@article {pmid39243797,
year = {2025},
author = {Rodriguez, J and Hassani, Z and Alves Costa Silva, C and Betsou, F and Carraturo, F and Fasano, A and Israelsen, M and Iyappan, A and Krag, A and Metwaly, A and Schierwagen, R and Trebicka, J and Zwart, H and Doré, J and Cordaillat-Simmons, M and Druart, C and , },
title = {State of the art and the future of microbiome-based biomarkers: a multidisciplinary Delphi consensus.},
journal = {The Lancet. Microbe},
volume = {6},
number = {2},
pages = {100948},
doi = {10.1016/j.lanmic.2024.07.011},
pmid = {39243797},
issn = {2666-5247},
mesh = {Humans ; *Biomarkers/analysis ; Delphi Technique ; *Microbiota ; Consensus ; Surveys and Questionnaires ; },
abstract = {Although microbiome signatures have been identified in various contexts (ie, pathogenesis of non-communicable diseases and treatment response), qualified microbiome-based biomarkers are currently not in use in clinical practice. The Human Microbiome Action consortium initiated a Delphi survey to establish a consensus on the needs, challenges, and limitations in developing qualified microbiome-based biomarkers. The questionnaire was developed by a scientific committee via literature review and expert interviews. To ensure broad applicability of the results, 307 experts were invited to participate; 114 of them responded to the first round of the survey, 93 of whom completed the second and final round as well. The survey highlighted the experts' confidence in the potential of microbiome-based biomarkers for several indications or pathologies. The paucity of validated analytical methods appears to be the principal factor hindering the qualification of these biomarkers. The survey also showed that clinical implementation of these biomarkers would only be possible if kitted and validated molecular assays with simple interpretation are developed. This initiative serves as a foundation for designing and implementing public-private collaborative projects to overcome the challenges and promote clinical application of microbiome-based biomarkers.},
}

Humans
*Biomarkers/analysis
Delphi Technique
*Microbiota
Consensus
Surveys and Questionnaires

@article {pmid39244168,
year = {2025},
author = {Govender, P and Ghai, M},
title = {Population-specific differences in the human microbiome: Factors defining the diversity.},
journal = {Gene},
volume = {933},
number = {},
pages = {148923},
doi = {10.1016/j.gene.2024.148923},
pmid = {39244168},
issn = {1879-0038},
mesh = {Humans ; Asian People ; Bacteria/genetics/classification ; Bacteriophages/genetics ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; White People ; Black People ; },
abstract = {Differences in microbial communities at different body habitats define the microbiome composition of the human body. The gut, oral, skin vaginal fluid and tissue microbiome, are pivotal for human development and immune response and cross talk between these microbiomes is evident. Population studies reveal that various factors, such as host genetics, diet, lifestyle, aging, and geographical location are strongly associated with population-specific microbiome differences. The present review discusses the factors that shape microbiome diversity in humans, and microbiome differences in African, Asian and Caucasian populations. Gut microbiome studies show that microbial species Bacteroides is commonly found in individuals living in Western countries (Caucasian populations), while Prevotella is prevalent in non-Western countries (African and Asian populations). This association is mainly due to the high carbohydrate, high fat diet in western countries in contrast to high fibre, low fat diets in African/ Asian regions. Majority of the microbiome studies focus on the bacteriome component; however, interesting findings reveal that increased bacteriophage richness, which makes up the virome component, correlates with decreased bacterial diversity, and causes microbiome dysbiosis. An increase of Caudovirales (bacteriophages) is associated with a decrease in enteric bacteria in inflammatory bowel diseases. Future microbiome studies should evaluate the interrelation between bacteriome and virome to fully understand their significance in the pathogenesis and progression of human diseases. With ethnic health disparities becoming increasingly apparent, studies need to emphasize on the association of population-specific microbiome differences and human diseases, to develop microbiome-based therapeutics. Additionally, targeted phage therapy is emerging as an attractive alternative to antibiotics for bacterial infections. With rapid rise in microbiome research, focus should be on standardizing protocols, advanced bioinformatics tools, and reducing sequencing platform related biases. Ultimately, integration of multi-omics data (genomics, transcriptomics, proteomics and metabolomics) will lead to precision models for personalized microbiome therapeutics advancement.},
}

Humans
Asian People
Bacteria/genetics/classification
Bacteriophages/genetics
Dysbiosis/microbiology
*Gastrointestinal Microbiome
*Microbiota
White People
Black People

@article {pmid39251326,
year = {2025},
author = {Zhou, Q and Lei, L and Cheng, J and Chen, J and Du, Y and Zhang, X and Li, Q and Li, C and Deng, H and Wong, CC and Zhuang, B and Li, G and Bai, X},
title = {Microbiota-induced S100A11-RAGE axis underlies immune evasion in right-sided colon adenomas and is a therapeutic target to boost anti-PD1 efficacy.},
journal = {Gut},
volume = {74},
number = {2},
pages = {214-228},
pmid = {39251326},
issn = {1468-3288},
mesh = {Animals ; *Colonic Neoplasms/immunology/pathology/microbiology/drug therapy ; *Adenoma/immunology/pathology/microbiology/drug therapy ; Mice ; Humans ; *Gastrointestinal Microbiome/immunology ; *S100 Proteins/metabolism ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; *Receptor for Advanced Glycation End Products/metabolism ; Myeloid-Derived Suppressor Cells/immunology ; Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Goblet Cells ; *Immune Evasion ; },
abstract = {BACKGROUND: Tumourigenesis in right-sided and left-sided colons demonstrated distinct features.

OBJECTIVE: We aimed to characterise the differences between the left-sided and right-sided adenomas (ADs) representing the early stage of colonic tumourigenesis.

DESIGN: Single-cell and spatial transcriptomic datasets were analysed to reveal alterations between right-sided and left-sided colon ADs. Cells, animal experiments and clinical specimens were used to verify the results.

RESULTS: Single-cell analysis revealed that in right-sided ADs, there was a significant reduction of goblet cells, and these goblet cells were dysfunctional with attenuated mucin biosynthesis and defective antigen presentation. An impairment of the mucus barrier led to biofilm formation in crypts and subsequent bacteria invasion into right-sided ADs. The regions spatially surrounding the crypts with biofilm occupation underwent an inflammatory response by lipopolysaccharide (LPS) and an apoptosis process, as revealed by spatial transcriptomics. A distinct S100A11[+] epithelial cell population in the right-sided ADs was identified, and its expression level was induced by bacterial LPS and peptidoglycan. S100A11 expression facilitated tumour growth in syngeneic immunocompetent mice with increased myeloid-derived suppressor cells (MDSC) but reduced cytotoxic CD8+ T cells. Targeting S100A11 with well-tolerated antagonists of its receptor for advanced glycation end product (RAGE) (Azeliragon) significantly impaired tumour growth and MDSC infiltration, thereby boosting the efficacy of anti-programmed cell death protein 1 therapy in colon cancer.

CONCLUSION: Our findings unravelled that dysfunctional goblet cells and consequential bacterial translocation activated the S100A11-RAGE axis in right-sided colon ADs, which recruits MDSCs to promote immune evasion. Targeting this axis by Azeliragon improves the efficacy of immunotherapy in colon cancer.},
}

Animals
*Colonic Neoplasms/immunology/pathology/microbiology/drug therapy
*Adenoma/immunology/pathology/microbiology/drug therapy
Mice
Humans
*Gastrointestinal Microbiome/immunology
*S100 Proteins/metabolism
Programmed Cell Death 1 Receptor/antagonists & inhibitors
*Receptor for Advanced Glycation End Products/metabolism
Myeloid-Derived Suppressor Cells/immunology
Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Goblet Cells
*Immune Evasion

@article {pmid39254049,
year = {2024},
author = {Harris, RM and Pace, F and Kuntz, TM and Morgan, XC and Hyland, P and Summers, K and McDermott, E and Blumen, K and Watnick, PI},
title = {Testosterone treatment impacts the intestinal microbiome of transgender individuals.},
journal = {mSphere},
volume = {9},
number = {10},
pages = {e0055724},
pmid = {39254049},
issn = {2379-5042},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Testosterone ; Male ; *Transgender Persons ; Female ; Pilot Projects ; *Feces/microbiology ; Adult ; Metagenomics ; Middle Aged ; Glutamic Acid/metabolism ; Bacteria/classification/genetics/drug effects/metabolism/isolation & purification ; },
abstract = {Medical modulation of sex hormone levels is a cornerstone of treatment for many conditions that impact well-being, including cancer, fertility/infertility, gender dysphoria, and chronic metabolic diseases such as diabetes and obesity. The microbial residents of the intestine, known as the microbiota, interact with sex hormones in the intestine, and there is correlative evidence that this interaction is bidirectional. Based on these published findings, we hypothesized that transgender individuals receiving exogenous testosterone as part of their gender-affirming medical treatment might undergo changes in their intestinal microbiome. To test this, we collected 26 stool samples from nine individuals before and up to 8 months after initiation of treatment with exogenous testosterone and subjected these samples to metagenomic analysis. While no species were significantly associated with the duration of testosterone therapy, pathways that generate glutamate increased in abundance, while those that consume glutamate decreased. Glutamate is a precursor of arginine, and testosterone is known to increase levels of arginine and its metabolites in the plasma. We hypothesize that testosterone increases the uptake of glutamate by enterocytes, thus decreasing access of the microbiota to this amino acid. While this pilot study establishes the impact of testosterone therapy on the intestinal microbiome, a more comprehensive study is necessary to establish the impact of testosterone-driven metagenomic shifts on the stool metatranscriptome, the stool metabolome, and the plasma metabolome.IMPORTANCEThe human intestine is inhabited by a large community of microbes known as the microbiome. Members of the microbiome consume the diet along with their human host. Thus, the metabolomes of the host and microbe are intricately linked. Testosterone alters the plasma metabolome. In particular, plasma levels of arginine and its metabolites and testosterone are positively correlated. To investigate the impact of exogenous testosterone on the microbiome, we analyzed the stool metagenomes of transgender individuals before and after the initiation of testosterone treatment. In this pilot project, we found a modest impact on the microbiome community structure but an increase in the abundance of metabolic pathways that generate glutamate and spare glutamate consumption. We propose that the host uses glutamate to generate arginine, decreasing the amount available for the microbiome.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Testosterone
Male
*Transgender Persons
Female
Pilot Projects
*Feces/microbiology
Adult
Metagenomics
Middle Aged
Glutamic Acid/metabolism
Bacteria/classification/genetics/drug effects/metabolism/isolation & purification

@article {pmid39255040,
year = {2024},
author = {Sanches Santos Rizzo Zuttion, M and Parimon, T and Bora, SA and Yao, C and Lagree, K and Gao, CA and Wunderink, RG and Kitsios, GD and Morris, A and Zhang, Y and McVerry, BJ and Modes, ME and Marchevsky, AM and Stripp, BR and Soto, CM and Wang, Y and Merene, K and Cho, S and Victor, BL and Vujkovic-Cvijin, I and Gupta, S and Cassel, SL and Sutterwala, FS and Devkota, S and Underhill, DM and Chen, P},
title = {Antibiotic use during influenza infection augments lung eosinophils that impair immunity against secondary bacterial pneumonia.},
journal = {The Journal of clinical investigation},
volume = {134},
number = {21},
pages = {},
pmid = {39255040},
issn = {1558-8238},
support = {R03 HL162655/HL/NHLBI NIH HHS/United States ; F32 HL162377/HL/NHLBI NIH HHS/United States ; K23 HL169815/HL/NHLBI NIH HHS/United States ; U19 AI135964/AI/NIAID NIH HHS/United States ; P01 HL154998/HL/NHLBI NIH HHS/United States ; U01 TR003528/TR/NCATS NIH HHS/United States ; KL2 TR001882/TR/NCATS NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; R01 HL164177/HL/NHLBI NIH HHS/United States ; R01 HL159953/HL/NHLBI NIH HHS/United States ; P01 HL114453/HL/NHLBI NIH HHS/United States ; R01 LM013337/LM/NLM NIH HHS/United States ; R01 HL155759/HL/NHLBI NIH HHS/United States ; R01 HL163646/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Eosinophils/immunology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Methicillin-Resistant Staphylococcus aureus/immunology ; *Lung/immunology/pathology ; *Influenza, Human/immunology/drug therapy ; Female ; *Orthomyxoviridae Infections/immunology/drug therapy ; Male ; Pneumonia, Bacterial/immunology/drug therapy ; Pneumonia, Staphylococcal/immunology/drug therapy ; },
abstract = {A leading cause of mortality after influenza infection is the development of a secondary bacterial pneumonia. In the absence of a bacterial superinfection, prescribing antibacterial therapies is not indicated but has become a common clinical practice for those presenting with a respiratory viral illness. In a murine model, we found that antibiotic use during influenza infection impaired the lung innate immunologic defenses toward a secondary challenge with methicillin-resistant Staphylococcus aureus (MRSA). Antibiotics augment lung eosinophils, which have inhibitory effects on macrophage function through the release of major basic protein. Moreover, we demonstrated that antibiotic treatment during influenza infection caused a fungal dysbiosis that drove lung eosinophilia and impaired MRSA clearance. Finally, we evaluated 3 cohorts of hospitalized patients and found that eosinophils positively correlated with antibiotic use, systemic inflammation, and worsened outcomes. Altogether, our work demonstrates a detrimental effect of antibiotic treatment during influenza infection that has harmful immunologic consequences via recruitment of eosinophils to the lungs, thereby increasing the risk of developing a secondary bacterial infection.},
}

Animals
Mice
*Eosinophils/immunology
Humans
*Anti-Bacterial Agents/pharmacology
*Methicillin-Resistant Staphylococcus aureus/immunology
*Lung/immunology/pathology
*Influenza, Human/immunology/drug therapy
Female
*Orthomyxoviridae Infections/immunology/drug therapy
Male
Pneumonia, Bacterial/immunology/drug therapy
Pneumonia, Staphylococcal/immunology/drug therapy

@article {pmid39255394,
year = {2024},
author = {Ginsberg, SD and Blaser, MJ},
title = {Alzheimer's Disease Has Its Origins in Early Life via a Perturbed Microbiome.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {Supplement_2},
pages = {S141-S149},
pmid = {39255394},
issn = {1537-6613},
support = {//Emch Foundation/ ; //Infectious Diseases Society of America/ ; U01 AI122285/AI/NIAID NIH HHS/United States ; RF1 AG077103/AG/NIA NIH HHS/United States ; U01 AI122285/NH/NIH HHS/United States ; P01 AG014449/AG/NIA NIH HHS/United States ; R01 AG074004/AG/NIA NIH HHS/United States ; R01 AG072599/AG/NIA NIH HHS/United States ; //C & D Fund/ ; },
mesh = {Animals ; Humans ; *Alzheimer Disease/microbiology/physiopathology ; Anti-Bacterial Agents/administration & dosage/adverse effects ; Brain/microbiology/pathology/physiopathology ; *Gastrointestinal Microbiome/drug effects/physiology ; Disease Models, Animal ; Brain-Gut Axis/drug effects/physiology ; },
abstract = {Alzheimer's disease (AD) is a neurodegenerative disorder with limited therapeutic options. Accordingly, new approaches for prevention and treatment are needed. One focus is the human microbiome, the consortium of microorganisms that live in and on us, which contributes to human immune, metabolic, and cognitive development and that may have mechanistic roles in neurodegeneration. AD and Alzheimer's disease-related dementias (ADRD) are recognized as spectrum disorders with complex pathobiology. AD/ADRD onset begins before overt clinical signs, but initiation triggers remain undefined. We posit that disruption of the normal gut microbiome in early life leads to a pathological cascade within septohippocampal and cortical brain circuits. We propose investigation to understand how early-life microbiota changes may lead to hallmark AD pathology in established AD/ADRD models. Specifically, we hypothesize that antibiotic exposure in early life leads to exacerbated AD-like disease endophenotypes that may be amenable to specific microbiological interventions. We propose suitable models for testing these hypotheses.},
}

Animals
Humans
*Alzheimer Disease/microbiology/physiopathology
Anti-Bacterial Agents/administration & dosage/adverse effects
Brain/microbiology/pathology/physiopathology
*Gastrointestinal Microbiome/drug effects/physiology
Disease Models, Animal
Brain-Gut Axis/drug effects/physiology

@article {pmid39256189,
year = {2024},
author = {Yılmaz, SS and Kuşkucu, MA and Çakan, H and Aygün, G},
title = {Effective use of skin microbiome signatures for fingerprint identification.},
journal = {Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)},
volume = {30},
number = {9},
pages = {e70052},
pmid = {39256189},
issn = {1600-0846},
support = {28100//Research Fund of Istanbul University-Cerrahpaşa/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Skin/microbiology ; Adult ; Male ; Female ; Staphylococcus epidermidis/isolation & purification/genetics ; Ribotyping/methods ; Dermatoglyphics ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Minisatellite Repeats ; },
abstract = {BACKGROUND: Recent advances have increased the importance of the human microbiome, including the skin microbiome. Despite the hand microbiome research, the factors affecting the composition of the hand microbiome and their personal characteristics are incompletely known.

OBJECTIVES: Despite changing environmental factors and personal variation, we aimed to indicate the interpersonal distinction between skin microbiota using simple and rapid molecular methods.

METHODS: Over a non-consecutive 10-day period, samples were taken from 10 adult individuals, and ribotyping analysis of the 16S and 23S genes of S. epidermidis was performed on each skin sample. Additionally, EcoRI and HindIII enzyme reactions and variable number tandem repeat (VNTR) reactions of S. epidermidis obtained from DNA samples were performed. The skin microbiomes of individuals were evaluated along with the microbiome profiles left on the surfaces they touched.

RESULTS: In the environmental samples taken, it has been observed that people preserve their core skin microbiota characters and carry them to their environment. It was determined that the highest similarity rate was 77.14%, and the lowest similarity rate was 31.74%.

CONCLUSION: Our study showed that the core skin microbiota retains its characteristics and leaves traces in environments. The fact that the personal microbiome remains unchanged despite environmental differences and has characteristic features has shown that it can be used in forensic sciences to distinguish individuals from each other. These results with simple and rapid methods further increased the importance and significance of the study. The findings indicate that personal skin microbiota can provide a significant contribution to criminal investigations by increasing accuracy and reliability, especially in forensic analyses.},
}

Humans
*Microbiota/genetics
*Skin/microbiology
Adult
Male
Female
Staphylococcus epidermidis/isolation & purification/genetics
Ribotyping/methods
Dermatoglyphics
RNA, Ribosomal, 16S/genetics
Young Adult
Minisatellite Repeats

@article {pmid39256307,
year = {2024},
author = {Rastegar, S and Skurnik, M and Niaz, H and Tadjrobehkar, O and Samareh, A and Hosseini-Nave, H and Sabouri, S},
title = {Isolation, characterization, and potential application of Acinetobacter baumannii phages against extensively drug-resistant strains.},
journal = {Virus genes},
volume = {60},
number = {6},
pages = {725-736},
pmid = {39256307},
issn = {1572-994X},
support = {KMU.AC.IR.400000652//Hossein Hosseini-Nave1/ ; },
mesh = {*Acinetobacter baumannii/virology/drug effects ; *Genome, Viral/genetics ; *Bacteriophages/genetics/isolation & purification/classification/physiology ; *Drug Resistance, Multiple, Bacterial ; *Host Specificity ; *Anti-Bacterial Agents/pharmacology ; Acinetobacter Infections/microbiology ; Phage Therapy ; Sewage/virology/microbiology ; Humans ; },
abstract = {One of the significant issues in treating bacterial infections is the increasing prevalence of extensively drug-resistant (XDR) strains of Acinetobacter baumannii. In the face of limited or no viable treatment options for extensively drug-resistant (XDR) bacteria, there is a renewed interest in utilizing bacteriophages as a treatment option. Three Acinetobacter phages (vB_AbaS_Ftm, vB_AbaS_Eva, and vB_AbaS_Gln) were identified from hospital sewage and analyzed for their morphology, host ranges, and their genome sequences were determined and annotated. These phages and vB_AbaS_SA1 were combined to form a phage cocktail. The antibacterial effects of this cocktail and its combinations with selected antimicrobial agents were evaluated against the XDR A. baumannii strains. The phages exhibited siphovirus morphology. Out of a total of 30 XDR A. baumannii isolates, 33% were sensitive to vB_AbaS_Ftm, 30% to vB_AbaS_Gln, and 16.66% to vB_AbaS_Eva. When these phages were combined with antibiotics, they demonstrated a synergistic effect. The genome sizes of vB_AbaS_Ftm, vB_AbaS_Eva, and vB_AbaS_Gln were 48487, 50174, and 50043 base pairs (bp), respectively, and showed high similarity. Phage cocktail, when combined with antibiotics, showed synergistic effects on extensively drug-resistant (XDR) strains of A. baumannii. However, the need for further study to fully understand the mechanisms of action and potential limitations of using these phages is highlighted.},
}

*Acinetobacter baumannii/virology/drug effects
*Genome, Viral/genetics
*Bacteriophages/genetics/isolation & purification/classification/physiology
*Drug Resistance, Multiple, Bacterial
*Host Specificity
*Anti-Bacterial Agents/pharmacology
Acinetobacter Infections/microbiology
Phage Therapy
Sewage/virology/microbiology
Humans

@article {pmid39271424,
year = {2024},
author = {Bokulich, NA and Robeson, MS},
title = {Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.},
journal = {Trends in microbiology},
volume = {32},
number = {12},
pages = {1163-1166},
doi = {10.1016/j.tim.2024.08.011},
pmid = {39271424},
issn = {1878-4380},
support = {R01 CA143130/CA/NCI NIH HHS/United States ; R01 CA245083/CA/NCI NIH HHS/United States ; R01 CA282198/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; *Computational Biology/methods ; *Metagenomics/methods ; *Machine Learning ; Sequence Analysis, DNA/methods ; },
abstract = {Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.},
}

Humans
*Neoplasms/microbiology
*Microbiota
*Computational Biology/methods
*Metagenomics/methods
*Machine Learning
Sequence Analysis, DNA/methods

@article {pmid39273475,
year = {2024},
author = {Larson, J and Sather, B and Wang, L and Westrum, J and Tokmina-Lukaszewska, M and Pauley, J and Copié, V and McDermott, TR and Bothner, B},
title = {Metalloproteomics Reveals Multi-Level Stress Response in Escherichia coli When Exposed to Arsenite.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273475},
issn = {1422-0067},
support = {P42ES031007//University of North Carolina's Superfund Program/ ; DE-SC0020246//U.S. Department of Energy/ ; S10 OD028650/OD/NIH HHS/United States ; MCB 1714556//National Science Foundation/ ; P42 ES031007/ES/NIEHS NIH HHS/United States ; R24 GM137786/GM/NIGMS NIH HHS/United States ; R24GM137786/GM/NIGMS NIH HHS/United States ; P20 GM103474/GM/NIGMS NIH HHS/United States ; },
mesh = {*Arsenites/toxicity ; *Escherichia coli/genetics/metabolism/drug effects ; *Escherichia coli Proteins/genetics/metabolism ; *Proteomics/methods ; *Stress, Physiological ; *Gene Expression Regulation, Bacterial/drug effects ; *Operon/genetics ; Metalloproteins/metabolism/genetics ; Humans ; },
abstract = {The arsRBC operon encodes a three-protein arsenic resistance system. ArsR regulates the transcription of the operon, while ArsB and ArsC are involved in exporting trivalent arsenic and reducing pentavalent arsenic, respectively. Previous research into Agrobacterium tumefaciens 5A has demonstrated that ArsR has regulatory control over a wide range of metal-related proteins and metabolic pathways. We hypothesized that ArsR has broad regulatory control in other Gram-negative bacteria and set out to test this. Here, we use differential proteomics to investigate changes caused by the presence of the arsR gene in human microbiome-relevant Escherichia coli during arsenite (As[III]) exposure. We show that ArsR has broad-ranging impacts such as the expression of TCA cycle enzymes during As[III] stress. Additionally, we found that the Isc [Fe-S] cluster and molybdenum cofactor assembly proteins are upregulated regardless of the presence of ArsR under these same conditions. An important finding from this differential proteomics analysis was the identification of response mechanisms that were strain-, ArsR-, and arsenic-specific, providing new clarity to this complex regulon. Given the widespread occurrence of the arsRBC operon, these findings should have broad applicability across microbial genera, including sensitive environments such as the human gastrointestinal tract.},
}

*Arsenites/toxicity
*Escherichia coli/genetics/metabolism/drug effects
*Escherichia coli Proteins/genetics/metabolism
*Proteomics/methods
*Stress, Physiological
*Gene Expression Regulation, Bacterial/drug effects
*Operon/genetics
Metalloproteins/metabolism/genetics
Humans

@article {pmid39283061,
year = {2024},
author = {McBurney, MI and Cho, CE},
title = {Understanding the role of the human gut microbiome in overweight and obesity.},
journal = {Annals of the New York Academy of Sciences},
volume = {1540},
number = {1},
pages = {61-88},
doi = {10.1111/nyas.15215},
pmid = {39283061},
issn = {1749-6632},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Obesity/microbiology/metabolism ; *Overweight/microbiology ; Probiotics ; Prebiotics/administration & dosage ; Fecal Microbiota Transplantation ; Diet ; },
abstract = {The gut microbiome may be related to the prevalence of overweight and obesity, but high interindividual variability of the human microbiome complicates our understanding. Obesity often occurs concomitantly with micronutrient deficiencies that impair energy metabolism. Microbiota composition is affected by diet. Host-microbiota interactions are bidirectional. We propose three pathways whereby these interactions may modulate the gut microbiome and obesity: (1) ingested compounds or derivatives affecting small intestinal transit, endogenous secretions, digestion, absorption, microbiome balance, and gut barrier function directly affect host metabolism; (2) substrate availability affecting colonic microbial composition and contact with the gut barrier; and (3) microbial end products affecting host metabolism. The quantity/concentration, duration, and/or frequency (circadian rhythm) of changes in these pathways can alter the gut microbiome, disrupt the gut barrier, alter host immunity, and increase the risk of and progression to overweight and obesity. Host-specific characteristics (e.g., genetic variations) may further affect individual sensitivity and/or resilience to diet- and microbiome-associated perturbations in the colonic environment. In this narrative review, the effects of selected interventions, including fecal microbiota transplantation, dietary calorie restriction, dietary fibers and prebiotics, probiotics and synbiotics, vitamins, minerals, and fatty acids, on the gut microbiome, body weight, and/or adiposity are summarized to help identify mechanisms of action and research opportunities.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Obesity/microbiology/metabolism
*Overweight/microbiology
Probiotics
Prebiotics/administration & dosage
Fecal Microbiota Transplantation
Diet

@article {pmid39292000,
year = {2024},
author = {Kilgore, PB and Sha, J and Hendrix, EK and Neil, BH and Lawrence, WS and Peel, JE and Hittle, L and Woolston, J and Sulakvelidze, A and Schwartz, JA and Chopra, AK},
title = {A bacteriophage cocktail targeting Yersinia pestis provides strong post-exposure protection in a rat pneumonic plague model.},
journal = {Microbiology spectrum},
volume = {12},
number = {11},
pages = {e0094224},
pmid = {39292000},
issn = {2165-0497},
support = {T32 AI141349/AI/NIAID NIH HHS/United States ; HHSN272201700040I/AI/NIAID NIH HHS/United States ; T32 AI060549/AI/NIAID NIH HHS/United States ; AI 141349//HHS | National Institutes of Health (NIH)/ ; HHSN272201700040I/75N93022F00003//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Yersinia pestis ; *Plague/prevention & control/microbiology ; Rats ; *Bacteriophages/physiology/genetics ; *Disease Models, Animal ; *Phage Therapy/methods ; Female ; Post-Exposure Prophylaxis/methods ; },
abstract = {Yersinia pestis, one of the deadliest bacterial pathogens ever known, is responsible for three plague pandemics and several epidemics, with over 200 million deaths during recorded history. Due to high genomic plasticity, Y. pestis is amenable to genetic mutations as well as genetic engineering that can lead to the emergence or intentional development of pan-drug-resistant strains. Indeed, antibiotic-resistant strains (e.g., strains carrying multidrug-resistant or MDR plasmids) have been isolated in various countries and endemic areas. Thus, there is an urgent need to develop novel, safe, and effective treatment approaches for managing Y. pestis infections. This includes infections by antigenically distinct strains for which vaccines (none FDA approved yet) may not be effective and those that cannot be managed by currently available antibiotics. Lytic bacteriophages provide one such alternative approach. In this study, we examined post-exposure efficacy of a bacteriophage cocktail, YPP-401, to combat pneumonic plague caused by Y. pestis CO92. YPP-401 is a four-phage preparation effective against a panel of at least 68 genetically diverse Y. pestis strains. Using a pneumonic plague aerosol challenge model in gender-balanced Brown Norway rats, YPP-401 demonstrated ~88% protection when delivered 18 h post-exposure for each of two administration routes (i.e., intraperitoneal and intranasal) in a dose-dependent manner. Our studies provide proof-of-concept that YPP-401 could be an innovative, safe, and effective approach for managing Y. pestis infections, including those caused by naturally occurring or intentionally developed multidrug-resistant strains.IMPORTANCECurrently, there are no FDA-approved plague vaccines. Since antibiotic-resistant strains of Y. pestis have emerged or are being intentionally developed to be used as a biothreat agent, new treatment modalities are direly needed. Phage therapy provides a viable option against potentially antibiotic-resistant strains. Additionally, phages are nontoxic and have been approved by the FDA for use in the food industry. Our study provides the first evidence of the protective effect of a cocktail of four phages against pneumonic plague, the most severe form of disease. When treatment was initiated 18 h post infection by either the intranasal or intraperitoneal route in Brown Norway rats, up to 87.5% protection was observed. The phage cocktail had a minimal impact on a representative human microbiome panel, unlike antibiotics. This study provides strong proof-of-concept data for the further development of phage-based therapy to treat plague.},
}

Animals
*Yersinia pestis
*Plague/prevention & control/microbiology
Rats
*Bacteriophages/physiology/genetics
*Disease Models, Animal
*Phage Therapy/methods
Female
Post-Exposure Prophylaxis/methods

@article {pmid39295776,
year = {2022},
author = {Puhlmann, ML and Jokela, R and van Dongen, KCW and Bui, TPN and van Hangelbroek, RWJ and Smidt, H and de Vos, WM and Feskens, EJM},
title = {Dried chicory root improves bowel function, benefits intestinal microbial trophic chains and increases faecal and circulating short chain fatty acids in subjects at risk for type 2 diabetes.},
journal = {Gut microbiome (Cambridge, England)},
volume = {3},
number = {},
pages = {e4},
pmid = {39295776},
issn = {2632-2897},
abstract = {We investigated the impact of dried chicory root in a randomised, placebo-controlled trial with 55 subjects at risk for type 2 diabetes on bowel function, gut microbiota and its products, and glucose homeostasis. The treatment increased stool softness (+1.1 ± 0.3 units; p = 0.034) and frequency (+0.6 ± 0.2 defecations/day; p < 0.001), strongly modulated gut microbiota composition (7 % variation; p = 0.001), and dramatically increased relative levels (3-4-fold) of Anaerostipes and Bifidobacterium spp., in a dose-dependent, reversible manner. A synthetic community, including selected members of these genera and a Bacteroides strain, generated a butyrogenic trophic chain from the product. Faecal acetate, propionate and butyrate increased by 25.8 % (+13.0 ± 6.3 mmol/kg; p = 0.023) as did their fasting circulating levels by 15.7 % (+7.7 ± 3.9 μM; p = 0.057). In the treatment group the glycaemic coefficient of variation decreased from 21.3 ± 0.94 to 18.3 ± 0.84 % (p = 0.004), whereas fasting glucose and HOMA-ir decreased in subjects with low baseline Blautia levels (-0.3 ± 0.1 mmol/L fasting glucose; p = 0.0187; -0.14 ± 0.1 HOMA-ir; p = 0.045). Dried chicory root intake rapidly and reversibly affects bowel function, benefits butyrogenic trophic chains, and promotes glycaemic control.},
}

@article {pmid39295904,
year = {2023},
author = {Ruxton, CHS and Kajita, C and Rocca, P and Pot, B},
title = {Microbiota and probiotics: chances and challenges - a symposium report.},
journal = {Gut microbiome (Cambridge, England)},
volume = {4},
number = {},
pages = {e6},
pmid = {39295904},
issn = {2632-2897},
abstract = {The 10th International Yakult Symposium was held in Milan, Italy, on 13-14 October 2022. Two keynote lectures covered the crewed journey to space and its implications for the human microbiome, and how current regulatory systems can be adapted and updated to ensure the safety of microorganisms used as probiotics or food processing ingredients. The remaining lectures were split into sections entitled "Chances" and "Challenges." The "Chances" section explored opportunities for the science of probiotics and fermented foods to contribute to diverse areas of health such as irritable bowel syndrome, major depression, Parkinson's disease, immune dysfunction, infant colic, intensive care, respiratory infections, and promoting healthy longevity. The "Challenges" section included selecting appropriate clinical trial participants and methodologies to minimise heterogeneity in responses, how to view probiotics in the context of One Health, adapting regulatory frameworks, and understanding how substances of bacterial origin can cross the blood-brain barrier. The symposium provided evidence from cutting-edge research that gut eubiosis is vital for human health and, like space, the microbiota deserves further exploration of its vast potential.},
}

@article {pmid39295911,
year = {2023},
author = {Panwar, S and Kumari, S and Verma, J and Bakshi, S and Narendrakumar, L and Paul, D and Das, B},
title = {Toxin-linked mobile genetic elements in major enteric bacterial pathogens.},
journal = {Gut microbiome (Cambridge, England)},
volume = {4},
number = {},
pages = {e5},
pmid = {39295911},
issn = {2632-2897},
abstract = {One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.},
}

@article {pmid39296724,
year = {2020},
author = {Hill, C},
title = {You have the microbiome you deserve.},
journal = {Gut microbiome (Cambridge, England)},
volume = {1},
number = {},
pages = {e3},
pmid = {39296724},
issn = {2632-2897},
abstract = {The human microbiome is one of the most exciting areas of microbiology. From a starting point of tens of papers annually a couple of decades ago, there are now thousands of papers published every year on the microbiome. Huge strides have been made in terms of defining the individual members of complex human microbiomes from different body sites. The individuality and diversity of the human microbiome almost surpasses our ability to comprehend it. Advances in metagenomics and computational sciences have increased the complexity of the field, while at the same time we have moved from regarding the human microbiome as a benign passenger to a situation where it has been linked to almost every chronic disease, including obesity, cancer and infectious disease. The microbiome tantalizes us with the promise of novel therapeutic molecules and modalities for a range of intractable diseases. And yet, very few microbiome-based therapies have made it to the clinic or the pharmacy and we still cannot really define a healthy microbiome. We are entering the most exciting phase of microbiome research, as we develop effective, evidence-based interventions to preserve and restore human health. But we need rigour and numeracy if we are to realize this vision.},
}

@article {pmid39298326,
year = {2024},
author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T},
title = {Establishing human microbial observatory programs in low- and middle-income countries.},
journal = {Annals of the New York Academy of Sciences},
volume = {1540},
number = {1},
pages = {13-20},
doi = {10.1111/nyas.15224},
pmid = {39298326},
issn = {1749-6632},
support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Developing Countries ; Global Health ; *Microbiota ; },
abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.},
}

Humans
*Developing Countries
Global Health
*Microbiota

@article {pmid39300165,
year = {2024},
author = {Bisht, V and Das, B and Hussain, A and Kumar, V and Navani, NK},
title = {Understanding of probiotic origin antimicrobial peptides: a sustainable approach ensuring food safety.},
journal = {NPJ science of food},
volume = {8},
number = {1},
pages = {67},
pmid = {39300165},
issn = {2396-8370},
abstract = {The practice of preserving and adding value to food dates back to over 10,000 BCE, when unintentional microbial-driven chemical reactions imparted flavor and extended the shelf life of fermented foods. The process evolved, and with the urbanization of society, significant shifts in dietary habits emerged, accompanied by sporadic food poisoning incidents. The repercussions of the COVID-19 pandemic have intensified the search for antibiotic alternatives owing to the rise in antibiotic-resistant pathogens, emphasizing the exploration of probiotic-origin antimicrobial peptides to alleviate human microbiome collateral damage. Often termed 'molecular knives', these peptides outstand as potent antimicrobials due to their compatibility with innate microflora, amenability to bioengineering, target specificity, versatility and rapidity in molecular level mode of action. This review centres on bacteriocins sourced from lactic acid bacteria found in ethnic fermented foods, accentuating their desirable attributes, technological applications as nanobiotics and potential future applications in the modern context of ensuring food safety.},
}

@article {pmid39303118,
year = {2024},
author = {Doré, J and Sansonetti, PJ},
title = {[The human microbiome: 340 years of history, 140 years of interrogations, technological innovations and emergence of "microbial medicine"].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {8-9},
pages = {654-660},
doi = {10.1051/medsci/2024101},
pmid = {39303118},
issn = {1958-5381},
mesh = {Humans ; Gastrointestinal Microbiome/physiology ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Inventions/history/trends ; *Microbiota/physiology ; Symbiosis ; History, 17th Century ; },
abstract = {For 350 years, we have known that the human body hosts microbes, then called "animalcules". For over a century, following the demonstration of the role of some of these microbes in diseases, questions have arisen about the role of the largely predominant ones colonizing human skin and mucous surfaces, particularly the rich microbial ecosystem of the intestine, the gut microbiota. From the invention of germ-free life - axenism - which experimentally validated the human-microbe symbiosis, resulting from a long coevolution, to the development of anaerobic culture methods, then to the invention of molecular diagnosis, deep sequencing opening up metagenomic and omics approaches in general, a remarkable race has taken place between technological innovations and conceptual advances. This race, beyond the exhaustive description of the microbiota in its intra- and inter-human diversity, and the essential symbiotic functions of the microbiome, has paved the way for a new field of medicine: microbial medicine.},
}

Humans
Gastrointestinal Microbiome/physiology
History, 18th Century
History, 19th Century
History, 20th Century
History, 21st Century
Inventions/history/trends
*Microbiota/physiology
Symbiosis
History, 17th Century

@article {pmid39304775,
year = {2024},
author = {Ray, K},
title = {A resource for the food microbiome and its links with the human microbiome.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {21},
number = {11},
pages = {746},
pmid = {39304775},
issn = {1759-5053},
}

@article {pmid39306588,
year = {2025},
author = {Sahin, TK and Sonmezer, MC},
title = {The role of the microbiome in head and neck squamous cell cancers.},
journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery},
volume = {282},
number = {2},
pages = {623-637},
pmid = {39306588},
issn = {1434-4726},
mesh = {Humans ; *Microbiota ; *Squamous Cell Carcinoma of Head and Neck/microbiology/therapy ; *Head and Neck Neoplasms/microbiology/therapy ; },
abstract = {The human microbiome has garnered tremendous interest in the field of oncology, and microbiota studies in head and neck oncology has also flourished. Given the increasing incidence and mortality of HNSCC, as well as the suboptimal outcomes of available treatments, there is an urgent need for innovative approaches involving the microbiome. This review evaluates the intricate relationship between the microbiome and HNSCC, highlighting the potential of the microbiome as a marker for cancer detection, its role in malignancy, and its impact on the efficacy of conventional treatments like chemotherapy and radiotherapy. The review also explores the effects of treatment modalities on the microbiome and discusses the potential of microbiome alterations to predict and influence treatment toxicities such as mucositis and xerostomia. Further research is warranted to characterize the microbiome-HNSCC association, which holds promise for advancing early diagnosis, enhancing prognostic accuracy, and personalizing treatment strategies to improve patient outcomes. The exploration of the microbiome in clinical trials indicates a burgeoning subject of microbiome-focused therapies, heralding a new frontier in most cancer care.},
}

Humans
*Microbiota
*Squamous Cell Carcinoma of Head and Neck/microbiology/therapy
*Head and Neck Neoplasms/microbiology/therapy

@article {pmid39307902,
year = {2024},
author = {Ma, Z and Zuo, T and Frey, N and Rangrez, AY},
title = {A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation.},
journal = {Signal transduction and targeted therapy},
volume = {9},
number = {1},
pages = {237},
pmid = {39307902},
issn = {2059-3635},
support = {RA 2717/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1289/17-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Probiotics/therapeutic use ; Symbiosis/genetics ; },
abstract = {The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.},
}

Humans
*Microbiota/genetics
Probiotics/therapeutic use
Symbiosis/genetics

@article {pmid39313228,
year = {2024},
author = {Kirtipal, N and Seo, Y and Son, J and Lee, S},
title = {Systems Biology of Human Microbiome for the Prediction of Personal Glycaemic Response.},
journal = {Diabetes & metabolism journal},
volume = {48},
number = {5},
pages = {821-836},
pmid = {39313228},
issn = {2233-6087},
support = {//Ministry of Science ICT/ ; 2021R1C1C1006336//National Research Foundation of Korea/ ; 2021M3A9G8022959//National Research Foundation of Korea/ ; RS-2024-00419699//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; HR22C141105//Ministry of Health and Welfare/ ; 2024-ER2108-00//Korea National Institute of Health/ ; 2024-ER0608-00//Korea National Institute of Health/ ; //GIST Research Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Precision Medicine/methods ; *Systems Biology/methods ; Machine Learning ; Dysbiosis ; Blood Glucose/analysis ; Diabetes Mellitus/microbiology ; Diabetes Mellitus, Type 2/microbiology ; Hypoglycemic Agents/therapeutic use ; },
abstract = {The human gut microbiota is increasingly recognized as a pivotal factor in diabetes management, playing a significant role in the body's response to treatment. However, it is important to understand that long-term usage of medicines like metformin and other diabetic treatments can result in problems, gastrointestinal discomfort, and dysbiosis of the gut flora. Advanced sequencing technologies have improved our understanding of the gut microbiome's role in diabetes, uncovering complex interactions between microbial composition and metabolic health. We explore how the gut microbiota affects glucose metabolism and insulin sensitivity by examining a variety of -omics data, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. Machine learning algorithms and genome-scale modeling are now being applied to find microbiological biomarkers associated with diabetes risk, predicted disease progression, and guide customized therapy. This study holds promise for specialized diabetic therapy. Despite significant advances, some concerns remain unanswered, including understanding the complex relationship between diabetes etiology and gut microbiota, as well as developing user-friendly technological innovations. This mini-review explores the relationship between multiomics, precision medicine, and machine learning to improve our understanding of the gut microbiome's function in diabetes. In the era of precision medicine, the ultimate goal is to improve patient outcomes through personalized treatments.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Precision Medicine/methods
*Systems Biology/methods
Machine Learning
Dysbiosis
Blood Glucose/analysis
Diabetes Mellitus/microbiology
Diabetes Mellitus, Type 2/microbiology
Hypoglycemic Agents/therapeutic use

@article {pmid39315152,
year = {2024},
author = {Zheng, B and Xu, J and Zhang, Y and Qin, J and Yuan, D and Fan, T and Wu, W and Chen, Y and Jiang, Y},
title = {MBCN: A novel reference database for Effcient Metagenomic analysis of human gut microbiome.},
journal = {Heliyon},
volume = {10},
number = {18},
pages = {e37422},
pmid = {39315152},
issn = {2405-8440},
abstract = {Metagenomic shotgun sequencing data can identify microbes and their proportions. But metagenomic shotgun data profiling results obtained from multiple projects using different reference databases are difficult to compare and apply meta-analysis. Our work aims to create a novel collection of human gut prokaryotic genomes, named Microbiome Collection Navigator (MBCN). 2379 human gut metagenomic samples are screened, and 16,785 metagenome-assembled genomes (MAGs) are assembled using a standardized pipeline. In addition, MAGs are combined with the representative genomes from public prokaryotic genomes collections to cluster, and pan-genomes for each cluster's genomes are constructed to build Kraken2 and Bracken databases. The databases built by MBCN are more comprehensive and accurate for profiling metagenomic reads comparing with other collections on simulated reads and virtual bio-projects. We profile 1082 human gut metagenomic samples with MBCN database and organize profiles and metadata on the web program. Meanwhile, using MBCN as a reference database, we also develop a unified, standardized, and systematic metagenomic analysis pipeline and platform, named MicrobiotaCN (http://www.microbiota.cn) and common statistical and visualization tools for microbiome research are integrated into the web program. Taken together, MBCN and MicrobiotaCN can be a valuable resource and a powerful tool that allows researchers to perform metagenomic analysis by a unified pipeline efficiently.},
}

@article {pmid39320132,
year = {2024},
author = {Bosland, MC and Gordon, T and Solomon, JJ and Shore, RE and Lippmann, M},
title = {Seventy-five years of impactful environmental and occupational health research at the Nelson Institute of Environmental Medicine at New York University.},
journal = {Annals of the New York Academy of Sciences},
volume = {1540},
number = {1},
pages = {147-165},
doi = {10.1111/nyas.15226},
pmid = {39320132},
issn = {1749-6632},
mesh = {Humans ; Academies and Institutes/history ; Biomedical Research/history/trends ; *Environmental Health/history ; *Environmental Medicine/history/trends ; History, 20th Century ; History, 21st Century ; New York ; New York City ; *Occupational Health/history ; Universities/history ; },
abstract = {Founded in 1947 as the Institute of Industrial Medicine, the Nelson Institute and Department of Environmental Medicine at New York University (NYU) Grossman School of Medicine (NYUGSOM) was supported by a National Institute of Environmental Health Science (NIEHS) Center Grant for over 56 years. Nelson Institute researchers generated 75 years of impactful research in environmental and occupational health, radiation effects, toxicology, and cancer. Environmental health research is continuing at NYUGSOM in its departments of medicine and population health. The objective of this historical commentary is to highlight the major achievements of the Nelson Institute and the department in the context of its history at facilities in Sterling Forest, Tuxedo, NY and Manhattan, NY. Aspects of our discussion include leadership, physical facilities, and research in many areas, including air pollution, health effects of environmental radiation exposures, inhalation toxicology methodology, carcinogenesis by chemicals, metals, and hormones, cancer chemoprevention, human microbiome, ecotoxicology, epidemiology, biostatistics, and community health concerns. The research of the institute and department benefited from unique facilities, strong leadership focused on team-based science, and outstanding investigators, students, and staff. A major lasting contribution has been the training of hundreds of graduate students and postdoctoral fellows, many of whom have been and are training the next generation of environmental and occupational health researchers at various institutions.},
}

Humans
Academies and Institutes/history
Biomedical Research/history/trends
*Environmental Health/history
*Environmental Medicine/history/trends
History, 20th Century
History, 21st Century
New York
New York City
*Occupational Health/history
Universities/history

@article {pmid39322314,
year = {2024},
author = {Van Hul, M and Cani, PD and Petitfils, C and De Vos, WM and Tilg, H and El-Omar, EM},
title = {What defines a healthy gut microbiome?.},
journal = {Gut},
volume = {73},
number = {11},
pages = {1893-1908},
pmid = {39322314},
issn = {1468-3288},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {The understanding that changes in microbiome composition can influence chronic human diseases and the efficiency of therapies has driven efforts to develop microbiota-centred therapies such as first and next generation probiotics, prebiotics and postbiotics, microbiota editing and faecal microbiota transplantation. Central to microbiome research is understanding how disease impacts microbiome composition and vice versa, yet there is a problematic issue with the term 'dysbiosis', which broadly links microbial imbalances to various chronic illnesses without precision or definition. Another significant issue in microbiome discussions is defining 'healthy individuals' to ascertain what characterises a healthy microbiome. This involves questioning who represents the healthiest segment of our population-whether it is those free from illnesses, athletes at peak performance, individuals living healthily through regular exercise and good nutrition or even elderly adults or centenarians who have been tested by time and achieved remarkable healthy longevity.This review advocates for delineating 'what defines a healthy microbiome?' by considering a broader range of factors related to human health and environmental influences on the microbiota. A healthy microbiome is undoubtedly linked to gut health. Nevertheless, it is very difficult to pinpoint a universally accepted definition of 'gut health' due to the complexities of measuring gut functionality besides the microbiota composition. We must take into account individual variabilities, the influence of diet, lifestyle, host and environmental factors. Moreover, the challenge in distinguishing causation from correlation between gut microbiome and overall health is presented.The review also highlights the resource-heavy nature of comprehensive gut health assessments, which hinders their practicality and broad application. Finally, we call for continued research and a nuanced approach to better understand the intricate and evolving concept of gut health, emphasising the need for more precise and inclusive definitions and methodologies in studying the microbiome.},
}

Humans
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid39322959,
year = {2024},
author = {Wirbel, J and Essex, M and Forslund, SK and Zeller, G},
title = {A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {247},
pmid = {39322959},
issn = {1474-760X},
mesh = {Humans ; *Microbiota ; *Benchmarking ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; },
abstract = {BACKGROUND: In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations.

RESULTS: Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications.

CONCLUSIONS: Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.},
}

Humans
*Microbiota
*Benchmarking
RNA, Ribosomal, 16S/genetics
Computer Simulation

@article {pmid39327438,
year = {2024},
author = {Schmartz, GP and Rehner, J and Gund, MP and Keller, V and Molano, LG and Rupf, S and Hannig, M and Berger, T and Flockerzi, E and Seitz, B and Fleser, S and Schmitt-Grohé, S and Kalefack, S and Zemlin, M and Kunz, M and Götzinger, F and Gevaerd, C and Vogt, T and Reichrath, J and Diehl, L and Hecksteden, A and Meyer, T and Herr, C and Gurevich, A and Krug, D and Hegemann, J and Bozhueyuek, K and Gulder, TAM and Fu, C and Beemelmanns, C and Schattenberg, JM and Kalinina, OV and Becker, A and Unger, M and Ludwig, N and Seibert, M and Stein, ML and Hanna, NL and Martin, MC and Mahfoud, F and Krawczyk, M and Becker, SL and Müller, R and Bals, R and Keller, A},
title = {Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8261},
pmid = {39327438},
issn = {2041-1723},
mesh = {Humans ; *Microbiota/genetics ; *Metagenome/genetics ; *Metagenomics/methods ; Bacteria/genetics/isolation & purification/classification ; Feces/microbiology ; Male ; Female ; Multigene Family ; Saliva/microbiology ; Adult ; },
abstract = {The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.},
}

Humans
*Microbiota/genetics
*Metagenome/genetics
*Metagenomics/methods
Bacteria/genetics/isolation & purification/classification
Feces/microbiology
Male
Female
Multigene Family
Saliva/microbiology
Adult

@article {pmid39331660,
year = {2024},
author = {Pasqualini, J and Facchin, S and Rinaldo, A and Maritan, A and Savarino, E and Suweis, S},
title = {Emergent ecological patterns and modelling of gut microbiomes in health and in disease.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012482},
pmid = {39331660},
issn = {1553-7358},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Models, Biological ; Computational Biology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Models, Biological
Computational Biology
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid39333099,
year = {2024},
author = {Hickman, B and Salonen, A and Ponsero, AJ and Jokela, R and Kolho, KL and de Vos, WM and Korpela, K},
title = {Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8323},
pmid = {39333099},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; *Feces/microbiology ; Female ; Male ; Infant, Newborn ; Cohort Studies ; Longitudinal Studies ; Child, Preschool ; Bifidobacterium/isolation & purification ; Bacteroides/isolation & purification ; },
abstract = {The human gut microbiota is central in regulating all facets of host physiology, and in early life it is thought to influence the host's immune system and metabolism, affecting long-term health. However, longitudinally monitored cohorts with parallel analysis of faecal samples and health data are scarce. In our observational study we describe the gut microbiota development in the first 2 years of life and create a gut microbiota wellbeing index based on the microbiota development and health data in a cohort of nearly 1000 infants using clustering and trajectory modelling. We show that infants' gut microbiota development is highly predictable, following one of five trajectories, dependent on infant exposures, and predictive of later health outcomes. We characterise the natural healthy gut microbiota trajectory and several different dysbiotic trajectories associated with different health outcomes. Bifidobacterium and Bacteroides appear as early keystone organisms, directing microbiota development and consistently predicting positive health outcomes. A microbiota wellbeing index, based on the healthy development trajectory, is predictive of general health over the first 5 years. The results indicate that gut microbiota succession is part of infant physiological development, predictable, and malleable. This information can be utilised to improve the predictions of individual health risks.},
}

Humans
*Gastrointestinal Microbiome/physiology
Infant
*Feces/microbiology
Female
Male
Infant, Newborn
Cohort Studies
Longitudinal Studies
Child, Preschool
Bifidobacterium/isolation & purification
Bacteroides/isolation & purification

@article {pmid39333143,
year = {2024},
author = {Wang, B and Wang, T and Du, X and Li, J and Wang, J and Wu, P},
title = {Microbe-drug association prediction model based on graph convolution and attention networks.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22327},
pmid = {39333143},
issn = {2045-2322},
support = {145209125//Basic scientific research operations of universities affiliated with Heilongjiang Province/ ; },
mesh = {Humans ; *Deep Learning ; Microbiota ; Computational Biology/methods ; Neural Networks, Computer ; Drug Discovery/methods ; Pharmaceutical Preparations ; },
abstract = {The human microbiome plays a key role in drug development and precision medicine, but understanding its complex interactions with drugs remains a challenge. Identifying microbe-drug associations not only enhances our understanding of their mechanisms but also aids in drug discovery and repurposing. Traditional experiments are expensive and time-consuming, making computational methods for predicting microbe-drug associations a new trend. Currently, computational methods specifically designed for this task are still scarce. Therefore, to address the shortcomings of traditional experimental methods in predicting potential microbe-drug associations, this paper proposes a new prediction model named GCNATMDA. The model combines two deep learning models, Graph Convolutional Network and Graph Attention Network, and aims to reveal potential relationships between microbes and drugs by learning related features. Thus improve the efficiency and accuracy of prediction. We first integrated the microbe-drug association matrix from the existing dataset, and then combined the calculated microbe-drug characteristic matrix as the model input. The GCN module is used to dig deeper into the potential characterization of microbes and drugs, while the GAT module further learns the more complex interactions between them and generates the corresponding score matrix. The experimental results show that the GCNATMDA model achieves 96.59% and 93.01% in AUC and AUPR evaluation indexes, respectively, which is significantly better than the existing prediction models. In addition, the reliability of the prediction results is verified by a series of experiments.},
}

Humans
*Deep Learning
Microbiota
Computational Biology/methods
Neural Networks, Computer
Drug Discovery/methods
Pharmaceutical Preparations

@article {pmid39333588,
year = {2024},
author = {Garcia-Vello, P and Tytgat, HLP and Elzinga, J and Van Hul, M and Plovier, H and Tiemblo-Martin, M and Cani, PD and Nicolardi, S and Fragai, M and De Castro, C and Di Lorenzo, F and Silipo, A and Molinaro, A and de Vos, WM},
title = {The lipooligosaccharide of the gut symbiont Akkermansia muciniphila exhibits a remarkable structure and TLR signaling capacity.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8411},
pmid = {39333588},
issn = {2041-1723},
support = {AdG 250172//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Lipopolysaccharides ; *Akkermansia ; Animals ; *Signal Transduction ; *Toll-Like Receptor 4/metabolism ; Humans ; *Toll-Like Receptor 2/metabolism ; Mice ; Symbiosis ; Mice, Inbred C57BL ; Lipid A/metabolism/chemistry ; Interleukin-10/metabolism ; Gastrointestinal Microbiome ; Liver/metabolism/microbiology ; Female ; },
abstract = {The cell-envelope of Gram-negative bacteria contains endotoxic lipopolysaccharides (LPS) that are recognized by the innate immune system via Toll-Like Receptors (TLRs). The intestinal mucosal symbiont Akkermansia muciniphila is known to confer beneficial effects on the host and has a Gram-negative architecture. Here we show that A. muciniphila LPS lacks the O-polysaccharide repeating unit, with the resulting lipooligosaccharide (LOS) having unprecedented structural and signaling properties. The LOS consists of a complex glycan chain bearing two distinct undeca- and hexadecasaccharide units each containing three 2-keto-3-deoxy-D-manno-octulosonic acid (Kdo) residues. The lipid A moiety appears as a mixture of differently phosphorylated and acylated species and carries either linear or branched acyl moieties. Peritoneal injection of the LOS in mice increased higher gene expression of liver TLR2 than TLR4 (100-fold) and induced high IL-10 gene expression. A. muciniphila LOS was found to signal both through TLR4 and TLR2, whereas lipid A only induced TLR2 in a human cell line. We propose that the unique structure of the A. muciniphila LOS allows interaction with TLR2, thus generating an anti-inflammatory response as to compensate for the canonical inflammatory signaling associated with LOS and TLR4, rationalizing its beneficial host interaction.},
}

*Lipopolysaccharides
*Akkermansia
Animals
*Signal Transduction
*Toll-Like Receptor 4/metabolism
Humans
*Toll-Like Receptor 2/metabolism
Mice
Symbiosis
Mice, Inbred C57BL
Lipid A/metabolism/chemistry
Interleukin-10/metabolism
Gastrointestinal Microbiome
Liver/metabolism/microbiology
Female

@article {pmid39333709,
year = {2024},
author = {Crunkhorn, S},
title = {Identifying antimicrobials in the human microbiome.},
journal = {Nature reviews. Drug discovery},
volume = {23},
number = {11},
pages = {816},
pmid = {39333709},
issn = {1474-1784},
}

@article {pmid39334849,
year = {2024},
author = {Mukherjee, S and Verma, A and Kong, L and Rengan, AK and Cahill, DM},
title = {Advancements in Green Nanoparticle Technology: Focusing on the Treatment of Clinical Phytopathogens.},
journal = {Biomolecules},
volume = {14},
number = {9},
pages = {},
pmid = {39334849},
issn = {2218-273X},
mesh = {*Nanoparticles/chemistry/therapeutic use ; Humans ; *Anti-Bacterial Agents/pharmacology/chemistry/therapeutic use ; Green Chemistry Technology/methods ; Plant Diseases/microbiology/prevention & control ; },
abstract = {Opportunistic pathogenic microbial infections pose a significant danger to human health, which forces people to use riskier, more expensive, and less effective drugs compared to traditional treatments. These may be attributed to several factors, such as overusing antibiotics in medicine and lack of sanitization in hospital settings. In this context, researchers are looking for new options to combat this worrying condition and find a solution. Nanoparticles are currently being utilized in the pharmaceutical sector; however, there is a persistent worry regarding their potential danger to human health due to the usage of toxic chemicals, which makes the utilization of nanoparticles highly hazardous to eukaryotic cells. Multiple nanoparticle-based techniques are now being developed, offering essential understanding regarding the synthesis of components that play a crucial role in producing anti-microbial nanotherapeutic pharmaceuticals. In this regard, green nanoparticles are considered less hazardous than other forms, providing potential options for avoiding the extensive harm to the human microbiome that is prevalent with existing procedures. This review article aims to comprehensively assess the current state of knowledge on green nanoparticles related to antibiotic activity as well as their potential to assist antibiotics in treating opportunistic clinical phytopathogenic illnesses.},
}

*Nanoparticles/chemistry/therapeutic use
Humans
*Anti-Bacterial Agents/pharmacology/chemistry/therapeutic use
Green Chemistry Technology/methods
Plant Diseases/microbiology/prevention & control

@article {pmid39335616,
year = {2024},
author = {Xiang, B and Zhang, Q and Wu, H and Lin, J and Xu, Z and Zhang, M and Zhu, L and Hu, J and Zhi, M},
title = {Impact of Mild COVID-19 History on Oral-Gut Microbiota and Serum Metabolomics in Adult Patients with Crohn's Disease: Potential Beneficial Effects.},
journal = {Biomedicines},
volume = {12},
number = {9},
pages = {},
pmid = {39335616},
issn = {2227-9059},
support = {2014008 (MZ)//the Sun Yat-sen University Clinical Research 5010 Program/ ; 82270544 (MZ)//the National Natural Science Foundation of China/ ; SL2022B03J00237 (MZ)//the Bureau of Science and Technology of Guangzhou Municipality/ ; 2022JBGS06 (MZ)//"Jie Bang Gua Shuai" project of The Sixth Affiliated Hospital of Sun Yat-sen University/ ; 2019ZT08Y464 (LZ)//Guangdong Province "Pearl River Talent Plan" Innovation and Entrepreneurship Team Project/ ; 2020B1111170004 (MZ)//the program of Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; },
abstract = {The impact of coronavirus disease 2019 (COVID-19) history on Crohn's disease (CD) is unknown. This investigation aimed to examine the effect of COVID-19 history on the disease course, oral-gut microbiota, and serum metabolomics in patients with CD. In this study, oral-gut microbiota and serum metabolomic profiles in 30 patients with CD and a history of mild COVID-19 (positive group, PG), 30 patients with CD without COVID-19 history (negative group, NG), and 60 healthy controls (HC) were assessed using 16S rDNA sequencing and targeted metabolomics. During follow-up, the CD activity index showed a stronger decrease in the PG than in the NG (p = 0.0496). PG patients demonstrated higher α-diversity and distinct β-diversity clustering in both salivary and fecal microbiota compared to NG and HC individuals. Notably, the gut microbiota composition in the PG patients showed a significantly greater similarity to that of HC than NG individuals. The interaction between oral and intestinal microbiota in the PG was reduced. Moreover, serum metabolome analysis revealed significantly increased anti-inflammatory metabolites, including short-chain fatty acids and N-Acetylserotonin, among PG patients; meanwhile, inflammation-related metabolites such as arachidonic acid were significantly reduced in this group. Our data suggest that the gut microbiota mediates a potential beneficial effect of a mild COVID-19 history in CD patients.},
}

@article {pmid39337215,
year = {2024},
author = {Falara, E and Metallinou, D and Nanou, C and Vlachou, M and Diamanti, A},
title = {Perinatal Exposure to Tobacco Smoke and Its Association with the Maternal and Offspring Microbiome: A Systematic Review.},
journal = {Healthcare (Basel, Switzerland)},
volume = {12},
number = {18},
pages = {},
pmid = {39337215},
issn = {2227-9032},
support = {The APC was partially funded by the "Special Account for Research Grants" of the University of West Attica, Athens, Greece.//The APC was partially funded by the "Special Account for Research Grants" of the University of West Attica, Athens, Greece./ ; },
abstract = {BACKGROUND: The human microbiome, comprising trillions of microorganisms, significantly influences human health and disease. During critical periods like the perinatal phase, the microbiome undergoes significant changes, impacting lifelong health. Tobacco smoke, a known environmental pollutant, has adverse effects on health, particularly during pregnancy. Despite this, its association with the perinatal microbiome remains understudied.

METHODS: We conducted a systematic review to integrate findings on perinatal tobacco smoke exposure and its association with the maternal and neonatal microbiomes. We conducted a comprehensive literature search in the PubMed, Scopus, and Web of Science databases from January 2000 to February 2024. We selected studies that met predefined inclusion criteria and performed data extraction.

RESULTS: The review included eight studies that revealed diverse associations of perinatal tobacco exposure with the maternal and neonatal microbiome. Active smoking during pregnancy was linked to alterations in microbiome composition and diversity in children. Maternal smoking correlated with increased Firmicutes abundance and decreased Akkermansia muciniphila abundance in offspring. Additionally, exposure to thirdhand smoke in neonatal intensive care units was related to infant microbiome diversity. Infants exposed to tobacco smoke showed various microbial changes, suggesting potential implications for childhood health outcomes, including obesity risk.

CONCLUSIONS: Perinatal exposure to tobacco smoke exerts significant influence on the maternal and neonatal microbiomes, with potential implications for long-term health outcomes. Addressing socioeconomic and psychological barriers to smoking cessation, implementing stricter smoking regulations, and promoting public health campaigns are essential steps towards reducing tobacco-related harm during the perinatal period. Further longitudinal studies and standardized assessment methods are needed to validate these findings and guide the development of effective preventive measures.},
}

@article {pmid39337688,
year = {2024},
author = {Fleshner, L and Roster, K and Farabi, B and Hirani, R and Tepper, K and Pitchumoni, CS and Safai, B and Marmon, S},
title = {Follicular Skin Disorders, Inflammatory Bowel Disease, and the Microbiome: A Systematic Review.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
pmid = {39337688},
issn = {1422-0067},
mesh = {Humans ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Hidradenitis Suppurativa/microbiology ; *Inflammatory Bowel Diseases/microbiology ; Microbiota ; Skin/microbiology ; Skin Diseases/microbiology ; },
abstract = {Follicular skin disorders, including hidradenitis suppurativa (HS), frequently coexist with systemic autoinflammatory diseases, such as inflammatory bowel disease (IBD) and its subtypes, Crohn's disease and ulcerative colitis. Previous studies suggest that dysbiosis of the human gut microbiome may serve as a pathogenic link between HS and IBD. However, the role of the microbiome (gut, skin, and blood) in the context of IBD and various follicular disorders remains underexplored. Here, we performed a systematic review to investigate the relationship between follicular skin disorders, IBD, and the microbiome. Of the sixteen included studies, four evaluated the impact of diet on the microbiome in HS patients, highlighting a possible link between gut dysbiosis and yeast-exclusion diets. Ten studies explored bacterial colonization and HS severity with specific gut and skin microbiota, including Enterococcus and Veillonella. Two studies reported on immunological or serological biomarkers in HS patients with autoinflammatory disease, including IBD, and identified common markers including elevated cytokines and T-lymphocytes. Six studies investigated HS and IBD patients concurrently. Our systematic literature review highlights the complex interplay between the human microbiome, IBD, and follicular disorders with a particular focus on HS. The results indicate that dietary modifications hold promise as a therapeutic intervention to mitigate the burden of HS and IBD. Microbiota analyses and the identification of key serological biomarkers are crucial for a deeper understanding of the impact of dysbiosis in these conditions. Future research is needed to more thoroughly delineate the causal versus associative roles of dysbiosis in patients with both follicular disorders and IBD.},
}

Humans
*Dysbiosis/microbiology
*Gastrointestinal Microbiome
Hidradenitis Suppurativa/microbiology
*Inflammatory Bowel Diseases/microbiology
Microbiota
Skin/microbiology
Skin Diseases/microbiology

@article {pmid39339787,
year = {2024},
author = {Fraiz, GM and Bonifácio, DB and Lacerda, UV and Cardoso, RR and Corich, V and Giacomini, A and Martino, HSD and Echeverría, SE and Barros, FAR and Milagro, FI and Bressan, J},
title = {Green Tea Kombucha Impacts Inflammation and Salivary Microbiota in Individuals with Excess Body Weight: A Randomized Controlled Trial.},
journal = {Nutrients},
volume = {16},
number = {18},
pages = {},
pmid = {39339787},
issn = {2072-6643},
support = {CAPE 507/2019 - APQ-00035-20//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; CB12/03/30002//Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; },
mesh = {Humans ; *Saliva/microbiology ; Male ; Female ; *Inflammation ; Adult ; *Microbiota ; Kombucha Tea ; Middle Aged ; Weight Loss ; Tea ; Overweight/microbiology ; Body Mass Index ; Caloric Restriction ; Body Composition ; },
abstract = {BACKGROUND: Green tea kombucha (GTK) is a fermented beverage with promising health benefits, but few studies proved its impact on human health. Thus, we aimed to investigate the impact of GTK on weight loss, inflammation, and salivary microbiota in individuals with excess body weight.

METHODS: This is a randomized controlled clinical trial that lasted 10 weeks with two groups of individuals with excess body weight: control (CG; n = 29; caloric restriction) and kombucha (KG; n = 30; caloric restriction + 200 mL GTK). Body composition, anthropometry, saliva, and blood collection were performed in the beginning and end of the intervention. Plasma interleukins were determined by flow cytometry. Salivary microbiota was analyzed by 16S rRNA sequencing.

RESULTS: Both groups decreased weight, BMI, and body fat (p < 0.001) after the intervention, but there were no differences between groups. The KG reduced lipid accumulation product (LAP) (p = 0.029). Both groups decreased IL-1β and IL-8, but IL-6 increased in the CG (p = 0.023) compared to the kombucha group. Alpha and beta diversity of salivary microbiota increased in the KG. Moreover, the KG presented lower Bacillota/Bacteroidota ratio (p = 0.028), and BMI was positively associated with the Bacillota phylum.

CONCLUSIONS: GTK did not enhance weight loss, but it decreased the LAP. GTK helped in the inflammatory profile and induced positive changes in oral microbiota composition.},
}

Humans
*Saliva/microbiology
Male
Female
*Inflammation
Adult
*Microbiota
Kombucha Tea
Middle Aged
Weight Loss
Tea
Overweight/microbiology
Body Mass Index
Caloric Restriction
Body Composition

@article {pmid39340867,
year = {2024},
author = {Moghaddam, HS and Abkar, L and Fowler, SJ},
title = {Making waves: From tap to gut- exploring the impact of drinking water on gut microbiota.},
journal = {Water research},
volume = {267},
number = {},
pages = {122503},
doi = {10.1016/j.watres.2024.122503},
pmid = {39340867},
issn = {1879-2448},
mesh = {*Drinking Water/microbiology ; *Gastrointestinal Microbiome ; Humans ; Diet ; },
abstract = {Drinking water (DW) harbours diverse microbial species and chemical attributes. Water comprises the greatest portion of our daily diet, ingested both on its own and used in the preparation of food. DW is our major source of liquids, which is vital to maintaining homeostasis, and can also supply essential minerals. Limited evidence suggests that DW plays a role in shaping the gut microbiome, which implies that it may impact human health. Despite its significant contribution to diet, DW is often overlooked in studies examining dietary influences on the gut microbiota. This perspective explores our current understanding of the link between DW and the gut microbiota - an area of human microbiome science that has been surprisingly understudied. Existing studies reveal links between DW source, microbiota composition, and gut health, emphasizing the need for comprehensive investigations. Understanding the interplay between DW and gut microbiota holds potential for tailored interventions to enhance human health.},
}

*Drinking Water/microbiology
*Gastrointestinal Microbiome
Humans
Diet

@article {pmid39341037,
year = {2024},
author = {Vogs, C and Lindqvist, D and Wai Tang, S and Gugescu, L and Alenius, H and Wincent, E},
title = {Transcriptomic and functional effects from a chemical mixture based on the exposure profile in Baltic Sea salmon, on metabolic and immune functions in zebrafish embryo.},
journal = {Environment international},
volume = {192},
number = {},
pages = {109018},
doi = {10.1016/j.envint.2024.109018},
pmid = {39341037},
issn = {1873-6750},
mesh = {Animals ; *Zebrafish ; *Water Pollutants, Chemical/toxicity ; *Transcriptome/drug effects ; *Salmon ; Embryo, Nonmammalian/drug effects ; Hydrocarbons, Halogenated/toxicity ; Gene Expression Profiling ; },
abstract = {The Baltic Sea is one of the world's most contaminated seas with long-standing adverse health status of its wildlife such as the Baltic Sea salmon, resulting in reduced fecundity and increased mortality. While adverse health effects have been reported among wild fish from the Baltic Sea, the toxicity mechanisms underlying these adversities, and the chemical effect drivers mediating them are poorly understood. To address this knowledge gap, we utilized the zebrafish (Danio rerio) embryo model to determine molecular and functional effects brought on by exposure to a technical mixture including 9 organohalogen compounds detected in serum from wild-caught Baltic Sea salmon. To align with the salmon exposure scenario, an internal dose regimen was opted to establish same relative proportions of the compounds in the zebrafish (whole body) as observed in the salmon serum. Through transcriptomic profiling, we identified dose-dependent effects on immune system and metabolism as two critical functions overlapping with adverse effects observed in wild fish from the Baltic Sea. We then determined likely effect drivers by comparing gene responses of the mixture with those of individual mixture components. Aligned with our transcriptome results, the number of total macrophages was reduced and the zebrafish's ability to respond to a tissue damage suppressed in a dose-dependent manner. This study brings forth a key advancement in delineating the impact of chemical pollutants on the health of wild fish in the Baltic Sea.},
}

Animals
*Zebrafish
*Water Pollutants, Chemical/toxicity
*Transcriptome/drug effects
*Salmon
Embryo, Nonmammalian/drug effects
Hydrocarbons, Halogenated/toxicity
Gene Expression Profiling

@article {pmid39342083,
year = {2024},
author = {Wang, X and Yao, S and Yang, X and Li, Y and Yu, Z and Huang, J and Wang, J},
title = {Peritoneal dialysis promotes microbial-driven biosynthesis pathways of sesquiterpenes and triterpenes compounds in end-stage renal disease patients.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {377},
pmid = {39342083},
issn = {1471-2180},
support = {32170071//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2022JJ40663//Natural Science Foundation of Hunan Province/ ; C2023045//Hunan Province Traditional Chinese Medicine Research Program Project/ ; },
mesh = {Humans ; *Kidney Failure, Chronic/therapy/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Peritoneal Dialysis ; *Sesquiterpenes/metabolism ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Triterpenes/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Biosynthetic Pathways ; Adult ; Metagenomics ; Aged ; },
abstract = {The concept of the gut-kidney axis is gaining significant attention due to the close relationship between gut microbiota and kidney disease. Peritoneal dialysis is recognized as a crucial renal replacement therapy for end-stage renal disease (ESRD). The alterations in gut microbiota and related mechanisms after receiving this dialysis method are not fully understood. This study conducted shotgun metagenomic sequencing on fecal samples from 11 end-stage renal disease patients who did not receive dialysis (ESRD_N) and 7 patients who received peritoneal dialysis (ESRD_P). After quality control and correlation analysis of the data, our study is aimed at exploring the impact of peritoneal dialysis on the gut microbiota and health of ESRD patients. Our research findings indicate that the complexity and aggregation characteristics of gut microbiota interactions increase in ESRD_P. In addition, the gut microbiota drives the biosynthesis pathways of sesquiterpenes and triterpenes in ESRD_P patients, which may contribute to blood purification and improve circulation. Therefore, our research will lay the foundation for the prevention and treatment of ESRD.},
}

Humans
*Kidney Failure, Chronic/therapy/metabolism/microbiology
*Gastrointestinal Microbiome
*Peritoneal Dialysis
*Sesquiterpenes/metabolism
Male
Female
*Feces/microbiology
Middle Aged
*Triterpenes/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification
Biosynthetic Pathways
Adult
Metagenomics
Aged

@article {pmid39345212,
year = {2024},
author = {Basting, CM and Langat, R and Broedlow, CA and Guerrero, CR and Bold, TD and Bailey, M and Velez, A and Schroeder, T and Short-Miller, J and Cromarty, R and Mayer, ZJ and Southern, PJ and Schacker, TW and Safo, SE and Bramante, CT and Tignanelli, CJ and Schifanella, L and Klatt, NR},
title = {SARS-CoV-2 infection is associated with intestinal permeability, systemic inflammation, and microbial dysbiosis in hospitalized patients.},
journal = {Microbiology spectrum},
volume = {12},
number = {11},
pages = {e0068024},
pmid = {39345212},
issn = {2165-0497},
mesh = {Humans ; *COVID-19/microbiology ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *SARS-CoV-2/isolation & purification ; *Inflammation ; *Gastrointestinal Microbiome ; Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; Permeability ; Cytokines/blood ; Hospitalization ; Bacteria/classification/isolation & purification/genetics ; Intestinal Barrier Function ; },
abstract = {Coronavirus disease 2019 (COVID-19) and its associated severity have been linked to uncontrolled inflammation and may be associated with changes in the microbiome of mucosal sites including the gastrointestinal tract and oral cavity. These sites play an important role in host-microbe homeostasis, and disruption of epithelial barrier integrity during COVID-19 may potentially lead to exacerbated inflammation and immune dysfunction. Outcomes in COVID-19 are highly disparate, ranging from asymptomatic to fatal, and the impact of microbial dysbiosis on disease severity is unclear. Here, we obtained plasma, rectal swabs, oropharyngeal swabs, and nasal swabs from 86 patients hospitalized with COVID-19 and 12 healthy volunteers. We performed 16S rRNA sequencing to characterize the microbial communities in the mucosal swabs and measured concentrations of circulating cytokines, markers of gut barrier integrity, and fatty acids in the plasma samples. We compared these plasma concentrations and microbiomes between healthy volunteers and COVID-19 patients, some of whom had unfortunately died by the end of the study enrollment, and performed a correlation analysis between plasma variables and bacterial abundances. Rectal swabs of COVID-19 patients had reduced abundances of several commensal bacteria including Faecalibacterium prausnitzii and an increased abundance of the opportunistic pathogens Eggerthella lenta and Hungatella hathewayi. Furthermore, the oral pathogen Scardovia wiggsiae was more abundant in the oropharyngeal swabs of COVID-19 patients who died. The abundance of both H. hathewayi and S. wiggsiae correlated with circulating inflammatory markers including IL-6, highlighting the possible role of the microbiome in COVID-19 severity and providing potential therapeutic targets for managing COVID-19.IMPORTANCEOutcomes in coronavirus disease 2019 (COVID-19) are highly disparate and are associated with uncontrolled inflammation; however, the individual factors that lead to this uncontrolled inflammation are not fully understood. Here, we report that severe COVID-19 is associated with systemic inflammation, microbial translocation, and microbial dysbiosis. The rectal and oropharyngeal microbiomes of COVID-19 patients were characterized by a decreased abundance of commensal bacteria and an increased abundance of opportunistic pathogens, which positively correlated with markers of inflammation and microbial translocation. These microbial perturbations may, therefore, contribute to disease severity in COVID-19 and highlight the potential for microbiome-based interventions in improving COVID-19 outcomes.},
}

Humans
*COVID-19/microbiology
*Dysbiosis/microbiology
Male
Female
Middle Aged
*SARS-CoV-2/isolation & purification
*Inflammation
*Gastrointestinal Microbiome
Aged
Adult
RNA, Ribosomal, 16S/genetics
Permeability
Cytokines/blood
Hospitalization
Bacteria/classification/isolation & purification/genetics
Intestinal Barrier Function

@article {pmid39349378,
year = {2024},
author = {Palmer, D and Henze, L and Murua Escobar, H and Walter, U and Kowald, A and Fuellen, G},
title = {Multicohort study testing the generalisability of the SASKit-ML stroke and PDAC prognostic model pipeline to other chronic diseases.},
journal = {BMJ open},
volume = {14},
number = {9},
pages = {e088181},
pmid = {39349378},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications ; Prognosis ; Female ; Male ; *Pancreatic Neoplasms ; *Stroke ; Middle Aged ; Arthritis, Rheumatoid ; Machine Learning ; Inflammatory Bowel Diseases ; Aged ; Longitudinal Studies ; Chronic Disease ; Prospective Studies ; Biomarkers/blood ; Cohort Studies ; },
abstract = {OBJECTIVES: To validate and test the generalisability of the SASKit-ML pipeline, a prepublished feature selection and machine learning pipeline for the prediction of health deterioration after a stroke or pancreatic adenocarcinoma event, by using it to identify biomarkers of health deterioration in chronic disease.

DESIGN: This is a validation study using a predefined protocol applied to multiple publicly available datasets, including longitudinal data from cohorts with type 2 diabetes (T2D), inflammatory bowel disease (IBD), rheumatoid arthritis (RA) and various cancers. The datasets were chosen to mimic as closely as possible the SASKit cohort, a prospective, longitudinal cohort study.

DATA SOURCES: Public data were used from the T2D (77 patients with potential pre-diabetes and 18 controls) and IBD (49 patients with IBD and 12 controls) branches of the Human Microbiome Project (HMP), RA Map (RA-MAP, 92 patients with RA, 22 controls) and The Cancer Genome Atlas (TCGA, 16 cancers).

METHODS: Data integration steps were performed in accordance with the prepublished study protocol, generating features to predict disease outcomes using 10-fold cross-validated random survival forests.

OUTCOME MEASURES: Health deterioration was assessed using disease-specific clinical markers and endpoints across different cohorts. In the HMP-T2D cohort, the worsening of glycated haemoglobin (HbA1c) levels (5.7% or more HbA1c in the blood), fasting plasma glucose (at least 100 mg/dL) and oral glucose tolerance test (at least 140) results were considered. For the HMP-IBD cohort, a worsening by at least 3 points of a disease-specific severity measure, the "Simple Clinical Colitis Activity Index" or "Harvey-Bradshaw Index" indicated an event. For the RA-MAP cohort, the outcome was defined as the worsening of the "Disease Activity Score 28" or "Simple Disease Activity Index" by at least five points, or the worsening of the "Health Assessment Questionnaire" score or an increase in the number of swollen/tender joints were evaluated. Finally, the outcome for all TCGA datasets was the progression-free interval.

RESULTS: Models for the prediction of health deterioration in T2D, IBD, RA and 16 cancers were produced. The T2D (C-index of 0.633 and Integrated Brier Score (IBS) of 0.107) and the RA (C-index of 0.654 and IBS of 0.150) models were modestly predictive. The IBD model was uninformative. TCGA models tended towards modest predictive power.

CONCLUSIONS: The SASKit-ML pipeline produces informative and useful features with the power to predict health deterioration in a variety of diseases and cancers; however, this performance is disease-dependent.},
}

Humans
*Diabetes Mellitus, Type 2/complications
Prognosis
Female
Male
*Pancreatic Neoplasms
*Stroke
Middle Aged
Arthritis, Rheumatoid
Machine Learning
Inflammatory Bowel Diseases
Aged
Longitudinal Studies
Chronic Disease
Prospective Studies
Biomarkers/blood
Cohort Studies

@article {pmid39351241,
year = {2024},
author = {Lu, S and Wang, C and Ma, J and Wang, Y},
title = {Metabolic mediators: microbial-derived metabolites as key regulators of anti-tumor immunity, immunotherapy, and chemotherapy.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1456030},
pmid = {39351241},
issn = {1664-3224},
mesh = {Humans ; *Neoplasms/immunology/therapy/metabolism/drug therapy ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology ; *Tumor Microenvironment/immunology ; Animals ; *Fatty Acids, Volatile/metabolism ; *Tryptophan/metabolism ; Methylamines/metabolism/immunology ; Antineoplastic Agents/therapeutic use ; },
abstract = {The human microbiome has recently emerged as a focal point in cancer research, specifically in anti-tumor immunity, immunotherapy, and chemotherapy. This review explores microbial-derived metabolites, emphasizing their crucial roles in shaping fundamental aspects of cancer treatment. Metabolites such as short-chain fatty acids (SCFAs), Trimethylamine N-Oxide (TMAO), and Tryptophan Metabolites take the spotlight, underscoring their diverse origins and functions and their profound impact on the host immune system. The focus is on SCFAs' remarkable ability to modulate immune responses, reduce inflammation, and enhance anti-tumor immunity within the intricate tumor microenvironment (TME). The review critically evaluates TMAO, intricately tied to dietary choices and gut microbiota composition, assessing its implications for cancer susceptibility, progression, and immunosuppression. Additionally, the involvement of tryptophan and other amino acid metabolites in shaping immune responses is discussed, highlighting their influence on immune checkpoints, immunosuppression, and immunotherapy effectiveness. The examination extends to their dynamic interaction with chemotherapy, emphasizing the potential of microbial-derived metabolites to alter treatment protocols and optimize outcomes for cancer patients. A comprehensive understanding of their role in cancer therapy is attained by exploring their impacts on drug metabolism, therapeutic responses, and resistance development. In conclusion, this review underscores the pivotal contributions of microbial-derived metabolites in regulating anti-tumor immunity, immunotherapy responses, and chemotherapy outcomes. By illuminating the intricate interactions between these metabolites and cancer therapy, the article enhances our understanding of cancer biology, paving the way for the development of more effective treatment options in the ongoing battle against cancer.},
}

Humans
*Neoplasms/immunology/therapy/metabolism/drug therapy
*Immunotherapy/methods
*Gastrointestinal Microbiome/immunology
*Tumor Microenvironment/immunology
Animals
*Fatty Acids, Volatile/metabolism
*Tryptophan/metabolism
Methylamines/metabolism/immunology
Antineoplastic Agents/therapeutic use

@article {pmid39352141,
year = {2024},
author = {Coclet, C and Camargo, AP and Roux, S},
title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0088824},
pmid = {39352141},
issn = {2379-5077},
mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; },
abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.},
}

*Metagenome/genetics
*Genome, Viral/genetics
*Metagenomics/methods
*Viruses/genetics/classification/isolation & purification
Software
Virome/genetics
Computational Biology/methods
Molecular Sequence Annotation

@article {pmid39358005,
year = {2025},
author = {Manning, S and Sinha, R and Rees, CJ},
title = {Need for standardised approaches to human microbiome research using the example of colorectal neoplasia research.},
journal = {Gut},
volume = {74},
number = {6},
pages = {875-877},
doi = {10.1136/gutjnl-2024-333765},
pmid = {39358005},
issn = {1468-3288},
}

@article {pmid39358771,
year = {2024},
author = {Kawano-Sugaya, T and Arikawa, K and Saeki, T and Endoh, T and Kamata, K and Matsuhashi, A and Hosokawa, M},
title = {A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {188},
pmid = {39358771},
issn = {2049-2618},
mesh = {Humans ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Mouth/microbiology ; *Genome, Bacterial ; Interspersed Repetitive Sequences/genetics ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Phylogeny ; },
abstract = {BACKGROUND: The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.

RESULTS: We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.

CONCLUSIONS: The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.},
}

Humans
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/genetics
*Metagenome
*Mouth/microbiology
*Genome, Bacterial
Interspersed Repetitive Sequences/genetics
Microbiota/genetics
Drug Resistance, Bacterial/genetics
Metagenomics/methods
Phylogeny

@article {pmid39359681,
year = {2024},
author = {Tian, S and Ding, T and Li, H},
title = {Oral microbiome in human health and diseases.},
journal = {mLife},
volume = {3},
number = {3},
pages = {367-383},
pmid = {39359681},
issn = {2770-100X},
abstract = {The oral cavity contains the second-largest microbiota in the human body. The cavity's anatomically and physiologically diverse niches facilitate a wide range of symbiotic bacteria living at distinct oral sites. Consequently, the oral microbiota exhibits site specificity, with diverse species, compositions, and structures influenced by specific aspects of their placement. Variations in oral microbiota structure caused by changes in these influencing factors can impact overall health and lead to the development of diseases-not only in the oral cavity but also in organs distal to the mouth-such as cancer, cardiovascular disease, and respiratory disease. Conversely, diseases can exacerbate the imbalance of the oral microbiota, creating a vicious cycle. Understanding the heterogeneity of both the oral microbiome and individual humans is important for investigating the causal links between the oral microbiome and diseases. Additionally, understanding the intricacies of the oral microbiome's composition and regulatory factors will help identify the potential causes of related diseases and develop interventions to prevent and treat illnesses in this domain. Therefore, turning to the extant research in this field, we systematically review the relationship between oral microbiome dynamics and human diseases.},
}

@article {pmid39362115,
year = {2024},
author = {Tian, H and Tang, R},
title = {Prediction of Crohn's disease based on deep feature recognition.},
journal = {Computational biology and chemistry},
volume = {113},
number = {},
pages = {108231},
doi = {10.1016/j.compbiolchem.2024.108231},
pmid = {39362115},
issn = {1476-928X},
mesh = {*Crohn Disease/genetics ; Humans ; *Deep Learning ; Support Vector Machine ; },
abstract = {BACKGROUND: Crohn's disease is a complex genetic disease that involves chronic gastrointestinal inflammation and results from a complex set of genetic, environmental, and immunological factors. By analyzing data from the human microbiome, genetic information can be used to predict Crohn's disease. Recent advances in deep learning have demonstrated its effectiveness in feature extraction and the use of deep learning to decode genetic information for disease prediction.

METHODS: In this paper, we present a deep learning-based model that utilizes a sequential convolutional attention network (SCAN) for feature extraction, incorporates adaptive additive interval losses to enhance these features, and employs support vector machines (SVM) for classification. To address the challenge of unbalanced Crohn's disease samples, we propose a random noise one-hot encoding data augmentation method.

RESULTS: Data augmentation with random noise accelerates training convergence, while SCAN-SVM effectively extracts features with adaptive additive interval loss enhancing differentiation. Our approach outperforms benchmark methods, achieving an average accuracy of 0.80 and a kappa value of 0.76, and we validate the effectiveness of feature enhancement.

CONCLUSIONS: In summary, we use deep feature recognition to effectively analyze the potential information in genes, which has a good application potential for gene analysis and prediction of Crohn's disease.},
}

*Crohn Disease/genetics
Humans
*Deep Learning
Support Vector Machine

@article {pmid39365053,
year = {2024},
author = {Silk, ET and Bayer, SB and Foster, M and Roy, NC and Taylor, MW and Vatanen, T and Gearry, RB},
title = {Advancing microbiome research in Māori populations: insights from recent literature exploring the gut microbiomes of underrepresented and Indigenous peoples.},
journal = {mSystems},
volume = {9},
number = {11},
pages = {e0090924},
pmid = {39365053},
issn = {2379-5077},
support = {Doctoral Scholarship//University of Otago (Te Whare Wānanga o Otāgo)/ ; HRC 23/314//Manatu Hauora | Health Research Council of New Zealand (HRC)/ ; UOAX1421,UOAX1902//High Value Nutrition (New Zealand)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Indigenous Peoples ; Maori People ; },
abstract = {The gut microbiome plays vital roles in human health, including mediating metabolism, immunity, and the gut-brain axis. Many ethnicities remain underrepresented in gut microbiome research, with significant variation between Indigenous and non-Indigenous peoples due to dietary, socioeconomic, health, and urbanization differences. Although research regarding the microbiomes of Indigenous peoples is increasing, Māori microbiome literature is lacking despite widespread inequities that Māori populations face. These inequities likely contribute to gut microbiome differences that exacerbate negative health outcomes. Characterizing the gut microbiomes of underrepresented populations is necessary to inform efforts to address health inequities. However, for microbiome research to be culturally responsible and meaningful, study design must improve to better protect the rights and interests of Indigenous peoples. Here, we discuss barriers to Indigenous participation in research and the role disparities may play in shaping the gut microbiomes of Indigenous peoples, with a particular focus on implications for Māori and areas for improvement.},
}

Humans
*Gastrointestinal Microbiome
*Indigenous Peoples
Maori People

@article {pmid39368472,
year = {2024},
author = {El Mouali, Y and Tawk, C and Huang, KD and Amend, L and Lesker, TR and Ponath, F and Vogel, J and Strowig, T},
title = {The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization.},
journal = {Cell host & microbe},
volume = {32},
number = {11},
pages = {1910-1926.e6},
doi = {10.1016/j.chom.2024.09.008},
pmid = {39368472},
issn = {1934-6069},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Symbiosis ; *RNA, Bacterial/genetics ; *Germ-Free Life ; Gene Expression Regulation, Bacterial ; Fructans/metabolism ; Mice, Inbred C57BL ; Gastrointestinal Tract/microbiology ; Transcriptome ; },
abstract = {The bacterium Segatella copri is a prevalent member of the human gut microbiota associated with health and disease states. However, the intrinsic factors that determine its ability to colonize the gut effectively remain largely unknown. By extensive transcriptome mapping of S. copri and examining human-derived samples, we discover a small RNA, which we name Segatella RNA colonization factor (SrcF), and show that SrcF is essential for S. copri gut colonization in gnotobiotic mice. SrcF regulates genes involved in nutrient acquisition, and complex carbohydrates, particularly fructans, control its expression. Furthermore, SrcF expression is strongly influenced by human microbiome composition and by the breakdown of fructans by cohabitating commensals, suggesting that the breakdown of complex carbohydrates mediates interspecies signaling among commensals beyond its established function in generating energy. Together, this study highlights the contribution of a small RNA as a critical regulator in gut colonization.},
}

Humans
Animals
*Gastrointestinal Microbiome/genetics
Mice
*Symbiosis
*RNA, Bacterial/genetics
*Germ-Free Life
Gene Expression Regulation, Bacterial
Fructans/metabolism
Mice, Inbred C57BL
Gastrointestinal Tract/microbiology
Transcriptome

@article {pmid39375475,
year = {2025},
author = {Turocy, T and Crawford, JM},
title = {Bacterial small molecule metabolites implicated in gastrointestinal cancer development.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {2},
pages = {106-121},
pmid = {39375475},
issn = {1740-1534},
support = {RM1 GM141649/GM/NIGMS NIH HHS/United States ; T32 GM067543/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Neoplasms/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; Animals ; Host Microbial Interactions ; },
abstract = {Numerous associations have been identified between cancer and the composition and function of the human microbiome. As cancer remains the second leading global cause of mortality, investigating the carcinogenic contributions of microbiome members could advance our understanding of cancer risk and support potential therapeutic interventions. Although fluctuations in bacterial species have been associated with cancer progression, studying their small molecule metabolites offers one avenue to establish support for causal relationships and the molecular mechanisms governing host-microorganism interactions. In this Review, we explore the expanding repertoire of small molecule metabolites and their mechanisms implicated in the risk of developing gastrointestinal cancers.},
}

Humans
*Gastrointestinal Neoplasms/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism
Animals
Host Microbial Interactions

@article {pmid39377779,
year = {2024},
author = {Porreca, A and Ibrahimi, E and Maturo, F and Marcos Zambrano, LJ and Meto, M and Lopes, MB},
title = {Robust prediction of colorectal cancer via gut microbiome 16S rRNA sequencing data.},
journal = {Journal of medical microbiology},
volume = {73},
number = {10},
pages = {},
doi = {10.1099/jmm.0.001903},
pmid = {39377779},
issn = {1473-5644},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Feces/microbiology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Introduction. The study addresses the challenge of utilizing human gut microbiome data for the early detection of colorectal cancer (CRC). The research emphasizes the potential of using machine learning techniques to analyze complex microbiome datasets, providing a non-invasive approach to identifying CRC-related microbial markers.Hypothesis/Gap Statement. The primary hypothesis is that a robust machine learning-based analysis of 16S rRNA microbiome data can identify specific microbial features that serve as effective biomarkers for CRC detection, overcoming the limitations of classical statistical models in high-dimensional settings.Aim. The primary objective of this study is to explore and validate the potential of the human microbiome, specifically in the colon, as a valuable source of biomarkers for colorectal cancer (CRC) detection and progression. The focus is on developing a classifier that effectively predicts the presence of CRC and normal samples based on the analysis of three previously published faecal 16S rRNA sequencing datasets.Methodology. To achieve the aim, various machine learning techniques are employed, including random forest (RF), recursive feature elimination (RFE) and a robust correlation-based technique known as the fuzzy forest (FF). The study utilizes these methods to analyse the three datasets, comparing their performance in predicting CRC and normal samples. The emphasis is on identifying the most relevant microbial features (taxa) associated with CRC development via partial dependence plots, i.e. a machine learning tool focused on explainability, visualizing how a feature influences the predicted outcome.Results. The analysis of the three faecal 16S rRNA sequencing datasets reveals the consistent and superior predictive performance of the FF compared to the RF and RFE. Notably, FF proves effective in addressing the correlation problem when assessing the importance of microbial taxa in explaining the development of CRC. The results highlight the potential of the human microbiome as a non-invasive means to detect CRC and underscore the significance of employing FF for improved predictive accuracy.Conclusion. In conclusion, this study underscores the limitations of classical statistical techniques in handling high-dimensional information such as human microbiome data. The research demonstrates the potential of the human microbiome, specifically in the colon, as a valuable source of biomarkers for CRC detection. Applying machine learning techniques, particularly the FF, is a promising approach for building a classifier to predict CRC and normal samples. The findings advocate for integrating FF to overcome the challenges associated with correlation when identifying crucial microbial features linked to CRC development.},
}

*RNA, Ribosomal, 16S/genetics
*Colorectal Neoplasms/microbiology
Humans
*Gastrointestinal Microbiome/genetics
*Machine Learning
*Feces/microbiology
Bacteria/genetics/classification/isolation & purification

@article {pmid39378356,
year = {2025},
author = {Yang, I and Alford, T and Brewster, G and Geurs, N and Wharton, W and Yeager, K and Houser, M},
title = {Oral Microbiome and Cognition Among Black Cancer Caregivers.},
journal = {Nursing research},
volume = {74},
number = {1},
pages = {47-55},
pmid = {39378356},
issn = {1538-9847},
support = {P30 NR018090/NR/NINR NIH HHS/United States ; UL1 TR002378/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *Black or African American/psychology ; *Caregivers/psychology ; Cognition/physiology ; Georgia ; *Microbiota ; Mouth/microbiology ; *Neoplasms/psychology/microbiology ; Oral Health/statistics & numerical data ; Saliva/microbiology ; },
abstract = {BACKGROUND: Despite known links between oral health and dementia and the growing understanding of the role of the human microbiome in health, few studies have explored the relationship between the oral microbiome and cognition. Additionally, there is a notable absence of research on how the oral microbiome is associated with cognitive function in Black adult caregivers of cancer patients despite their elevated risk for both oral disease and cognitive impairment.

OBJECTIVES: This study aimed to characterize the oral microbiome of Black caregivers of people living with cancer and explore the association of the oral microbiome with cognitive performance.

METHODS: Thirty-one self-identified Black or African American caregivers of cancer patients in the greater metropolitan Atlanta area participated in the study. They provided oral microbiome samples. Cognitive performance was assessed using the Montreal Cognitive Assessment (MoCA), depressive symptoms with the Center for Epidemiological Studies-Depression Scale, and individual race-related stress with the Index of Race-Related Stress-Brief. Salivary microbiome diversity was analyzed using alpha and beta diversity metrics, and taxa associated with cognition were identified through differential abundance testing, adjusting for potential confounders.

RESULTS: The mean age of participants was 54.8 years. MoCA scores ranged from 18 to 30, with a mean of 25. Participants were categorized into normal cognition (MoCA ≥ 26, n = 12) and low cognition (MoCA < 26, n = 16) groups. Education level and individual race-related stress were associated with cognition group and were controlled for in the oral microbiome analysis. Alpha and beta diversity analyses showed no significant overall differences between cognition groups. Differential abundance testing suggested 48 taxa were associated with cognition status, many of which are known to be associated with periodontal disease and cognition.

DISCUSSION: This study revealed associations between cognition status and specific oral bacteria, many of which are known to be associated with periodontal disease and cognitive impairment. These findings underscore the complex relationship between oral health and cognitive function, suggesting a need for further research to develop oral microbiome profiles capable of identifying individuals at risk for cognitive decline and guiding targeted interventions for promoting overall well-being and cognitive health.},
}

Adult
Aged
Female
Humans
Male
Middle Aged
*Black or African American/psychology
*Caregivers/psychology
Cognition/physiology
Georgia
*Microbiota
Mouth/microbiology
*Neoplasms/psychology/microbiology
Oral Health/statistics & numerical data
Saliva/microbiology

@article {pmid39383990,
year = {2024},
author = {Wang, C and Song, Y and Liang, J and Wang, Y and Zhang, D and Zhao, Z},
title = {Antibiotic resistance genes are transferred from manure-contaminated water bodies to the gut microbiota of animals through the food chain.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {363},
number = {Pt 1},
pages = {125087},
doi = {10.1016/j.envpol.2024.125087},
pmid = {39383990},
issn = {1873-6424},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Food Chain ; *Drug Resistance, Microbial/genetics ; *Manure/microbiology ; Daphnia/genetics ; Feces/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Water Pollutants, Chemical ; },
abstract = {Fecal-contaminated water may enter the food chain and become an important route for the transmission of antibiotic resistance genes (ARGs) to the human microbiome. However, little is known about the spread of ARGs from fecal contamination in water bodies along the aquatic food chain. In this study, laboratory-raised Daphnia magna and Aristichthys nobilis were used to investigate the effects of the addition of manure on target ARGs in water and their intestinal contents to determine the potential transmission route of ARGs in the aquatic food chain system. The abundance of target ARGs in water as well as D. magna and A. nobilis intestinal contents significantly increased when fecal contamination was present. ARGs bioaccumulated along the food chain, with four ARGs (tetM-01, tetX, qnrS, and sul2) detected regularly. Mn and Cr were key environmental factors that promoted the transfer of ARGs along the food chain. Fecal addition significantly changed the structure of microbial communities in water, D. magna gut, and A. nobilis gut. The ARG spectrum was significantly correlated with the composition and structure of the bacterial community. Proteobacteria, Bacteroidetes, and Firmicutes were identified as the main host bacteria and were likely to act as carriers of ARGs to promote the spread of antibiotic resistance in the food chain. The composition and structure of bacterial communities, along with mobile genetic elements, were two key drivers of ARG transfer. These findings provide new insights into the distribution and spread of ARGs along the freshwater food chain.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Food Chain
*Drug Resistance, Microbial/genetics
*Manure/microbiology
Daphnia/genetics
Feces/microbiology
Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Bacteria/genetics
Water Pollutants, Chemical

@article {pmid39386965,
year = {2024},
author = {Muhi, S and Marshall, JL and O'Brien, DP and Johnson, PDR and Ross, G and Ramakrishnan, A and Mackay, LK and Doerflinger, M and McCarthy, JS and Jamrozik, E and Osowicki, J and Stinear, TP},
title = {A human model of Buruli ulcer: Provisional protocol for a Mycobacterium ulcerans controlled human infection study.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {488},
pmid = {39386965},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Critical knowledge gaps have impeded progress towards reducing the global burden of disease due to Mycobacterium ulcerans, the cause of the neglected tropical disease Buruli ulcer (BU). Development of a controlled human infection model of BU has been proposed as an experimental platform to explore host-pathogen interactions and evaluate tools for prevention, diagnosis, and treatment. We have previously introduced the use case for a new human model and identified M. ulcerans JKD8049 as a suitable challenge strain. Here, we present a provisional protocol for an initial study, for transparent peer review during the earliest stages of protocol development. Following simultaneous scientific peer review and community/stakeholder consultation of this provisional protocol, we aim to present a refined protocol for institutional review board (IRB) evaluation.},
}

@article {pmid39387683,
year = {2024},
author = {Li, Z and Wang, Q and Huang, X and Wu, Y and Shan, D},
title = {Microbiome's role in musculoskeletal health through the gut-bone axis insights.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2410478},
pmid = {39387683},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/microbiology ; *Musculoskeletal Diseases/microbiology/physiopathology ; Animals ; Osteoarthritis/microbiology/therapy ; Osteoporosis/microbiology ; Bone Density ; Musculoskeletal System/microbiology ; },
abstract = {The interplay between the human microbiome and the musculoskeletal system represents a burgeoning field of research with profound implications for understanding and treating musculoskeletal disorders. This review articulates the pivotal role of the microbiome in modulating bone health, highlighting the gut-bone axis as a critical nexus for potential therapeutic intervention. Through a meticulous analysis of recent clinical research, we underscore the microbiome's influence on osteoporosis, sarcopenia, osteoarthritis, and rheumatoid arthritis, delineating both the direct and indirect mechanisms by which microbiota could impact musculoskeletal integrity and function. Our investigation reveals novel insights into the microbiota's contribution to bone density regulation, hormone production, immune modulation, and nutrient absorption, laying the groundwork for innovative microbiome-based strategies in musculoskeletal disease management. Significantly, we identify the challenges hindering the translation of research into clinical practice, including the limitations of current microbial sequencing techniques and the need for standardized methodologies in microbiome studies. Furthermore, we highlight promising directions for future research, particularly in the realm of personalized medicine, where the microbiome's variability offers unique opportunities for tailored treatment approaches. This review sets a new agenda for leveraging gut microbiota in the diagnosis, prevention, and treatment of musculoskeletal conditions, marking a pivotal step toward integrating microbiome science into clinical musculoskeletal care.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bone and Bones/microbiology
*Musculoskeletal Diseases/microbiology/physiopathology
Animals
Osteoarthritis/microbiology/therapy
Osteoporosis/microbiology
Bone Density
Musculoskeletal System/microbiology

@article {pmid39392836,
year = {2024},
author = {Daisley, BA and Allen-Vercoe, E},
title = {Microbes as medicine.},
journal = {Annals of the New York Academy of Sciences},
volume = {1541},
number = {1},
pages = {63-82},
pmid = {39392836},
issn = {1749-6632},
support = {950-232131//Canada Research Chairs/ ; PDF-402947//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Sciences and Engineering Research Council of Canada/ ; 2023//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Humans ; *Probiotics/therapeutic use ; *Microbiota/drug effects/physiology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Precision Medicine/methods ; Animals ; },
abstract = {Over the last two decades, advancements in sequencing technologies have significantly deepened our understanding of the human microbiome's complexity, leading to increased concerns about the detrimental effects of antibiotics on these intricate microbial ecosystems. Concurrently, the rise in antimicrobial resistance has intensified the focus on how beneficial microbes can be harnessed to treat diseases and improve health and offer potentially promising alternatives to traditional antibiotic treatments. Here, we provide a comprehensive overview of both established and emerging microbe-centric therapies, from probiotics to advanced microbial ecosystem therapeutics, examine the sophisticated ways in which microbes are used medicinally, and consider their impacts on microbiome homeostasis and health outcomes through a microbial ecology lens. In addition, we explore the concept of rewilding the human microbiome by reintroducing "missing microbes" from nonindustrialized societies and personalizing microbiome modulation to fit individual microbial profiles-highlighting several promising directions for future research. Ultimately, the advancements in sequencing technologies combined with innovative microbial therapies and personalized approaches herald a new era in medicine poised to address antibiotic resistance and improve health outcomes through targeted microbiome management.},
}

Humans
*Probiotics/therapeutic use
*Microbiota/drug effects/physiology
Anti-Bacterial Agents/therapeutic use/pharmacology
Precision Medicine/methods
Animals

@article {pmid39394961,
year = {2024},
author = {Branck, T and Hu, Z and Nickols, WA and Walsh, AM and Bhosle, A and Short, MI and Nearing, JT and Asnicar, F and McIver, LJ and Maharjan, S and Rahnavard, A and Louyakis, AS and Badri, DV and Brockel, C and Thompson, KN and Huttenhower, C},
title = {Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39394961},
issn = {1751-7370},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Dogs/microbiology ; Cats ; *Pets/microbiology ; *Feces/microbiology ; *Phylogeny ; *Metagenome ; Humans ; *Metagenomics ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g. differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the "One Health" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.},
}

Animals
*Gastrointestinal Microbiome/genetics
Dogs/microbiology
Cats
*Pets/microbiology
*Feces/microbiology
*Phylogeny
*Metagenome
Humans
*Metagenomics
Bacteria/genetics/classification/isolation & purification

@article {pmid39396734,
year = {2025},
author = {Kajova, M and Khawaja, T and Kainulainen, K and Kantele, A},
title = {Carbapenemase-producing Enterobacterales emerging in Finland's capital region over 2010-2023: increasing proportion of CPE cases first detected in clinical samples.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {31},
number = {2},
pages = {296-297},
doi = {10.1016/j.cmi.2024.10.005},
pmid = {39396734},
issn = {1469-0691},
}

@article {pmid39401296,
year = {2024},
author = {Wang, S and Ilves, M and Mäenpää, K and Zhao, L and El-Nezami, H and Karisola, P and Alenius, H},
title = {ZnO Nanoparticles as Potent Inducers of Dermal Immunosuppression in Contact Hypersensitivity in Mice.},
journal = {ACS nano},
volume = {18},
number = {43},
pages = {29479-29491},
pmid = {39401296},
issn = {1936-086X},
mesh = {Animals ; *Zinc Oxide/chemistry/pharmacology ; Mice ; *Dermatitis, Contact/immunology/pathology ; Humans ; Female ; Skin/drug effects/immunology/pathology ; Nanoparticles/chemistry ; Oxazolone ; Mice, Inbred BALB C ; THP-1 Cells ; Disease Models, Animal ; Metal Nanoparticles/chemistry ; },
abstract = {Nanosized zinc oxide (nZnO) metal particles are used in skin creams and sunscreens to enhance their texture and optical properties as UV filters. Despite their common use, little is known about the molecular mechanisms of nZnO exposure on damaged skin. We studied the effects of topically applied nZnO particles on allergic skin inflammation in an oxazolone (OXA)-induced contact hypersensitivity (CHS) mouse model. We investigated whether exposure to nZnO during the sensitization or challenge phase would induce immunological changes and modulate transcriptional responses. We followed skin thickness, cellular infiltration, and changes in the local transcriptome up to 28 days after the challenge. The responses peaked at 24 h and were fully resolved by 28 days. Co-exposure to nZnO and hapten did not interfere with the formation of the sensitization process. Conversely, during the hapten challenge, the application of nZnO fully suppressed the development of the CHS response by the inhibition of pro-inflammatory pathways, secretion of pro-inflammatory cytokines, and proliferation of immune cells. In differentiated and stimulated THP-1 cells and the CHS mouse model, we found that nZnO particles and Zn ions contributed to anti-inflammatory responses. The immunosuppressive properties of nZnO in inflamed skin are mediated by impaired IL-1R-, CXCR2-, and LTB4-mediated pathways. nZnO-induced dermal immunosuppression may be beneficial for individuals with contact allergies who use nZnO-containing cosmetic products. Our findings also provide a deeper understanding of the mechanisms of nZnO, which could be considered when developing nanoparticle-containing skin products.},
}

Animals
*Zinc Oxide/chemistry/pharmacology
Mice
*Dermatitis, Contact/immunology/pathology
Humans
Female
Skin/drug effects/immunology/pathology
Nanoparticles/chemistry
Oxazolone
Mice, Inbred BALB C
THP-1 Cells
Disease Models, Animal
Metal Nanoparticles/chemistry

@article {pmid39403892,
year = {2024},
author = {Wang, B and Shen, Y and Fang, J and Su, X and Xu, ZZ},
title = {DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {11},
number = {45},
pages = {e2404277},
pmid = {39403892},
issn = {2198-3844},
support = {2022YFA1304200//National Key RD Program of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Phylogeny ; Data Analysis ; Inflammatory Bowel Diseases/microbiology ; Female ; Male ; },
abstract = {Microbial data analysis poses significant challenges due to its high dimensionality, sparsity, and compositionality. Recent advances have shown that integrating abundance and phylogenetic information is an effective strategy for uncovering robust patterns and enhancing the predictive performance in microbiome studies. However, existing methods primarily focus on the hierarchical structure of phylogenetic trees, overlooking the evolutionary distances embedded within them. This study introduces DeepPhylo, a novel method that employs phylogeny-aware amplicon embeddings to effectively integrate abundance and phylogenetic information. DeepPhylo improves both the unsupervised discriminatory power and supervised predictive accuracy of microbiome data analysis. Compared to the existing methods, DeepPhylo demonstrates superiority in informing biologically relevant insights across five real-world microbiome use cases, including clustering of skin microbiomes, prediction of host chronological age and gender, diagnosis of inflammatory bowel disease (IBD) across 15 studies, and multilabel disease classification.},
}

Humans
*Microbiota/genetics
*Phylogeny
Data Analysis
Inflammatory Bowel Diseases/microbiology
Female
Male

@article {pmid39406893,
year = {2025},
author = {Ioannou, A and Berkhout, MD and Geerlings, SY and Belzer, C},
title = {Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {3},
pages = {162-177},
pmid = {39406893},
issn = {1740-1534},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Akkermansia/physiology/genetics/classification ; Probiotics/therapeutic use ; *Host Microbial Interactions ; *Verrucomicrobia/physiology/genetics/classification ; Animals ; Intestinal Mucosa/microbiology ; Phylogeny ; Mucins/metabolism ; },
abstract = {Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Akkermansia/physiology/genetics/classification
Probiotics/therapeutic use
*Host Microbial Interactions
*Verrucomicrobia/physiology/genetics/classification
Animals
Intestinal Mucosa/microbiology
Phylogeny
Mucins/metabolism

@article {pmid39408199,
year = {2024},
author = {Iannotti, L and Rueda García, AM and Palma, G and Fontaine, F and Scherf, B and Neufeld, LM and Zimmerman, R and Fracassi, P},
title = {Terrestrial Animal Source Foods and Health Outcomes for Those with Special Nutrient Needs in the Life Course.},
journal = {Nutrients},
volume = {16},
number = {19},
pages = {},
pmid = {39408199},
issn = {2072-6643},
support = {P30 DK056341/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Animals ; Child ; Female ; Humans ; Pregnancy ; *Dairy Products ; *Diet ; *Eggs ; Food Hypersensitivity/epidemiology/prevention & control ; *Meat ; Milk ; Nutrients/analysis ; },
abstract = {Background. Animal source foods are under scrutiny for their role in human health, yet some nutritionally vulnerable populations are largely absent from consideration. Methods. Applying a Population Intervention/Exposure Comparator Outcome (PICO/PECO) framework and prioritizing systematic review and meta-analyses, we reviewed the literature on terrestrial animal source foods (TASFs) and human health, by life course phase. Results. There were consistent findings for milk and dairy products on positive health outcomes during pregnancy and lactation, childhood, and among older adults. Eggs were found to promote early childhood growth, depending on context. Unprocessed meat consumption was associated with a reduced risk for anemia during pregnancy, improved cognition among school-age children, and muscle health in older adults. Milk and eggs represent a risk for food sensitivities/allergies, though prevalence is low, and individuals tend to outgrow the allergies. TASFs affect the human microbiome and associated metabolites with both positive and negative health repercussions, varying by type and quantity. Conclusions. There were substantial gaps in the evidence base for studies limiting our review, specifically for studies in populations outside high-income countries and for several TASF types (pig, poultry, less common livestock species, wild animals, and insects). Nonetheless, sufficient evidence supports an important role for TASFs in health during certain periods of the life course.},
}

Adult
Animals
Child
Female
Humans
Pregnancy
*Dairy Products
*Diet
*Eggs
Food Hypersensitivity/epidemiology/prevention & control
*Meat
Milk
Nutrients/analysis

@article {pmid39415150,
year = {2024},
author = {Ma, J and Wang, F and Zhu, Y and Tian, Y and Du, C and Yan, L and Ding, C and Wang, D},
title = {Oral microbiome dysbiosis may be associated with intra cranial aneurysms.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {1235},
pmid = {39415150},
issn = {1472-6831},
support = {2021J01217//Fujian Provincial Nature Foundation/ ; 2021Y2001//Technology Platform Construction Project of Fujian Province/ ; },
mesh = {Humans ; *Intracranial Aneurysm/microbiology ; Female ; Male ; Middle Aged ; *Dysbiosis/microbiology ; *Microbiota ; Case-Control Studies ; *Saliva/microbiology ; Mouth/microbiology ; RNA, Ribosomal, 16S/analysis ; Adult ; Aged ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Although the etiology of aneurysms remains elusive, recent advances in high-throughput sequencing technology and ongoing human microbiome investigations suggest a potential link between microbiome composition and the onset of various human diseases.

OBJECTIVE: This study aimed to utilize high-throughput 16 S rRNA gene sequencing to analyze the oral flora bacterial profiles of individuals, comparing patients with intracranial aneurysms to a healthy control group. Importantly, we sought to identify differences in the oral microbiota and offer novel insights and methods for early diagnosis and identification of intracranial aneurysms.

METHOD: Saliva samples were collected from 60 patients with cerebral aneurysms (case group) and 130 healthy individuals (control group). The V3-V4 region of the bacterial 16 S rRNA gene was amplified and sequenced using the HiSeq high-throughput sequencing platform to establish the bacterial profile. Sequencing data were analyzed using QIIME2 and Metastats software to compare composition differences and relative abundance at the phylum and genus levels in the oral microbiota of the two groups.

RESULTS: Significant differences in oral microbiota composition were observed between patients in the case and control groups (P < 0.05). Genus-level identification highlighted key positions occupied by Eubacterium, Saccharimonadaceae, Rothia, Gemella, Streptococcus, Lactobacillales, Phocaeicola, Bacteroides, Saccharimonadales, and Abiotrophia.

CONCLUSION: This study revealed noteworthy distinctions in the composition, abundance, and diversity of oral microbiota between intracranial aneurysm patients and healthy controls. These disparities suggest a potential correlation between oral microbiota and the development of intracranial aneurysms, offering new avenues for early diagnosis and intervention. However, limitations such as a small sample size, lack of prospective design, and absence of causal inference warrant further validation and exploration.},
}

Humans
*Intracranial Aneurysm/microbiology
Female
Male
Middle Aged
*Dysbiosis/microbiology
*Microbiota
Case-Control Studies
*Saliva/microbiology
Mouth/microbiology
RNA, Ribosomal, 16S/analysis
Adult
Aged
High-Throughput Nucleotide Sequencing

@article {pmid39419193,
year = {2024},
author = {Chen, H and Zeng, M and Batool, SS and Zhao, Y and Yu, Z and Zhou, J and Liu, K and Huang, J},
title = {Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer.},
journal = {Genomics},
volume = {116},
number = {6},
pages = {110951},
doi = {10.1016/j.ygeno.2024.110951},
pmid = {39419193},
issn = {1089-8646},
mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome ; *Neoadjuvant Therapy ; Chemoradiotherapy ; Female ; Male ; Middle Aged ; Metagenomics ; Aged ; Metagenome ; Feces/microbiology ; Bacteria/genetics/classification/metabolism ; },
abstract = {Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.},
}

Humans
*Rectal Neoplasms/therapy/microbiology/genetics/metabolism
*Gastrointestinal Microbiome
*Neoadjuvant Therapy
Chemoradiotherapy
Female
Male
Middle Aged
Metagenomics
Aged
Metagenome
Feces/microbiology
Bacteria/genetics/classification/metabolism

@article {pmid39421250,
year = {2024},
author = {Puhlmann, ML and van de Rakt, E and Kerezoudi, EN and Rangel, I and Brummer, RJ and Smidt, H and Kaper, FS and de Vos, WM},
title = {Analysis of the fermentation kinetics and gut microbiota modulatory effect of dried chicory root reveals the impact of the plant-cell matrix rationalizing its conversion in the distal colon.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {28},
pmid = {39421250},
issn = {2771-5965},
abstract = {Aim: The cell matrix of plant foods has received little attention in prebiotic fiber research. We aimed to understand the impact of the plant cell matrix in dried chicory root on its breakdown in the human gut to explain its reported beneficial effects on gut and metabolic health. Methods: We applied in vitro digestion and fermentation models together with an ex vivo gut barrier integrity model. Plant cell matrix intactness in the upper gastrointestinal tract was investigated by scanning electron microscopy. Colonic breakdown of inulin, and chicory root cubes and powder was assessed by gut microbiota analysis using 16S rRNA gene amplicon sequencing and determining the kinetics of changes in pH, gas, and short-chain fatty acid (SCFA) production. Finally, effects on gut barrier integrity were explored by exposing colonic biopsies to fermentation supernatants in an Ussing chamber model. Results: The plant cell matrix of dried chicory root cubes remained intact throughout upper gastrointestinal transit. Dried chicory root fermentation resulted in higher final relative abundances of pectin-degrading Monoglobus and butyrate-producing Roseburia spp. compared to inulin and a seven-fold increase in Bifidobacterium spp. in donors where these species were present. Dried chicory root cubes yielded similar total SCFAs but higher final butyrate levels than chicory root powder or isolated inulin with less gas produced. No uniform but donor-specific effects of fermentation supernatants on the maintenance of gut barrier integrity were detected. Conclusion: The intact plant cell matrix of dried chicory root affected its colonic breakdown kinetics and microbiota, underpinning its beneficial effect in vivo.},
}

@article {pmid39421255,
year = {2024},
author = {Geerlings, SY and van der Ark, K and Nijsse, B and Boeren, S and van Loosdrecht, M and Belzer, C and de Vos, WM},
title = {Omics-based analysis of Akkermansia muciniphila cultivation in food-grade media.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {36},
pmid = {39421255},
issn = {2771-5965},
abstract = {Background and Aim: Over the past years, the gut microbiota and its correlation to health and disease has been studied extensively. In terms of beneficial microbes, an increased interest in Akkermansia muciniphila (A. muciniphila) has been observed since its discovery. Direct evidence for the role of A. muciniphila in host health has been provided in both mice and human studies. However, for human interventions with A. muciniphila cells, industrial-scale fermentations are needed, and hence, the used cultivation media should be free of animal-derived components, food-grade, non-allergenic and allow for efficient growth to high densities to provide cost-effective production platforms. In this study, we assessed the growth and performance of A. muciniphila in batch bioreactors using newly developed plant-based media. Methods: The bioreactors were supplemented with varying carbon sources, including different ratios of N-acetylglucosamine (GlcNAc) and glucose. We monitored the growth of A. muciniphila in the plant-based medium using optical density (OD600) measurements and microscopy. In addition, we used a combination of biochemical analysis as well as transcriptional and proteomics analysis to gain detailed insight into the physiology. Results: Comparisons between growth on these media and that on mucin revealed differences at both transcriptome and proteome levels, including differences in the expression of glycosyltransferases, signaling proteins, and stress response. Furthermore, elongated cells and higher OD600 values were observed using the plant-based media as compared to cultivation media containing mucin. Conclusion: These differences do not hamper growth, and therefore, our data suggest that the food-grade medium composition described here could be used to produce A. muciniphila with high yields for therapeutic purposes.},
}

@article {pmid39421627,
year = {2024},
author = {Beschastnov, VV and Shirokova, IY and Belyanina, NA and Pogodin, IE and Tulupov, AA and Tochilina, AG and Belova, IV and Tyumenkov, YO and Kovalishena, OV and Soloveva, IV},
title = {Evaluation of the Feasibility of Using Commercial Wound Coatings as a Carrier Matrix for Bacteriophages.},
journal = {Sovremennye tekhnologii v meditsine},
volume = {16},
number = {1},
pages = {45-52},
pmid = {39421627},
issn = {2309-995X},
mesh = {Humans ; *Bacteriophages ; *Wound Infection/therapy ; Staphylococcus aureus/virology/drug effects ; Wound Healing ; Phage Therapy ; Bandages ; Feasibility Studies ; },
abstract = {UNLABELLED: The aim of the investigation is to study the possibility of applying commercial wound coatings for treating infected wounds as a carrier matrix for bacteriophages.

MATERIALS AND METHODS: Twelve varieties of commercial wound coverings based on biopolymers of natural and synthetic origin, a biological preparation Staphylophag produced by scientific-industrial association Microgen (Russia), registration certificate P N001973/01, and the S. aureus 3196 test strain (GenBank JARQZO000000000) isolated from a patient with a burn wound have been used in our work. The ability of commercial biological wound coatings to absorb solutions was examined by immersing them in a physiological solution (pH 7.0-7.2) followed by weighing. The lytic activity of three bacteriophage series against the test strain was studied using the Appelman method and a spot test. The lytic activity of the bacteriophage in the wound samples was studied within 7 days after its absorption by the wound coatings.

RESULTS: The greatest volume of fluid was absorbed by the LycoSorb, NEOFIX FibroSorb Ag, Biatravm, and Chitocol-S wound coatings. All bacteriophage series have been found to have a high lytic activity against the test strain. It has also been shown that Chitocol-S, Collachit-FA, Algipran, and Aquacel Ag Extra possessed their own inherent antibacterial activity under in vitro conditions stable for 7 days; moreover, the lysis zones of the test strain increased after their saturation with bacteriophage. On day 0, a high level of bacteriophage lytic activity with the maximum size of the test strain lysis zones from 49 to 59 mm have been found to remain in all samples of the wound coverings. The bacteriophage activity persisted for 1 day in the samples of Hydrofilm, Polypran, and NEOFIX FibroCold Ag coatings, up to 4 days in Algipran, Nano-Aseptica, and Biatravm coatings; and for 7 days in the Chitocol-S, Collachit-FA, Opsite Post-Op Visible, NEOFIX FibroSorb Ag, Aquacel Ag Extra, and LycoSorb samples.

CONCLUSION: Modern commercial wound dressings based on chitosan-collagen complex (Chitocol-S, Collachit-FA), polyurethane (Opsite Post-Op Visible, LycoSorb, NEOFIX FibroSorb Ag), and Hydrofiber (Aquacel Ag Extra) have a sufficient level of bacteriophage solution absorption, provide a stable preservation of the bacteriophage lytic activity under in vitro conditions up to 7 days. Thus, the in vitro studies prove the possibility of their use as a carrier matrix for bacteriophages.},
}

Humans
*Bacteriophages
*Wound Infection/therapy
Staphylococcus aureus/virology/drug effects
Wound Healing
Phage Therapy
Bandages
Feasibility Studies

@article {pmid39425798,
year = {2024},
author = {Goladze, S and Patpatia, S and Tuomala, H and Ylänne, M and Gachechiladze, N and de Oliveira Patricio, D and Skurnik, M and Sundberg, LR},
title = {Isolation and characterization of Yersinia phage fMtkYen3-01.},
journal = {Archives of virology},
volume = {169},
number = {11},
pages = {226},
pmid = {39425798},
issn = {1432-8798},
support = {PHDF-21-2176//Shota Rustaveli National Science Foundation/ ; #346772//Research Council of Finland/ ; },
mesh = {*Yersinia enterocolitica/virology/genetics ; *Genome, Viral/genetics ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; Yersinia Infections/microbiology/therapy/virology ; Base Composition ; Humans ; Phage Therapy/methods ; },
abstract = {Yersinia enterocolitica causes yersiniosis, the third most common gastrointestinal infection in humans throughout Europe. The emergence of multidrug resistance and the lack of effective new antibiotics have drawn attention to phage therapy as a treatment option. Here, we report the complete genome sequence of phage fMtkYen3-01, which infects Y. enterocolitica serotype O:3 strains. This phage has a genome 40,415 bp in length with 45.1% GC content and 49 predicted genes. fMtkYen3-01 infected 9.5% of the 42 Y. enterocolitica strains tested and showed stability at 25-40 °C, as well as pH 5.0-10.0. These results suggest the therapeutic potential of this phage.},
}

*Yersinia enterocolitica/virology/genetics
*Genome, Viral/genetics
*Bacteriophages/genetics/classification/isolation & purification/physiology
Yersinia Infections/microbiology/therapy/virology
Base Composition
Humans
Phage Therapy/methods

@article {pmid39429878,
year = {2024},
author = {Chen, J and Luo, J and Pouwels, S and Li, B and Wu, B and Abdelbaki, TN and Arcot, J and Yang, W},
title = {Dietary therapies interlinking with gut microbes toward human health: Past, present, and future.},
journal = {iMeta},
volume = {3},
number = {5},
pages = {e230},
pmid = {39429878},
issn = {2770-596X},
abstract = {Overview of personalized dietary therapies. This flow chart exhibits the future prospect for integrating human microbiome and bio-medical research to revolutionize the precise personalized dietary therapies. With the development of artificial intelligence (AI), incorporating database may achieve personalized dietary therapies with high precision.},
}

@article {pmid39435653,
year = {2024},
author = {Rastegar, S and Sabouri, S and Tadjrobehkar, O and Samareh, A and Niaz, H and Sanjari, N and Hosseini-Nave, H and Skurnik, M},
title = {Characterization of bacteriophage vB_AbaS_SA1 and its synergistic effects with antibiotics against clinical multidrug-resistant Acinetobacter baumannii isolates.},
journal = {Pathogens and disease},
volume = {82},
number = {},
pages = {},
pmid = {39435653},
issn = {2049-632X},
support = {//University of Helsinki/ ; KMU.AC.IR.400000652//Kerman University of Medical Sciences/ ; },
mesh = {*Acinetobacter baumannii/virology/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; *Bacteriophages/genetics/isolation & purification/physiology/classification ; *Acinetobacter Infections/microbiology ; Humans ; *Genome, Viral ; *Host Specificity ; Microbial Sensitivity Tests ; Sewage/virology/microbiology ; Phage Therapy ; DNA, Viral/genetics ; Viral Plaque Assay ; },
abstract = {Acinetobacter baumannii is a major cause of nosocomial infections globally. The increasing prevalence of multidrug-resistant (MDR) A. baumannii has become an important public health concern. To combat drug resistance, alternative methods such as phage therapy have been suggested. In total, 30 MDR A. baumannii strains were isolated from clinical specimens, and their antibiotic susceptibilities were determined. The Acinetobacter phage vB_AbaS_SA1, isolated from hospital sewage, was characterized. In addition to its plaque size, particle morphology, and host range, its genome sequence was determined and annotated. Finally, the antibacterial effects of phage alone, antibiotics alone, and phage/antibiotic combinations were assessed against the A. baumannii strains. Phage vB_AbaS_SA1 had siphovirus morphology, showed a latent period of 20 min, and a 250 PFU/cell (plaque forming unit/cell) burst size. When combined with antibiotics, vB_AbaS_SA1 (SA1) showed a significant phage-antibiotic synergy effect and reduced the overall effective concentration of antibiotics in time-kill assessments. The genome of SA1 is a linear double-stranded DNA of 50 108 bp in size with a guanine-cytosine (GC) content of 39.15%. Despite the potent antibacterial effect of SA1, it is necessary to perform additional research to completely elucidate the mechanisms of action and potential constraints associated with utilizing this bacteriophage.},
}

*Acinetobacter baumannii/virology/drug effects
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Multiple, Bacterial
*Bacteriophages/genetics/isolation & purification/physiology/classification
*Acinetobacter Infections/microbiology
Humans
*Genome, Viral
*Host Specificity
Microbial Sensitivity Tests
Sewage/virology/microbiology
Phage Therapy
DNA, Viral/genetics
Viral Plaque Assay

@article {pmid39439268,
year = {2025},
author = {Weinkove, D},
title = {Folates, bacteria and ageing: insights from the model organism C. elegans in the study of nutrition and ageing.},
journal = {The Proceedings of the Nutrition Society},
volume = {84},
number = {3},
pages = {259-263},
pmid = {39439268},
issn = {1475-2719},
support = {BB/H01974X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Caenorhabditis elegans/microbiology/physiology ; Animals ; *Folic Acid/metabolism/biosynthesis ; *Aging/physiology ; *Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/metabolism ; Models, Animal ; Diet ; Nutritional Status ; },
abstract = {The relationship between nutrition and ageing is complex. The metabolism and synthesis of micronutrients within the gut microbiome can influence human health but is challenging to study. Furthermore, studying ageing in humans is time-consuming and difficult to control for environmental factors. Studies in model organisms can guide research efforts in this area. This review describes how the nematode Caenorhabditis elegans can be used to study how bacteria and diet influence ageing and inform follow-on studies in humans. It is known that certain bacteria accelerate ageing in C. elegans. This age-accelerating effect is prevented by inhibiting folate synthesis within the bacteria, and we propose that in the human microbiome, certain bacteria also accelerate ageing in a way that can be modulated by interfering with bacterial folate synthesis. Bacterial-derived folates do not promote ageing themselves; rather, ageing is accelerated by bacteria in some way, either through secondary metabolites or other bacterial activity, which is dependent on bacterial folate synthesis. In humans, it may be possible to inhibit bacterial folate synthesis in the human gut while maintaining healthy folate status in the body via food and supplementation. The supplement form of folic acid has a common breakdown product that can be used by bacteria to increase folate synthesis. Thus, supplementation with folic acid may not be good for health in certain circumstances such as in older people or those with an excess of proteobacteria in their microbiome. For these groups, alternative supplement strategies may be a safer way to ensure adequate folate levels.},
}

*Caenorhabditis elegans/microbiology/physiology
Animals
*Folic Acid/metabolism/biosynthesis
*Aging/physiology
*Gastrointestinal Microbiome/physiology
Humans
*Bacteria/metabolism
Models, Animal
Diet
Nutritional Status

@article {pmid39440978,
year = {2024},
author = {Soto Ocaña, J and Friedman, ES and Keenan, O and Bayard, NU and Ford, E and Tanes, C and Munneke, MJ and Beavers, WN and Skaar, EP and Bittinger, K and Zemel, BS and Wu, GD and Zackular, JP},
title = {Metal availability shapes early life microbial ecology and community succession.},
journal = {mBio},
volume = {15},
number = {11},
pages = {e0153424},
pmid = {39440978},
issn = {2150-7511},
support = {R01DK107565, P30DK050306//HHS | National Institutes of Health (NIH)/ ; R35GM138369//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; UL1 TR001878/TR/NCATS NIH HHS/United States ; R01DK107565//HHS | National Institutes of Health (NIH)/ ; P30 DK050306/DK/NIDDK NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Metals/metabolism ; *Leukocyte L1 Antigen Complex/metabolism/analysis ; Bacteria/metabolism/classification/genetics ; Breast Feeding ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Infant, Newborn ; Microbiota ; Infant Formula ; },
abstract = {The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, assembly of this microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life. To date, the role of host-mediated nutritional immunity and metal availability in shaping microbial community assembly and succession early in life has not been explored in depth. Using a human infant cohort, we show that the metal-chelating protein calprotectin is highly abundant in infants. Taxa previously shown to be successful early colonizers of the infant gut, such as Enterococcus, Enterobacteriaceae, and Bacteroides, are highly resistant to experimental metal starvation in culture. Lactobacillus, meanwhile, is highly susceptible to metal restriction, pointing to a possible mechanism by which host-mediated metal limitation shapes the fitness of early colonizing taxa in the infant gut. We further demonstrate that formula-fed infants harbor markedly higher levels of metals in their gastrointestinal tract compared to breastfed infants. Formula-fed infants with high levels of metals harbor distinct microbial communities compared to breastfed infants, with higher levels of Enterococcus, Enterobacter, and Klebsiella, taxa which show increased resistance to the toxic effects of high metal concentrations. These data highlight a new paradigm in microbial community assembly and suggest an unappreciated role for nutritional immunity and dietary metals in shaping the earliest colonization events of the microbiota.IMPORTANCEEarly life represents a critical window for microbial colonization of the human gastrointestinal tract. Surprisingly, we still know little about the rules that govern the successful colonization of infants and the factors that shape the success of early life microbial colonizers. In this study, we report that metal availability is an important factor in the assembly and succession of the early life microbiota. We show that the host-derived metal-chelating protein, calprotectin, is highly abundant in infants and successful early life colonizers can overcome metal restriction. We further demonstrate that feeding modality (breastmilk vs formula) markedly impacts metal levels in the gut, potentially influencing microbial community succession. Our work suggests that metals, a previously unexplored aspect of early life ecology, may play a critical role in shaping the early events of microbiota assembly in infants.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Metals/metabolism
*Leukocyte L1 Antigen Complex/metabolism/analysis
Bacteria/metabolism/classification/genetics
Breast Feeding
Feces/microbiology
Gastrointestinal Tract/microbiology
Infant, Newborn
Microbiota
Infant Formula

@article {pmid39443812,
year = {2025},
author = {Joos, R and Boucher, K and Lavelle, A and Arumugam, M and Blaser, MJ and Claesson, MJ and Clarke, G and Cotter, PD and De Sordi, L and Dominguez-Bello, MG and Dutilh, BE and Ehrlich, SD and Ghosh, TS and Hill, C and Junot, C and Lahti, L and Lawley, TD and Licht, TR and Maguin, E and Makhalanyane, TP and Marchesi, JR and Matthijnssens, J and Raes, J and Ravel, J and Salonen, A and Scanlan, PD and Shkoporov, A and Stanton, C and Thiele, I and Tolstoy, I and Walter, J and Yang, B and Yutin, N and Zhernakova, A and Zwart, H and , and Doré, J and Ross, RP},
title = {Examining the healthy human microbiome concept.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {3},
pages = {192-205},
pmid = {39443812},
issn = {1740-1534},
mesh = {Humans ; *Microbiota/physiology ; },
abstract = {Human microbiomes are essential to health throughout the lifespan and are increasingly recognized and studied for their roles in metabolic, immunological and neurological processes. Although the full complexity of these microbial communities is not fully understood, their clinical and industrial exploitation is well advanced and expanding, needing greater oversight guided by a consensus from the research community. One of the most controversial issues in microbiome research is the definition of a 'healthy' human microbiome. This concept is complicated by the microbial variability over different spatial and temporal scales along with the challenge of applying a unified definition to the spectrum of healthy microbiome configurations. In this Perspective, we examine the progress made and the key gaps that remain to be addressed to fully harness the benefits of the human microbiome. We propose a road map to expand our knowledge of the microbiome-health relationship, incorporating epidemiological approaches informed by the unique ecological characteristics of these communities.},
}

Humans
*Microbiota/physiology

@article {pmid39443987,
year = {2024},
author = {Levi Mortera, S and Marzano, V and Rapisarda, F and Marangelo, C and Pirona, I and Vernocchi, P and Di Michele, M and Del Chierico, F and Quintero, MA and Fernandez, I and Hazime, H and Killian, RM and Solis, N and Ortega, M and Damas, OM and Proksell, S and Kerman, DH and Deshpande, AR and Garces, L and Scaldaferri, F and Gasbarrini, A and Abreu, MT and Putignani, L},
title = {Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn's disease location.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {217},
pmid = {39443987},
issn = {2049-2618},
mesh = {Humans ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Feces/microbiology ; Adult ; *Proteomics ; Middle Aged ; Diet ; Dietary Fiber/administration & dosage ; Bacteria/classification/isolation & purification/genetics ; Colon/microbiology ; Young Adult ; Faecalibacterium/isolation & purification ; },
abstract = {BACKGROUND: Crohn's disease (CD) is characterized by chronic intestinal inflammation. Diet is a key modifiable factor influencing the gut microbiome (GM) and a risk factor for CD. However, the impact of diet modulation on GM function in CD patients is understudied. Herein, we evaluated the effect of a high-fiber, low-fat diet (the Mi-IBD diet) on GM function in CD patients. All participants were instructed to follow the Mi-IBD diet for 8 weeks. One group of CD patients received one-time diet counseling only (Gr1); catered food was supplied for the other three groups, including CD patients (Gr2) and dyads of CD patients and healthy household controls (HHCs) residing within the same household (Gr3-HHC dyads). Stool samples were collected at baseline, week 8, and week 36, and analyzed by liquid chromatography-tandem mass spectrometry.

RESULTS: At baseline, the metaproteomic profiles of CD patients and HHCs differed. The Mi-IBD diet significantly increased carbohydrate and iron transport and metabolism. The predicted microbial composition underlying the metaproteomic changes differed between patients with ileal only disease (ICD) or colonic involvement: ICD was characterized by decreased Faecalibacterium abundance. Even on the Mi-IBD diet, the CD patient metaproteome displayed significant underrepresentation of carbohydrate and purine/pyrimidine synthesis pathways compared to that of HHCs. Human immune-related proteins were upregulated in CD patients compared to HHCs.

CONCLUSIONS: The Mi-IBD diet changed the microbial function of CD patients and enhanced carbohydrate metabolism. Our metaproteomic results highlight functional differences in the microbiome according to disease location. Notably, our dietary intervention yielded the most benefit for CD patients with colonic involvement compared to ileal-only disease. Video Abstract.},
}

Humans
*Crohn Disease/microbiology
*Gastrointestinal Microbiome
Male
Female
*Feces/microbiology
Adult
*Proteomics
Middle Aged
Diet
Dietary Fiber/administration & dosage
Bacteria/classification/isolation & purification/genetics
Colon/microbiology
Young Adult
Faecalibacterium/isolation & purification

@article {pmid39447121,
year = {2024},
author = {Jia, B and Baek, JH and Lee, JK and Sun, Y and Kim, KH and Jung, JY and Jeon, CO},
title = {Expanding the β-Lactamase Family in the Human Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {11},
number = {46},
pages = {e2403563},
pmid = {39447121},
issn = {2198-3844},
support = {2024SSY0104//Pioneer"and"Leading Goose"R&DProgram of Zhejiang/ ; 2023C4S01002//Xianghu Laboratory/ ; 2018R1A5A1025077//Xianghu Laboratory/ ; 2018R1A5A1025077//Ministry of Science and ICT of the Ministry of Science and ICT, Republic of Korea/ ; 2021003420003//Korea Environment Industry & Technology Institute (KEITI) through the Project to make multi-ministerial national biological research resources more advanced, funded by Korea Ministry of Environment (MOE), Republic of Korea/ ; },
mesh = {Humans ; *beta-Lactamases/metabolism/genetics ; Female ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics/physiology/drug effects ; Male ; Adult ; Anti-Bacterial Agents/pharmacology ; beta-Lactams/pharmacology ; Middle Aged ; },
abstract = {β-lactams, the most common antibiotics globally, have resistance primarily determined by β-lactamases. Human microbiota and β-lactams influence mutually; however, β-lactamase variety and abundance in the human microbiome remain partially understood. This study aimed to elucidate the diversity, abundance, and substrate spectrum of β-lactamases. 1369 characterized β-lactamases and 16 204 putative sequences are collected from protein databases. Upon clustering analysis and biochemical assays, nine proteins exhibiting less than 35% identity to those previously characterized are confirmed as β-lactamases. These newly identified β-lactamases originated from eight distinct clusters comprising 1163 β-lactamases. Quantifying healthy participants (n = 2394) across 19 countries using functionally confirmed clusters revealed that Japan have the highest gut β-lactamase abundance (log2[reads per million (RPM)] = 6.52) and Fiji have the lowest (log2[RPM] = 2.31). The β-lactamase abundance is correlated with β-lactam consumption (R = 0.50, p = 0.029) and income (R = 0.51, p = 0.024). Comparing individuals with ailments with healthy participants, β-lactamase abundance in the gut is increased significantly in patients with colorectal cancer, cardiovascular diseases, breast cancer, and epilepsy. These outcomes provide insights into investigating antibiotic resistance, antibiotic stewardship, and gut microbiome-antibiotic interactions.},
}

Humans
*beta-Lactamases/metabolism/genetics
Female
Microbiota/genetics
Gastrointestinal Microbiome/genetics/physiology/drug effects
Male
Adult
Anti-Bacterial Agents/pharmacology
beta-Lactams/pharmacology
Middle Aged

@article {pmid39450961,
year = {2024},
author = {Sansonetti, PJ and Doré, J},
title = {[The human microbiome proofed by the Anthropocene: from correlation to causality and intervention].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {10},
pages = {757-765},
doi = {10.1051/medsci/2024121},
pmid = {39450961},
issn = {1958-5381},
mesh = {Humans ; *Microbiota/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Biodiversity ; Causality ; Climate Change ; },
abstract = {The deleterious effects of human activities on biodiversity in the vegetal and animal world, and on climate changes are now well-established facts. However, little is yet known on the impact of human activities on microbial diversity on the planet and more specifically on the human microbiota Large implementation of metagenomics allows exaustive microbial cataloguing with broad spatio-temporal resolution of human microbiota. A reduction in bacterial richness and diversity in the human microbiota, particularly in the intestinal tract, is now established and particularly obvious in the most industrialized regions of the planet. Massive, uncontrolled use of antibiotics, drastic changes in traditional food habits and some elements of the "global exposome" that remain to identify are usually considered as stressors accounting for this situation of "missing microbes". As a consequence, a dysbiotic situation develops, a "dysbiosis" being characterized by the erosion of the central core of shared bacterial species across individuals and the development of opportunistic "pathobionts" in response to a weaker barrier capacity of these impoverished microbiota. The current challenge is to establish a causality link between the extension of these dysbiotic situations and the steady emergence of epidemic, non-communicable diseases such as asthma, allergy, obesity, diabetes, autoimmune diseases and some cancers. Experimental animal models combined with controlled, prospective clinical interventions are in demand to consolidate causality links, with the understanding that in the deciphering of the mechanisms of alteration of the human-microbiome symbiosis resides a novel exciting chapter of medicine: "microbial medicine".},
}

Humans
*Microbiota/physiology
Animals
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
Biodiversity
Causality
Climate Change

@article {pmid39452183,
year = {2024},
author = {Otava, UE and Tervo, L and Havela, R and Vuotari, L and Ylänne, M and Asplund, A and Patpatia, S and Kiljunen, S},
title = {Phage-Antibiotic Combination Therapy against Recurrent Pseudomonas Septicaemia in a Patient with an Arterial Stent.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {39452183},
issn = {2079-6382},
support = {336519//Research Council of Finland/ ; PROFI7//Research Council of Finland/ ; n.a.//Jane and Aatos Erkko Foundation/ ; },
abstract = {Background: Intravascular stent infections are often associated with high risks of morbidity and mortality. We report here a case of a patient with an arterial stent and recurrent Pseudomonas septicaemias successfully treated with phage-meropenem combination therapy. Methods: A 75-year-old female with arteriosclerosis and comorbidities went through a femoropopliteal bypass with prosthesis in the right inguinal area. After the bypass, she developed a recurring Pseudomonas aeruginosa infection and also neutropenia during different antibiotics. A rapidly growing pseudoaneurysm in the right inguinal area led to an emergency intra-arterial stent placement during blood stream infection, later suspected to host a P. aeruginosa biofilm. Removing the stent was deemed precarious, and phage therapy was considered as a compassionate treatment option. A three-phage cocktail infecting the P. aeruginosa strain was prepared and administered intravenously together with meropenem for two weeks, after which, a ten-month follow-up was carried out. Results: No adverse reactions occurred during the phage therapy treatment, while infection markers were normalized. In addition, recovery was seen in a PET-CT scan. During the 10-month follow-up, no further P. aeruginosa septicaemias occurred. Conclusions: Phage-meropenem combination therapy was thus found safe and effective in the treatment of recurrent Pseudomonas septicaemia in a patient with an arterial stent.},
}

@article {pmid39455951,
year = {2024},
author = {Rastegar, S and Skurnik, M and Tadjrobehkar, O and Samareh, A and Samare-Najaf, M and Lotfian, Z and Khajedadian, M and Hosseini-Nave, H and Sabouri, S},
title = {Synergistic effects of bacteriophage cocktail and antibiotics combinations against extensively drug-resistant Acinetobacter baumannii.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1208},
pmid = {39455951},
issn = {1471-2334},
support = {402000840//Hossein Hosseini-Nave/ ; },
mesh = {*Acinetobacter baumannii/virology/drug effects ; *Biofilms/drug effects/growth & development ; *Anti-Bacterial Agents/pharmacology ; *Bacteriophages/physiology ; *Acinetobacter Infections/microbiology/therapy ; Humans ; *Drug Resistance, Multiple, Bacterial ; Phage Therapy/methods ; Microbial Sensitivity Tests ; },
abstract = {BACKGROUND: The extensively drug-resistant (XDR) strains of Acinetobacter baumannii have become a major cause of nosocomial infections, increasing morbidity and mortality worldwide. Many different treatments, including phage therapy, are attractive ways to overcome the challenges of antibiotic resistance.

METHODS: This study investigates the biofilm formation ability of 30 XDR A. baumannii isolates and the efficacy of a cocktail of four tempetate bacteriophages (SA1, Eve, Ftm, and Gln) and different antibiotics (ampicillin/sulbactam, meropenem, and colistin) in inhibiting and degrading the biofilms of these strains.

RESULTS: The majority (83.3%) of the strains exhibited strong biofilm formation. The bacteriophage cocktail showed varying degrees of effectiveness against A. baumannii biofilms, with higher concentrations generally leading to more significant inhibition and degradation rates. The antibiotics-bacteriophage cocktail combinations also enhanced the inhibition and degradation of biofilms.

CONCLUSION: The findings suggested that the bacteriophage cocktail is an effective tool in combating A. baumannii biofilms, with its efficacy depending on the concentration. Combining antibiotics with the bacteriophage cocktail improved the inhibition and removal of biofilms, indicating a promising strategy for managing A. baumannii infections. These results contribute to our understanding of biofilm dynamics and the potential of bacteriophage cocktails as a novel therapeutic approach to combat antibiotic-resistant bacteria.},
}

*Acinetobacter baumannii/virology/drug effects
*Biofilms/drug effects/growth & development
*Anti-Bacterial Agents/pharmacology
*Bacteriophages/physiology
*Acinetobacter Infections/microbiology/therapy
Humans
*Drug Resistance, Multiple, Bacterial
Phage Therapy/methods
Microbial Sensitivity Tests

@article {pmid39458307,
year = {2024},
author = {Krause, JL and Engelmann, B and Lallinger, DJD and Rolle-Kampczyk, U and von Bergen, M and Chang, HD},
title = {Multi-Omics Analysis Unravels the Impact of Stool Sample Logistics on Metabolites and Microbial Composition.},
journal = {Microorganisms},
volume = {12},
number = {10},
pages = {},
pmid = {39458307},
issn = {2076-2607},
support = {NNF21OC0066551//Novo Nordisk Foundation/ ; //Dr. Rolf M. Schwiete Stiftung/ ; 375876048//Deutsche Forschungsgemeinschaft/ ; 831434//Innovative Medicines Initiative/ ; },
abstract = {Human health and the human microbiome are inevitably intertwined, increasing their relevance in clinical research. However, the collection, transportation and storage of faecal samples may introduce bias due to methodological differences, especially since postal shipping is a common practise in large-scale clinical cohort studies. Using four different Omics layer, we determined the structural (16S rRNA sequencing, cytometric microbiota profiling) and functional integrity (SCFAs, global metabolome) of the microbiota in relation to different easy-to-handle conditions. These conditions were storage at -20 °C, -20 °C as glycerol stock, 4 °C and room temperature with and without oxygen exposure for a maximum of one week. Storage time affected the microbiota on all Omics levels. However, the magnitude was donor-dependent, highlighting the need for purpose-optimized sample collection in clinical multi-donor studies. The effects of oxygen exposure were negligible for all analyses. At ambient temperature, SCFA and compositional profiles were stable for 24 h and 48 h, respectively, while at 4 °C, SCFA profiles were maintained for 48 h. The global metabolome was highly susceptible, already changing at 24 h in non-frozen conditions. Thus, faecal microbiota was best preserved on all levels when transported as a native sample frozen within 24 h, leading to the least biased outcomes in the analysis. We conclude that the immediate freezing of native stool samples for transportation to the lab is best suited for planned multi-Omics analyses that include metabolomics to extend standard sequencing approaches.},
}

@article {pmid39458350,
year = {2024},
author = {Marangelo, C and Vernocchi, P and Del Chierico, F and Scanu, M and Marsiglia, R and Petrolo, E and Fucà, E and Guerrera, S and Valeri, G and Vicari, S and Putignani, L},
title = {Stratification of Gut Microbiota Profiling Based on Autism Neuropsychological Assessments.},
journal = {Microorganisms},
volume = {12},
number = {10},
pages = {},
pmid = {39458350},
issn = {2076-2607},
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Investigations of gut microbiota (GM) play an important role in deciphering disease severity and symptoms. Overall, we stratified 70 ASD patients by neuropsychological assessment, based on Calibrated Severity Scores (CSSs) of the Autism Diagnostic Observation Schedule-Second edition (ADOS-2), Child Behavior Checklist (CBCL) and intelligent quotient/developmental quotient (IQ/DQ) parameters. Hence, metataxonomy and PICRUSt-based KEGG predictions of fecal GM were assessed for each clinical subset. Here, 60% of ASD patients showed mild to moderate autism, while the remaining 40% showed severe symptoms; 23% showed no clinical symptoms, 21% had a risk of behavior problems and 56% had clinical symptoms based on the CBCL, which assesses internalizing problems; further, 52% had no clinical symptoms, 21% showed risk, and 26% had clinical symptoms classified by CBCL externalizing problems. Considering the total CBCL index, 34% showed no clinical symptoms, 13% showed risk, and 52% had clinical symptoms. Here, 70% of ASD patients showed cognitive impairment/developmental delay (CI/DD). The GM of ASDs with severe autism was characterized by an increase in Veillonella, a decrease in Monoglobus pectinilyticus and a higher microbial dysbiosis index (MDI) when compared to mild-moderate ASDs. Patients at risk for behavior problems and showing clinical symptoms were characterized by a GM with an increase of Clostridium, Eggerthella, Blautia, Intestinibacter, Coprococcus, Ruminococcus, Onthenecus and Bariatricus, respectively. Peptidoglycan biosynthesis and biofilm formation KEGGs characterized patients with clinical symptoms, while potential microbiota-activated PPAR-γ-signaling was seen in CI/DD patients. This evidence derived from GM profiling may be used to further improve ASD understanding, leasing to a better comprehension of the neurological phenotype.},
}

@article {pmid39458569,
year = {2024},
author = {Toivio, L and Launonen, H and Lindén, J and Lehto, M and Vapaatalo, H and Salmenkari, H and Korpela, R},
title = {Correction: Toivio et al. Ketogenic Diet High in Saturated Fat Promotes Colonic Claudin Expression without Changes in Intestinal Permeability to Iohexol in Healthy Mice. Nutrients 2024, 16, 18.},
journal = {Nutrients},
volume = {16},
number = {20},
pages = {},
pmid = {39458569},
issn = {2072-6643},
abstract = {Text Correction [...].},
}

@article {pmid39465215,
year = {2024},
author = {Lam, MI and Gleason, K and Repp, AB and Yeo, S and Vojnits, K and MacNaughton, P and Pakpour, S},
title = {The spatial and temporal effect of electrochromic windows on indoor and human microbiome in an inpatient hospital.},
journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE},
volume = {4},
number = {1},
pages = {e188},
pmid = {39465215},
issn = {2732-494X},
abstract = {OBJECTIVE: Improving the hospital environment and developing novel disinfection strategies are critical for infection control in healthcare settings. In this study, we explored the effects of electrochromic (EC) windows on indoor and patient microbiome in an inpatient hospital.

PATIENT AND SETTING: Hematology-Oncology patients at the University of Vermont Medical Center.

METHODS: We conducted a prospective study in ten occupied patient rooms. Five of the patient rooms had active EC windows that tint dynamically to control for heat and glare, and the other five rooms had deactivated EC windows that simulated traditional windows and blinds. Samples were collected one day before patient admission as baseline and on the 1st, 3rd, and 5th day of the patient stay. Total bacterial abundance and bacterial community structure were determined through quantitative PCR and 16s rRNA Illumina MiSeq sequencing, respectively.

RESULTS: Patient rooms with active EC windows had significantly lower light intensity and temperature than traditional patient rooms with blinds. The absolute bacterial abundance and diversities on windows were significantly lower in rooms with EC windows and the bacterial composition changed after one day EC window activation. Compared to baseline, relative abundance of the Staphylococcus genus was significantly lower on EC window surface during the five-day experiment. In contrast, the air microbiome was more diverse in rooms with EC windows.

CONCLUSION: Active electrochromic (EC) windows in patient rooms result in lower light intensity and temperature, reduced bacterial abundance and diversities on window surfaces, and a more diverse air microbiome, informing future healthcare design.},
}

@article {pmid39466852,
year = {2024},
author = {Chen, H and Huang, S and Yao, S and Wang, J and Huang, J and Yu, Z},
title = {Multi-omics analyses of Bacillus amyloliquefaciens treated mice infected with Schistosoma japonicum reveal dynamics change of intestinal microbiome and its associations with host metabolism.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {10},
pages = {e0012583},
pmid = {39466852},
issn = {1935-2735},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Bacillus amyloliquefaciens/metabolism/genetics ; *Schistosoma japonicum/metabolism ; *Schistosomiasis japonica ; *Probiotics/administration & dosage ; Female ; Multiomics ; },
abstract = {BACKGROUND: Schistosomiasis japonica is a serious threat to human health. It causes damage to the intestine and liver. Probiotic therapy has been shown to be effective in alleviating intestinal diseases and improving host health. Previous studies have found that Bacillus amyloliquefaciens could alleviate the pathological symptoms of schistosomiasis japonica, but the regulatory mechanism of alleviating schistosomiasis japonica is still unknown.

PRINCIPAL FINDINGS: This study analyzed the dynamic changes of intestinal microbiome in mice infected with Schistosoma japonicum after the intervention of B. amyloliquefaciens and its connection to host metabolism by multi-omics sequencing technology. B. amyloliquefaciens was found to significantly regulate the homeostasis of intestinal microbiota by promoting the growth of beneficial bacteria and inhibiting potential pathogenic bacteria and protect the number of core microbes. Meanwhile, the genes related to the metabolism of glycerophospholipids and amino acid from intestinal microbiome changed significantly, and were shown to be significantly positively correlated with the associated metabolites of microbial origin. Moreover, host metabolism (lipid metabolism and steroid hormone biosynthesis) was also found to be significantly regulated.

CONCLUSIONS: The recovery of intestinal microbial homeostasis and the regulation of host metabolism revealed the potential probiotic properties of B. amyloliquefaciens, which also provided new ideas for the prevention and adjuvant treatment of schistosomiasis japonica.},
}

Animals
Mice
*Gastrointestinal Microbiome
*Bacillus amyloliquefaciens/metabolism/genetics
*Schistosoma japonicum/metabolism
*Schistosomiasis japonica
*Probiotics/administration & dosage
Female
Multiomics

@article {pmid39470190,
year = {2024},
author = {Toyomane, K and Kimura, Y and Fukagawa, T and Yamagishi, T and Watanabe, K and Akutsu, T and Asahi, A and Kubota, S and Sekiguchi, K},
title = {Metagenomic sequencing of CRISPRs as a new marker to aid in personal identification with low-biomass samples.},
journal = {mSystems},
volume = {9},
number = {11},
pages = {e0103824},
pmid = {39470190},
issn = {2379-5077},
support = {20K18991,24K20264//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Humans ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Metagenomics/methods ; *Skin/microbiology ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Metagenome/genetics ; Genetic Markers/genetics ; },
abstract = {The high specificity of the human skin microbiome is expected to provide a new marker for personal identification. Metagenomic sequencing of clustered regularly interspaced short palindromic repeats (CRISPRs), which we call metaCRISPR typing, was shown to achieve personal identification accurately. However, the intra-individual variability observed in previous studies, which may be due to poor DNA yields from skin samples, has resulted in non-reproducible results. Furthermore, whether metaCRISPR typing can assist in the forensic human DNA analysis of low-biomass samples, from which the information obtained is insufficient, is unknown. In the present study, we sequenced serially diluted control streptococcal CRISPRs cloned into plasmids to determine the minimum copy number required to obtain reproducible results from metaCRISPR typing. We found that at least 10[2] copies of CRISPRs are necessary to obtain reproducible results. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA typing. When the DNA extracted from the skin swabs was diluted, no information was obtained from six out of eight samples by human DNA typing. On the other hand, beta diversity indices of spacer sequences compared with reference samples were below 0.8 for three out of six samples, for which no information was obtained from human DNA analysis, indicating that the spacers observed in these samples were similar to those in the references. These results indicate that metaCRISPR typing may contribute to the identification of individuals from whom the samples were obtained, even in cases where human DNA yields are insufficient to perform human DNA analysis.IMPORTANCEPrevious studies have developed new personal identification methods utilizing personal differences in the skin microbiome. However, intra-individual diversity of skin microbiome may preclude the application of microbiome-based personal identification. Moreover, no study has compared microbiome-based personal identification and practical human DNA analysis. Here, we revealed that the results of metaCRISPR typing, a previously developed microbiome-based personal identification method, are stable if the copy number of the marker gene is sufficient. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA analysis. Our results indicate that metaCRISPR typing may provide additional information for personal identification using low-biomass samples that cannot be used for conventional human DNA analysis.},
}

Humans
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics
*Metagenomics/methods
*Skin/microbiology
Microbiota/genetics
Sequence Analysis, DNA/methods
Metagenome/genetics
Genetic Markers/genetics

@article {pmid39470240,
year = {2024},
author = {Dumann, G and Rohland, O and Abdel-Glil, MY and Allen, RJ and Bauer, M and Busch, A},
title = {Draft genomes of the bile duct microbiome strains Klebsiella pneumoniae and Enterococcus lactis isolated from bilioenteric drainages with biofilm-forming abilities.},
journal = {Microbiology resource announcements},
volume = {13},
number = {12},
pages = {e0020224},
pmid = {39470240},
issn = {2576-098X},
support = {EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; },
abstract = {We describe the genetic properties of two strains isolated from the elusive bile duct microbiome from solid organ transplant patients. Bacterial strains Enterococcus lactis (MS-STENT-08-E-001) and Klebsiella pneumoniae (MS-STENT-01-M-001) were isolated from the biofilms of bile duct catheters.},
}

@article {pmid39470241,
year = {2024},
author = {Bouchier, C and Touak, G and Rei, D and Clermont, D},
title = {Complete genome sequence of two Christensenella minuta strains CIP 112228 and CIP 112229, isolated from human fecal samples.},
journal = {Microbiology resource announcements},
volume = {13},
number = {12},
pages = {e0076624},
pmid = {39470241},
issn = {2576-098X},
abstract = {Christensenella minuta is one of the representative bacterial species of the human gut microbiome. We report the complete genome sequence of two strains, Christensenella minuta CIP 112228 and CIP 112229, isolated from two healthy volunteers.},
}

@article {pmid39470277,
year = {2024},
author = {Xie, J and Zhang, X and Cheng, L and Deng, Y and Ren, H and Mu, M and Zhao, L and Mu, C and Chen, J and Liu, K and Ma, R},
title = {Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0180824},
pmid = {39470277},
issn = {2165-0497},
support = {No. YNWR-MY-2020-044//Yunnan Provincial Health Commission/ ; No. 202102AA310002//Fuwai Yunnan Hospital,Chinese Academy of Medical Sciences/ ; },
mesh = {Humans ; Male ; Female ; *Heart Defects, Congenital/complications/microbiology ; Child ; Gastrointestinal Microbiome ; *Pulmonary Arterial Hypertension/microbiology ; Child, Preschool ; Lung/microbiology ; Metabolome ; *Microbiota ; Bacteria/classification/genetics/isolation & purification/metabolism ; Adolescent ; Multiomics ; },
abstract = {Dysregulation of immune and inflammatory cells around blood vessels and metabolic dysfunction are key mechanisms in the development of pulmonary arterial hypertension (PAH). The homeostasis of the human microbiome plays a crucial role in regulating immune responses and the progression of diseases. For pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD), the potential impact of the microbiome on the "gut-lung axis" remains underexplored. This study recruited 15 healthy individuals and 15 patients with pulmonary arterial hypertension due to congenital heart disease from Fuwai Yunnan Hospital, Chinese Academy of Medical Sciences, and Kunming Children's Hospital. We performed differential analyses of metabolites and microbiota from both the gut and lower respiratory tract for these two groups. The goal was to investigate the "gut-lung axis" microbiome and metabolome profiles in children with PAH-CHD and to analyze the interrelationships between these profiles. Ultimately, we aim to propose the potential value of these profiles in aiding diagnosis. The results indicated that the gut and pulmonary microbiota of children with PAH-CHD are characterized by an increased abundance of beneficial symbionts, which are closely linked to changes in the metabolome. Metabolite functional enrichment analysis revealed energy metabolism reprogramming in the PAH-CHD group, with active metabolic pathways associated with bile acid secretion and carnitine homeostasis. Moreover, the differential expression of metabolites was correlated with right heart function and growth development.IMPORTANCEPrevious studies have primarily focused on the relationship between the gut microbiome and PAH. However, the impact of microbial homeostasis on the progression of PAH-CHD from the perspective of the gut-lung axis has not been adequately elucidated. Our study utilizes an integrated multi-omics approach to report on the differential characteristics of gut and lung microbiota between children with PAH-CHD and reference subjects. We found that microbiota influence the pathological changes and disease manifestations of PAH-CHD through their metabolic activity. Additionally, alterations in metabolites impact the microbial ecological structure. Our findings suggest that modulating the microbiome composition may have positive implications for maintaining and regulating the immune environment and pathological progression of PAH-CHD.},
}

Humans
Male
Female
*Heart Defects, Congenital/complications/microbiology
Child
Gastrointestinal Microbiome
*Pulmonary Arterial Hypertension/microbiology
Child, Preschool
Lung/microbiology
Metabolome
*Microbiota
Bacteria/classification/genetics/isolation & purification/metabolism
Adolescent
Multiomics

@article {pmid39472801,
year = {2024},
author = {Valiei, A and Dickson, AM and Aminian-Dehkordi, J and Mofrad, MRK},
title = {Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {441},
pmid = {39472801},
issn = {1471-2180},
mesh = {*Bacteria/metabolism/classification/growth & development/genetics ; *Biofilms/growth & development ; Humans ; *Gastrointestinal Microbiome ; Microbial Interactions ; Bacterial Physiological Phenomena ; Models, Biological ; Kinetics ; Symbiosis ; Ecosystem ; Nutrients/metabolism ; },
abstract = {Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.},
}

*Bacteria/metabolism/classification/growth & development/genetics
*Biofilms/growth & development
Humans
*Gastrointestinal Microbiome
Microbial Interactions
Bacterial Physiological Phenomena
Models, Biological
Kinetics
Symbiosis
Ecosystem
Nutrients/metabolism

@article {pmid39474048,
year = {2023},
author = {Wu, J and Zhang, S and Chen, Y and Zhao, J and Prosun, T and O'Brien, JW and Mueller, JF and Tscharke, BJ and Coin, LJM and Luby, SP and Hai, FI and Buchanan, T and Jiang, G},
title = {Associations between Wastewater Microbiome and Population Smoking Rate Identified Using Wastewater-Based Epidemiology.},
journal = {Environment & health (Washington, D.C.)},
volume = {1},
number = {6},
pages = {394-404},
pmid = {39474048},
issn = {2833-8278},
abstract = {Tobacco use is known to cause health damage, partly by changing the mouth, respiratory tract, and gut-related microbiomes. This study aims to identify the associations between the human microbiome detected in domestic wastewater and the population smoking rate. Metagenomic sequencing and a biomarker discovery algorithm were employed to identify microorganisms as potential microbial biomarkers of smoking through wastewater-based epidemiology. Wastewater samples were collected from selected catchments with low and high smoking rates, i.e., 11.2 ± 1.5% and 17.0 ± 1.6%, respectively. Using the linear discriminant analysis effect size (LEfSe) method, Neisseria, Desulfovibrio, Megamonas, Blautia, Fusicatenibacter, Granulicatella and Enterococcus were suggested as potential biomarker microorganisms. A higher abundance of pathogens, including Neisseria, Eikenella and Haemophilus, was associated with the high smoking rate, likely because of their colonization in smoking-disturbed human guts. The identified potential microbial biomarkers reflect the change of the human gut microbiome due to the long-term smoking behavior. The metagenomic analysis also indicates that smoking upregulates microbial gene expression of genetic information processing, environmental information processing, and cell wall peptidoglycan cleavage, while it downregulates amino acid, lipid, and galactose metabolisms. The findings demonstrate the potential of microbial biomarkers for the surveillance of smoking through a wastewater-based epidemiology approach.},
}

@article {pmid39478172,
year = {2024},
author = {Collado, MC and Devkota, S and Ghosh, TS},
title = {Gut microbiome: a biomedical revolution.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {21},
number = {12},
pages = {830-833},
pmid = {39478172},
issn = {1759-5053},
}

@article {pmid39478225,
year = {2024},
author = {Lu, Z and Mo, S and Xie, D and Zhai, X and Deng, S and Zhou, K and Wang, K and Kang, X and Zhang, H and Tong, J and Hou, L and Hu, H and Li, X and Zhou, D and Lee, LTO and Liu, L and Zhu, Y and Yu, J and Lan, P and Wang, J and He, Z and He, X and Hu, Z},
title = {Polyclonal-to-monoclonal transition in colorectal precancerous evolution.},
journal = {Nature},
volume = {636},
number = {8041},
pages = {233-240},
pmid = {39478225},
issn = {1476-4687},
support = {//National Key R&D Program of China/ ; //National Natural Sciences Foundation of China/ ; //Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Animals ; Humans ; Male ; Mice ; Carcinogenesis/genetics/pathology ; *Cell Lineage ; Cell Transformation, Neoplastic/genetics/pathology ; *Clonal Evolution ; *Clone Cells/metabolism ; Colonic Polyps/pathology/genetics ; *Colorectal Neoplasms/genetics/pathology ; Disease Models, Animal ; DNA Barcoding, Taxonomic ; Exome Sequencing ; Genes, APC ; Inflammation/pathology/genetics ; *Precancerous Conditions/genetics/pathology ; *Single-Cell Analysis ; Single-Cell Gene Expression Analysis ; Whole Genome Sequencing ; Intestines/cytology/pathology ; },
abstract = {Unravelling the origin and evolution of precancerous lesions is crucial for effectively preventing malignant transformation, yet our current knowledge remains limited[1-3]. Here we used a base editor-enabled DNA barcoding system[4] to comprehensively map single-cell phylogenies in mouse models of intestinal tumorigenesis induced by inflammation or loss of the Apc gene. Through quantitative analysis of high-resolution phylogenies including 260,922 single cells from normal, inflamed and neoplastic intestinal tissues, we identified tens of independent cell lineages undergoing parallel clonal expansions within each lesion. We also found polyclonal origins of human sporadic colorectal polyps through bulk whole-exome sequencing and single-gland whole-genome sequencing. Genomic and clinical data support a model of polyclonal-to-monoclonal transition, with monoclonal lesions representing a more advanced stage. Single-cell RNA sequencing revealed extensive intercellular interactions in early polyclonal lesions, but there was significant loss of interactions during monoclonal transition. Therefore, our data suggest that colorectal precancer is often founded by many different lineages and highlight their cooperative interactions in the earliest stages of cancer formation. These findings provide insights into opportunities for earlier intervention in colorectal cancer.},
}

Animals
Humans
Male
Mice
Carcinogenesis/genetics/pathology
*Cell Lineage
Cell Transformation, Neoplastic/genetics/pathology
*Clonal Evolution
*Clone Cells/metabolism
Colonic Polyps/pathology/genetics
*Colorectal Neoplasms/genetics/pathology
Disease Models, Animal
DNA Barcoding, Taxonomic
Exome Sequencing
Genes, APC
Inflammation/pathology/genetics
*Precancerous Conditions/genetics/pathology
*Single-Cell Analysis
Single-Cell Gene Expression Analysis
Whole Genome Sequencing
Intestines/cytology/pathology

@article {pmid39479472,
year = {2024},
author = {Mousa, WK and Shaikh, AY and Ghemrawi, R and Aldulaimi, M and Al Ali, A and Sammani, N and Khair, M and Helal, MI and Al-Marzooq, F and Oueis, E},
title = {Human microbiome derived synthetic antimicrobial peptides with activity against Gram-negative, Gram-positive, and antibiotic resistant bacteria.},
journal = {RSC medicinal chemistry},
volume = {16},
number = {1},
pages = {312-323},
pmid = {39479472},
issn = {2632-8682},
abstract = {The prevalence of antibacterial resistance has become one of the major health threats of modern times, requiring the development of novel antibacterials. Antimicrobial peptides are a promising source of antibiotic candidates, mostly requiring further optimization to enhance druggability. In this study, a series of new antimicrobial peptides derived from lactomodulin, a human microbiome natural peptide, was designed, synthesized, and biologically evaluated. Within the most active region of the parent peptide, linear peptide LM6 with the sequence LSKISGGIGPLVIPV-NH2 and its cyclic derivatives LM13a and LM13b showed strong antibacterial activity against Gram-positive bacteria, including resistant strains, and Gram-negative bacteria. The peptides were found to have a rapid onset of bactericidal activity and transmission electron microscopy clearly shows the disintegration of the cell membrane, suggesting a membrane-targeting mode of action.},
}

@article {pmid39481381,
year = {2024},
author = {Zheludev, IN and Edgar, RC and Lopez-Galiano, MJ and de la Peña, M and Babaian, A and Bhatt, AS and Fire, AZ},
title = {Viroid-like colonists of human microbiomes.},
journal = {Cell},
volume = {187},
number = {23},
pages = {6521-6536.e18},
pmid = {39481381},
issn = {1097-4172},
support = {R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; R35 GM130366/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; *Phylogeny ; Feces/microbiology ; RNA, Circular/genetics/metabolism ; Open Reading Frames/genetics ; RNA, Catalytic/metabolism/genetics ; Gastrointestinal Microbiome/genetics ; },
abstract = {Here, we describe "obelisks," a class of heritable RNA elements sharing several properties: (1) apparently circular RNA ∼1 kb genome assemblies, (2) predicted rod-like genome-wide secondary structures, and (3) open reading frames encoding a novel "Oblin" protein superfamily. A subset of obelisks includes a variant hammerhead self-cleaving ribozyme. Obelisks form their own phylogenetic group without detectable similarity to known biological agents. Surveying globally, we identified 29,959 distinct obelisks (clustered at 90% sequence identity) from diverse ecological niches. Obelisks are prevalent in human microbiomes, with detection in ∼7% (29/440) and ∼50% (17/32) of queried stool and oral metatranscriptomes, respectively. We establish Streptococcus sanguinis as a cellular host of a specific obelisk and find that this obelisk's maintenance is not essential for bacterial growth. Our observations identify obelisks as a class of diverse RNAs of yet-to-be-determined impact that have colonized and gone unnoticed in human and global microbiomes.},
}

Humans
*Microbiota/genetics
*Phylogeny
Feces/microbiology
RNA, Circular/genetics/metabolism
Open Reading Frames/genetics
RNA, Catalytic/metabolism/genetics
Gastrointestinal Microbiome/genetics

@article {pmid39483755,
year = {2024},
author = {Pita, S and Myers, PN and Johansen, J and Russel, J and Nielsen, MC and Eklund, AC and Nielsen, HB},
title = {CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1425489},
pmid = {39483755},
issn = {1664-302X},
abstract = {INTRODUCTION: Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed for the profiling of prokaryotes, eukaryotes, and viruses across all body sites.

METHODS: CHAMP uses a reference database derived from 30,382 human microbiome samples, covering 6,567 prokaryotic and 244 eukaryotic species, as well as 64,003 viruses. We benchmarked CHAMP against established profiling tools (MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta) using a diverse set of in silico metagenomes and DNA mock communities.

RESULTS: CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives compared to all other tools benchmarked. The false positive relative abundance (FPRA) for CHAMP was, on average, 50-fold lower than the second-best performing profiler. CHAMP also proved to be more robust than other tools at low sequencing depths, highlighting its application for low biomass samples.

DISCUSSION: Taken together, this establishes CHAMP as a best-in-class human microbiome profiler of prokaryotes, eukaryotes, and viruses in diverse and complex communities across low and high biomass samples. CHAMP profiling is offered as a service by Clinical Microbiomics A/S and is available for a fee at https://cosmosidhub.com.},
}

@article {pmid39484071,
year = {2024},
author = {Nurkolis, F and Utami, TW and Alatas, AI and Wicaksono, D and Kurniawan, R and Ratmandhika, SR and Sukarno, KT and Pahu, YGP and Kim, B and Tallei, TE and Tjandrawinata, RR and Alhasyimi, AA and Surya, R and Helen, H and Halim, P and Muhar, AM and Syahputra, RA},
title = {Can salivary and skin microbiome become a biodetector for aging-associated diseases? Current insights and future perspectives.},
journal = {Frontiers in aging},
volume = {5},
number = {},
pages = {1462569},
pmid = {39484071},
issn = {2673-6217},
abstract = {Growth and aging are fundamental elements of human development. Aging is defined by a decrease in physiological activities and higher illness vulnerability. Affected by lifestyle, environmental, and hereditary elements, aging results in disorders including cardiovascular, musculoskeletal, and neurological diseases, which accounted for 16.1 million worldwide deaths in 2019. Stress-induced cellular senescence, caused by DNA damage, can reduce tissue regeneration and repair, promoting aging. The root cause of many age-related disorders is inflammation, encouraged by the senescence-associated secretory phenotype (SASP). Aging's metabolic changes and declining immune systems raise illness risk via promoting microbiome diversity. Stable, individual-specific skin and oral microbiomes are essential for both health and disease since dysbiosis is linked with periodontitis and eczema. Present from birth to death, the human microbiome, under the influence of diet and lifestyle, interacts symbiotically with the body. Poor dental health has been linked to Alzheimer's and Parkinson's diseases since oral microorganisms and systemic diseases have important interactions. Emphasizing the importance of microbiome health across the lifetime, this study reviews the understanding of the microbiome's role in aging-related diseases that can direct novel diagnosis and treatment approaches.},
}

@article {pmid39486524,
year = {2024},
author = {Kapoor, B and Biswas, P and Gulati, M and Rani, P and Gupta, R},
title = {Gut microbiome and Alzheimer's disease: What we know and what remains to be explored.},
journal = {Ageing research reviews},
volume = {102},
number = {},
pages = {102570},
doi = {10.1016/j.arr.2024.102570},
pmid = {39486524},
issn = {1872-9649},
mesh = {Animals ; Humans ; *Alzheimer Disease/metabolism/microbiology/physiopathology ; Brain/metabolism/physiopathology ; *Brain-Gut Axis/physiology ; *Dysbiosis/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; },
abstract = {With advancement in human microbiome research, an increasing number of scientific evidences have endorsed the key role of gut microbiota in the pathogenesis of Alzheimer disease. Microbiome dysbiosis, characterized by altered diversity and composition, as well as rise of pathobionts influence not only various gut disorder but also central nervous system disorders such as AD. On the basis of accumulated evidences of past few years now it is quite clear that the gut microbiota can control the functions of the central nervous system (CNS) through the gut-brain axis, which provides a new prospective into the interactions between the gut and brain. The main focus of this review is on the molecular mechanism of the crosstalk between the gut microbiota and the brain through the gut-brain axis, and on the onset and development of neurological disorders triggered by the dysbiosis of gut microbiota. Due to microbiota dysbiosis the permeability of the gut and blood brain barrier is increased which may mediate or affect AD. Along with this, bacterial population of the gut microbiota can secrete amyloid proteins and lipopolysaccharides in a large quantity which may create a disturbance in the signaling pathways and the formation of proinflammatory cytokines associated with the pathogenesis of AD. These topics are followed by a critical analysis of potential intervention strategies targeting gut microbiota dysbiosis, including the use of probiotics, prebiotics, metabolites, diets and fecal microbiota transplantation. The main purpose of this review includes the summarization and discussion on the recent finding that may explain the role of the gut microbiota in the development of AD. Understanding of these fundamental mechanisms may provide a new insight into the novel therapeutic strategies for AD.},
}

Animals
Humans
*Alzheimer Disease/metabolism/microbiology/physiopathology
Brain/metabolism/physiopathology
*Brain-Gut Axis/physiology
*Dysbiosis/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology

@article {pmid39504483,
year = {2024},
author = {Chen, H and Chen, K},
title = {Predicting disease-associated microbes based on similarity fusion and deep learning.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39504483},
issn = {1477-4054},
support = {20242BAB25083//Jiangxi Provincial Natural Science Foundation, China/ ; },
mesh = {*Deep Learning ; Humans ; *Computational Biology/methods ; *Microbiota/genetics ; Algorithms ; },
abstract = {Increasing studies have revealed the critical roles of human microbiome in a wide variety of disorders. Identification of disease-associated microbes might improve our knowledge and understanding of disease pathogenesis and treatment. Computational prediction of microbe-disease associations would provide helpful guidance for further biomedical screening, which has received lots of research interest in bioinformatics. In this study, a deep learning-based computational approach entitled SGJMDA is presented for predicting microbe-disease associations. Specifically, SGJMDA first fuses multiple similarities of microbes and diseases using a nonlinear strategy, and extracts feature information from homogeneous networks composed of the fused similarities via a graph convolution network. Second, a heterogeneous microbe-disease network is built to further capture the structural information of microbes and diseases by employing multi-neighborhood graph convolution network and jumping knowledge network. Finally, potential microbe-disease associations are inferred through computing the linear correlation coefficients of their embeddings. Results from cross-validation experiments show that SGJMDA outperforms 6 state-of-the-art computational methods. Furthermore, we carry out case studies on three important diseases using SGJMDA, in which 19, 20, and 11 predictions out of their top 20 results are successfully checked by the latest databases, respectively. The excellent performance of SGJMDA suggests that it could be a valuable and promising tool for inferring disease-associated microbes.},
}

*Deep Learning
Humans
*Computational Biology/methods
*Microbiota/genetics
Algorithms

@article {pmid39505118,
year = {2024},
author = {Ferrara, F and Valacchi, G},
title = {Role of microbiota in the GUT-SKIN AXIS responses to outdoor stressors.},
journal = {Free radical biology & medicine},
volume = {225},
number = {},
pages = {894-909},
doi = {10.1016/j.freeradbiomed.2024.11.003},
pmid = {39505118},
issn = {1873-4596},
mesh = {Humans ; *Skin/microbiology/immunology ; *Gastrointestinal Microbiome ; *Oxidative Stress ; Dysbiosis/microbiology/immunology ; Air Pollutants/adverse effects ; Microbiota ; Animals ; },
abstract = {Beside the respiratory tract, the skin and the gut represent the first defensive lines of our body against the external insults displaying many important biochemical features able to maintain the epithelial barrier integrity and to regulate the tissue immune responses. The human microbiome is essential in maintaining the tissue homeostasis and its dysregulation may lead to tissue conditions including inflammatory pathologies. Among all external insults, air pollutants have been shown to cause oxidative stress damage within the target tissues via an OxInflammatory response. Dysregulation of the gut microbiome (dysbiosis) by outdoor stressors, including air pollutants, may promote the exacerbation of the skin tissue damage via the interplay between the gut-skin axis. The intent of this review is to highlight the ability of exogenous stressors to modulate the human gut-skin axis via a redox regulated mechanism affecting the microbiome and therefore contributing to the development and aggravation of gut and skin conditions.},
}

Humans
*Skin/microbiology/immunology
*Gastrointestinal Microbiome
*Oxidative Stress
Dysbiosis/microbiology/immunology
Air Pollutants/adverse effects
Microbiota
Animals