old TSNO mice n = 5; 5-week-old TSOD mice n = 5; 12-week-old TSNO mice n = 5; 12-week-old TSOD mice n = 5 | qPCR | ↑ Lactobacillus in TSOD vs. TSNO ↑ Bacteroidales and Lachnospiraceae in TSNO vs. TSOD ↑ Turicibacter and SMB53 in TSOD |
Larsen et al. [72] | Human Type 2 diabetes | NA | n = 36; HC n = 18; T2D n = 18 | MiSeq platform (Illumina) V4 region of the 16S rRNA gene | ↑ Firmicutes in HC ↑ Bacteroidetes and Betaproteobacteria in T2D ↓ Clostridia in T2D |
Sedighi et al. [73] | Human Type 2 diabetes | NA | n = 36; HC n = 18; T2D n = 18 | qPCR | ↑ Lactobacillus in T2D ↑ Bifidobacterium in HC ↑ Fusobacterium in T2D |
Moghadam et al. [74] | Human Tipe 2 diabetes | NA | n = 36; HC n = 18; T2D n = 18 | qPCR | ↑ Faecalibacterium prausnitzii in HC |
Ahmad et al. [75] | Human Type 2 diabetes Obesity | Eastern dietary habits (high carbohydrate and fat intake, low fiber intake) | n = 60; HC n = 20; Obese-T2D n = 40 | MiSeq platform (Illumina) V3–V4 region of the 16S rRNA gene | ↑ Firmicutes in Obese-T2D ↑ Clostridia, Negativicutes, Coriobacteria, Acidobacteria, Deferribacteres, and Gemmatimonadetes in obese-T2D ↑ Verrucomicrobia, Bacteroidetes, Proteobacteria, and Elusimicrobia in HC ↑ Prevotella P4_76, Clostridiales, Porphyromonadaceae bacterium DJF B175, Candidatus Alistipes marseilloanorexic AP11, Bacillus sporothermodurans, Staphylococcus SV3, and Iamia in obese-T2D |
Ejtahed et al. [76] | Human Type 2 diabetes Type 1 diabetes | NA | n = 110; HC n = 40; T2D n = 49; T1D n = 21 | qPCR | ↑ Escherichia, Prevotella, and Lactobacillus in T1D and T2D ↑ Bifidobacterium, Roseburia, and Bacteroides in HC ↓ Faecalibacterium in T1D vs. HC and T2D |
Takagi et al. [77] | Human Type 2 diabetes Hypertension Hyperlipidemia | NA | n = 239; HC n = 54; HT n = 97; HL n = 96; T2D n = 162 | MiSeq platform (Illumina) V3–V4 region of the 16S rRNA gene | ↑ Actinobacteria in HT, HL, T2D, RISK2, and RISK3 ↓ Bacteroidetes in HT, HL, T2D and RISK3 ↑ Bifidobacterium in HL, T2D, RISK1 and RISK2 ↑ Collinsella in HT, HL, T2D, RISK2 and RISK3 ↑ Escherichia in RISK 3 ↓ Alistipes in HL |
Wang et al. [78] | Human Non-alcoholic fatty liver disease | Omnivorous Chinese diet | n = 126; HC n = 83; NAFLD n = 43 | 454 Life Sciences Genome Sequencer FLX system (Roche) V3 region of the 16S rRNA gene | ↓ Firmicutes ↑Bacteroidetes in NAFLD ↑ Bacteroidia ↓ Clostridia in NAFLD ↓ Coprococcus, Pseudobutyrivibrio, Moryella, Roseburia, Anaerotruncus, Ruminococcus, Anaerosporobacter, andLactobacillus in NAFLD |
Li et al. [79] | Human Non-alcoholic fatty liver disease | No dietary restrictions imposed | n = 67; HC n = 37; NAFLD n = 30 | MiSeq platform (Illumina) V4 region of the16S rRNA gene | ↑ Lactobacillaceae, Peptostreptococcaceae, Veillonellaceae, EtOH8, Coprobacillaceae, and Erysipelotrichaceae in NAFLD ↑ Porphyromonas and Succinivibrio in NAFLD ↓ Odoribacter and Proteus in NAFLD |
Shen et al. [80] | Human Non-alcoholic fatty liver disease | NA | n = 47; HC n = 22; NAFLD n = 25 | 454 GS-FLX platform (Roche) V3-V5 region of the 16S rRNA gene | ↑ Proteobacteria, Fusobacteria, Lachnospiraceae_Incertae_Sedis and Blautia in NAFLD ↑ Bacteroidetes and Prevotella in HC ↑ Escherichia_Shigella, Clostridium_XVIII, and Staphylococcus in NAFLD |
Raman et al. [81] | Human Non-alcoholic fatty liver disease | No dietary restrictions imposed | n = 60; HC n = 30; NAFLD n = 30 | qPCR | ↑ Lactobacillus, Roseburia, Dorea, and Robinsoniella in NAFLD ↓Oscillibacterin NAFLD |
Michail et al. [82] | Human Non-alcoholic fatty liver disease Obesity | No dietary restrictions imposed | n = 50; HC n = 26; NAFLD n = 13; Obese non-NAFLD n = 11 | qPCR | ↑ Gammaproteobacteria, Prevotella, and Epsilonproteobacteria in NAFLD ↓ Clostridia ↑ Alphaproteobacteria in obese non-NAFLD |
Nistal et al. [83] | Human Non-alcoholic fatty liver disease Obesity | NA | n = 73; HC n = 20; Obese-NAFLD n = 36; Obese non-NAFLD n = 17 | MiSeq platform (Illumina) V3–V4 region of the 16S rRNA gene | ↑ Bacilli in obese-NAFLD ↓ Betaproteobacteria in obese-NAFLD vs. obese non-NAFLD ↓ Oscillospira, Akkermansia, and Eubacterium in obese-NAFLD and obese non-NAFLD vs. HC ↑ Megasphaera, Lactobacillus, Acidominococcus in obese-NAFLD, and obese non-NAFLD vs. HC ↓ Blautia, Alkaliphilus, and Flavobacterium in obese-NAFLD ↑ Staphylococcus in obese-NAFLD |
Loomba et al. [84] | Human Non-alcoholic fatty liver disease Fibrosis | NA | n= 86; NAFLD n = 72; Fibrosis n = 14 | qPCR | ↑ Firmicutes in NAFLD, ↑ Proteobacteria in fibrosis ↑ Eubacterium rectale and Bacteroides vulgatus in NAFLD ↑ Bacteroides vulgatus and Escherichia coli in fibrosis ↓ Ruminococcus obeum, and Eubacterium rectale in fibrosis |
Del Chierico et al. [85] | Human Non-alcoholic fatty liver disease Non-alcoholic steatohepatitis Obesity | NA | n= 115; HC n = 54, OB n = 8; NAFLD n = 27; NASH n = 26 | 454- Junior Genome Sequencer FLX system (Roche) V1-V3 region of the 16S rRNA gene | ↑ Bradyrhizobium, Anaerococcus, Peptoniphilus, Propionibacterium acnes, Dorea, and Ruminococcus ↓ Oscillospira and Rikenellaceae in NAFLD ↑ Ruminococcus, Dorea, and Blautia in NASH |
Da Silva et al. [86] | Human Non-alcoholic steatohepatitis Simple steatosis | 7-day food record | n = 67; HC n = 28; SS n = 15: NASH n = 24 | MiSeq platform (Illumina) | ↓ Ruminococcus, Faecalibacteriumprausnitzii, and Coprococcus in NASH and SS vs. HC |
Mouzaki et al. [87] | Human Non-alcoholic steatohepatitis Simple steatosis | HC patients were consuming more calories per kg compared to patients with NASH | n = 50; HC n = 17; SS n = 11; NASH n = 22 | qPCR | ↓ Bacteroidetes in NASH vs. SS and HC ↑ Clostridium coccoides in NASH vs. SS |
Zhu et al. [88] | Human Non-alcoholic steatohepatitis Obesity | NA | n= 63; HC n = 16; OB n = 25; NASH n = 22 | qPCR | ↑ Bacteroides ↓ Firmicutes in NASH and OB ↓ Blautia and Faecalibacterium in NASH and OB |
Boursier et al. [89] | Human Non-alcoholic steatohepatitis Fibrosis | NA | n = 57; Non-NASH n = 20 NASH n = 10; Fibrosis ≥ 2 n = 27 | Illumina V4 region of 16S rRNA gene | ↑ Bacteroides ↓Prevotella in NASH ↑ Bacteroides and Ruminococcus in fibrosis ≥ 2 ↓ Prevotella in fibrosis ≥ 2 |
Qin et al. [90] | Human Cirrhosis | NA | n= 179; HC n = 83; Cirrhosis n = 96 | qPCR | ↑ Streptococcus, Veillonella, Clostridium and Prevotella in cirrhosis ↑ Eubacterium and Alistipes in HC ↓ Bacteroides in cirrhosis |
Lim et al. [91] | Human Methabolic syndrome | NA | n = 655; Monozygotic twins n = 306; Dizygotic twins n = 74; Siblings n = 275 | MiSeq platform (Illumina) V4 region of the 16S rRNA gene | ↑ Lactobacillus, Sutterella and Methanobrevibacter in MetS ↓ Parabacteroides, Bifidobacterium, Odoribacter, Akkermansia and Christensenella in MetS |
Reference/Sample | Culture Media | Culture Media Modifications | Selected Favored Cultured Microorganisms | Outcome and Observations: New Species Cultured: Potential NGP |
---|---|---|---|---|
Browne et al. [118] Human | YCFA | Glucose (0.2%), maltose (0.2%), and cellobiose (0.2%) | Aero-intolerant genus and species | 68 new isolated species: 16S RNA similarity 86–97% Anaerotruncus colihominis Blautia luti; B. hydrogenotrophica Clostridium boltae; C. celerecrescens; C. celerescens; C. clostridioforme; C. cocleatum; C. disporicum; C. ghonii; C. hathewayi; C. innocuum; C. lituseburense; C. methylpentosum; C. nexile; C. oroticum; C. saccharogumia; C. saccharolyticum; C. thermocellum; C. xylanolyticum Coprococcus eutactus Oscillibacter valericigenes Roseburia faecis; R. inulinivorans Ruminococcus albus; R.bromii; R. flavefaciens; R. gnavus; R.obeum; R. torques |
YCFA | Pre-treatment with ethanol 70% (v/v), glucose (0.2%), maltose (0.2%), cellobiose (0.2%), sodium taurocholate (0.1%). Spore-forming gut aero-intolerant bacteria | Alistipes finegoldii Anaerotruncus colihominis Blautia hydrogenotrophica; B. obeum; B. wexlerae Clostridum baratti; C. bartlettii; C. clostridioforme; C. disporicum; C. hathewayi; C.innocuum; C. paraputrificum; C.perfringens Coprococcus comes; C. eutactus Prevotella copri Roseburia hominis; R. intestinalis; R. inulinvorans; Ruminococcus bromii; R. gnavus; R. obeum; R. torques | ||
Chang et al. [119] Human | YCFA | Pre-incubation in blood culture bottles supplemented with 10% sheep blood and 10% rumen | Aero-intolerant bacteria Alistipes shahii; A. onderdonkii, Clostridium bifermentans, C. innocuum, C. hiranonis, C. butiricum, C. hathewayi, C. bolteae, C. sporogenes, Odoribacter splanchnicus | 22% of species isolated increase: 16S RNA similarity 93–97% 3 new species isolated: Longicatena caemuris Bacillus alcalophilus Pseudogracilibacillus auburnensis |
Gotoh et al. [120] Microbial bank | GAM | NA | Aero-intolerant bacteria 72% of species of the top 56 species listed in the “human gut microbial gene catalogue” cultured in GAM | Isolated species in GAM: Anaerotruncus colihominis, Blautia hansenii, Clostridium nexile, C. asparagiforme, C. scindens, Coprococcus comes Roseburia intestinalis Ruminococcus torques, R. lactaris, R. obeum, R. gnavus. |
Lagier et al. [121] 16-years-old male | BHI | Preincubation of the stool with lytic E. coli T1 and T4 phages | Non-fastidious aerobic and facultatively anaerobic bacteria | Enterobactermassiliensis strain JC163T |
Bailey and Coe [122] Rhesus Monkeys | BHI | NA | Non-fastidious aerobic and facultatively anaerobic bacteria | NA |
EMB | NA | Gram-negative aerobic and facultatively anaerobic bacteria | NA | |
LBS | NA | Aerobic members of lactobacilli | Lactobacillusspp. | |
Lei et al. [123] Female mice | GMM | NA | Gut aero-intolerant bacteria | |
López-Moreno [117] | BHI | Supplemented with Obesogens: BPA, BPS | Anaerobic facultative Firmicutes | Staphylococcus, Bacillusamyloliquefaciens group, Streptococcussalivarius |
López-Moreno [117] | MRS | Supplemented with Obesogens: BPA, BPS | Lactobacillus, Enterobacteria | Latilactobacillus sakei, Enterococcus faecium |
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López-Moreno, A.; Acuña, I.; Torres-Sánchez, A.; Ruiz-Moreno, Á.; Cerk, K.; Rivas, A.; Suárez, A.; Monteoliva-Sánchez, M.; Aguilera, M. Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies. Nutrients 2021, 13, 1617. https://doi.org/10.3390/nu13051617
López-Moreno A, Acuña I, Torres-Sánchez A, Ruiz-Moreno Á, Cerk K, Rivas A, Suárez A, Monteoliva-Sánchez M, Aguilera M. Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies. Nutrients. 2021; 13(5):1617. https://doi.org/10.3390/nu13051617
Chicago/Turabian StyleLópez-Moreno, Ana, Inmaculada Acuña, Alfonso Torres-Sánchez, Ángel Ruiz-Moreno, Klara Cerk, Ana Rivas, Antonio Suárez, Mercedes Monteoliva-Sánchez, and Margarita Aguilera. 2021. "Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies" Nutrients 13, no. 5: 1617. https://doi.org/10.3390/nu13051617
APA StyleLópez-Moreno, A., Acuña, I., Torres-Sánchez, A., Ruiz-Moreno, Á., Cerk, K., Rivas, A., Suárez, A., Monteoliva-Sánchez, M., & Aguilera, M. (2021). Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies. Nutrients, 13(5), 1617. https://doi.org/10.3390/nu13051617