@article {pmid39608999,
year = {2024},
author = {Climacosa, FMM and Anlacan, VMM and Gordovez, FJA and Reyes, JCB and Tabios, IKB and Manalo, RVM and Cruz, JMC and Asis, JLB and Razal, RB and Abaca, MJM and Dacasin, AB and Espiritu, APN and Gapaz, NCLL and Lee Yu, MHL},
title = {Monitoring drug Efficacy through Multi-Omics Research initiative in Alzheimer's Disease (MEMORI-AD): A protocol for a multisite exploratory prospective cohort study on the drug response-related clinical, genetic, microbial and metabolomic signatures in Filipino patients with Alzheimer's disease.},
journal = {BMJ open},
volume = {14},
number = {11},
pages = {e078660},
pmid = {39608999},
issn = {2044-6055},
mesh = {Humans ; *Alzheimer Disease/drug therapy/genetics ; Philippines ; Prospective Studies ; Aged ; Cholinesterase Inhibitors/therapeutic use ; Rivastigmine/therapeutic use ; Donepezil/therapeutic use ; Cross-Sectional Studies ; Memantine/therapeutic use ; Male ; Female ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; Multiomics ; },
abstract = {INTRODUCTION: Dementia is one of the leading causes of disability among older people aged 60 years and above, with majority eventually being diagnosed with Alzheimer's disease (AD). Pharmacological agents approved for dementia include acetylcholinesterase enzyme (AChE) inhibitors like rivastigmine, donepezil and galantamine and the N-methyl-D-aspartate (NMDA) receptor antagonist memantine, prescribed as monotherapy or in combination with each other, depending on the severity of disease. There is currently no available study demonstrating the clinical response to these drugs for AD in the Filipino population. Hence, this protocol aims to characterise the clinical, genetic, microbial and metabolic factors associated with drug responses to donepezil, rivastigmine and/or memantine for AD in a cohort of Filipinos with late-onset AD.

METHODS AND ANALYSIS: This protocol involves a multisite descriptive study that will use two study designs: (1) a descriptive, cross-sectional study to characterise the clinical profile of Filipino dementia patients with AD and (2) an exploratory prospective cohort study to investigate drug response-related genetic, gut microbiome and metabolome signatures of a subset of the recruited AD patients. At least 153 patients with mild or moderate AD aged 65 years old and above will be recruited regardless of their treatment status. A subset of these patients (n=60) who meet inclusion and exclusion criteria will be included further in the exploratory cohort study. These patients will be grouped according to their baseline medications and will be observed for treatment response in 6 months. The cognitive, functional and behavioural domains of patients and levels of functioning will be measured using different assessment tools. Drug responses of Filipino patients will then be investigated employing multi-omics technology to characterise genetic variations via whole exome sequencing, gut microbiome profile via shotgun metagenomic sequencing and metabolome profile via liquid chromatography with mass spectrometry.

ETHICS AND DISSEMINATION: The study has received ethical clearance from the Department of Health Single Joint Research Ethics Board (SJREB-2022-15). Results of psychometric scales will be made available to enrolled patients. The study results will be presented at national/international conferences and published in international peer-reviewed scientific journals, and summaries of the results will be provided to the study funders and institutional review boards of the three tertiary referral hospitals.

TRIAL REGISTRATION NUMBER: Philippine Health Research Registry ID PHRR230220-0054116; ClinicalTrials.gov ID NCT05801380.},
}

Humans
*Alzheimer Disease/drug therapy/genetics
Philippines
Prospective Studies
Aged
Cholinesterase Inhibitors/therapeutic use
Rivastigmine/therapeutic use
Donepezil/therapeutic use
Cross-Sectional Studies
Memantine/therapeutic use
Male
Female
Metabolomics
Gastrointestinal Microbiome/drug effects
Multiomics

@article {pmid39608384,
year = {2024},
author = {Gopal, RK and Sankar Ganesh, P and Pathoor, NN and Viswanathan, A},
title = {Enhancing microbiome-based biomarkers: challenges and opportunities.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101032},
doi = {10.1016/j.lanmic.2024.101032},
pmid = {39608384},
issn = {2666-5247},
}

@article {pmid39608378,
year = {2024},
author = {Hussain, A and Koser, N and Aun, SM and Siddiqui, MF and Malik, S and Ali, SA},
title = {Deciphering the role of probiotics in mental health: a systematic literature review of psychobiotics.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-22},
doi = {10.1163/18762891-bja00053},
pmid = {39608378},
issn = {1876-2891},
abstract = {Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit to the host. The selection criteria for probiotics include strain safety, viability, tolerance, metabolite production and/or the ability to modulate the immune system. Probiotics are commonly used in industries, such as food, agriculture, medicine, biotechnology, pharmaceuticals, and aquaculture. Recently, the medicinal applications of probiotics have gained attention and are being explored for the prevention and treatment of various diseases. One emerging area of interest is their potential role in psychological disorders. Mental illnesses, characterised by disturbances in behaviour, mood, thinking, and emotions, affect over one billion people globally. While various preventive and treatment options for mental disorders exists, each is associated with certain limitations. A new avenue being explored is the gut-brain axis, a complex bi-directional communication between the gut and the brain, that is facilitated by hormonal, neuronal, humoral, and immunological pathways. This system plays an important role in mental health. Probiotics, as a key modulator of the gut microbiome, could play a vital role in this communication. However, the underlying mechanisms remain to be explored. Probiotics may act through the production of metabolites and neuroactive substances, as well as through immunomodulation and cytokine production. Current data shows promising effects on stress, mood, and depression, presenting probiotics as a potential natural treatment option for psychological disorders. Nevertheless, major limitations in the existing research include insufficient clinical outcomes, limited sample sizes, and variable dosing. Future advancements may be achieved through stratifications based on gut microbiota, the use of next-generation probiotic strains, and the conduct of comprehensive validation studies.},
}

@article {pmid39608339,
year = {2024},
author = {Gu, Y and Jiao, J and Xu, H and Chen, Y and He, X and Wu, X and Wang, J and Chen, X and He, H and Yan, W},
title = {Intercropping improves the yield by increasing nutrient metabolism capacity and crucial microbial abundance in root of Camellia oleifera in purple soil.},
journal = {Plant physiology and biochemistry : PPB},
volume = {219},
number = {},
pages = {109318},
doi = {10.1016/j.plaphy.2024.109318},
pmid = {39608339},
issn = {1873-2690},
abstract = {Intercropping system influences the endophytic microbial abundance, hormone balance, nutrient metabolism and yield, but the molecular mechanism of yield advantage in Camellia oleifera intercropping with peanut is not clear. In this study, the C. oleifera monoculture (CK) and C. oleifera-peanut intercropping (CP) treatments in purple soil were conducted, and the physicochemical properties, gene expressions, signal pathways and crucial microbial abundances were investigated to reveal the molecular mechanism of the yield advantage of intercropped C. oleifera. The results showed that the intercropping system increased in contents of pigment, carbohydrate, available nitrogen and phosphorus in leaf and root, as well as the abundances of Burkholderia, Ralstonia, Delftia, Pseudoalteromonas and Caulobacter, enhanced the relative expression levels of CoSPS, CoGBE, CoGlgP, CoGBSS/GlgA genes to promote sugar metabolism, decreased the relative expression levels of CoASA, CoTSB, CoPAI, CoTDC and CoCYP71A13 genes for inhibiting IAA biosynthesis and signal transduction, as well as microbial diversity, Fusarium, Albifimbria and Coniosporium abundances in root, ultimately improved the fruit yield of C. oleifera. These findings indicate that intercropping system improves the fruit yield by enhancing the nutrient metabolism capability and crucial microbial abundances in root of C. oleifera in purple soil.},
}

@article {pmid39608222,
year = {2024},
author = {Padilha, MDM and Melo, FTV and Laurentino, RV and da Silva, ANMR and Feitosa, RNM},
title = {Dysregulation in the microbiota by HBV and HCV infection induces an altered cytokine profile in the pathobiome of infection.},
journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases},
volume = {29},
number = {1},
pages = {104468},
doi = {10.1016/j.bjid.2024.104468},
pmid = {39608222},
issn = {1678-4391},
abstract = {Viral hepatitis is a public health problem, about 1 million people die due to complications of this viral disease, the etiological agents responsible for inducing cirrhosis and cellular hepatocarcinoma are HBV and HCV, both hepatotropic viruses that cause asymptomatic infection in most cases. The regulation of the microbiota performs many physiological functions, which can induce normal intestinal function and produce essential nutrients for the human body. Metabolites derived from gut microbiota or direct regulation of host immunity and metabolism have been reported to profoundly affect tumorigenesis in liver disease. If the microbiota is unbalanced, both exogenous and symbiotic microorganisms can affect a pathological process. It is well understood that the microbiota plays a role in viral diseases and infections, specifically the hepatic portal pathway has been linked to the gut-liver axis. In HBV and HCV infections, the altered bacterial representatives undergo a state of dysbiosis, with subsequent establishment of the pathobiome with overexpression of taxons such as Bacteroides, Clostridium, Lactobacillus, Enterobacter, and Enterococcus. This dysregulated microbiome induces a microenvironment conducive to the development of hepatic complications in patients with acute and chronic HBV and HCV infection, with subsequent dysregulation of cytokines IFN-α/β, TNF-α, IL-1β, TGF-β, IL-6 and IL-10, which alter the dysfunction and damage of the hepatic portal system. In view of the above, this review aimed to correlate the pathophysiological mechanisms in HBV and HCV infection, the dysregulation of the microbiome in patients infected with HBV and HCV, the most altered cytokines in the microbiome, and the most altered bacterial representatives in the pathobiome of infection.},
}

@article {pmid39608199,
year = {2024},
author = {Bhat, AH and Malik, IM and Tak, H and Ganai, BA and Bharti, P},
title = {Host, parasite, and microbiome interaction: Trichuris ovis and its effect on sheep gut microbiota.},
journal = {Veterinary parasitology},
volume = {333},
number = {},
pages = {110356},
doi = {10.1016/j.vetpar.2024.110356},
pmid = {39608199},
issn = {1873-2550},
abstract = {Sheep that are infected with gastrointestinal helminths experience a significant impact on their health and productivity. Among the helminths, nematodes like Haemonchus contortus, Oesophagostomum spp., Bunostomum trigonocephalum, Nematodirus battus, Trichostrongylus spp. and Teladorsagia circumcincta are particularly pathogenic. Understanding the interactions among parasites, hosts, and their microbiomes is crucial in developing new approaches in the management of parasites. This study examines the bacterial profile of Trichuris ovis, a highly prevalent nematode among Kashmir Merino sheep, and the influence of nematode infection on the caecal microbiome of its host. Sheep were selected based on T. ovis infection status, and samples were collected from infected and non-infected caecum. The 16S rRNA metagenomic analysis revealed distinct microbial communities in T. ovis, infected caecum, and non-infected caecum. Proteobacteria dominated the T. ovis microbiome, while infected caecum was rich in Bacteroidota and Spirochaetota, and non-infected caecum had a higher proportion of Firmicutes and Verrucomicrobiota. At the genus level, T. ovis was predominantly associated with Escherichia/Shigella, while infected caecum had higher proportions of Bacteroides, Prevotella, and Treponema. Non-infected caecum was characterized by WCHB1-41, Prevotella, and Succiniclasticum like genera. Alpha and beta diversity indicated significant differences in microbiome among the groups, with higher diversity observed in infected caecum. The study found T. ovis infection significantly alters the caecal microbiome of sheep, introducing potentially pathogenic bacteria and reducing beneficial ones. These findings underscore the complex relationship between host, parasite, and microbiome, highlighting the need for comprehensive strategies to manage helminth infections and their broader ecological impacts.},
}

@article {pmid39607975,
year = {2024},
author = {Abbasi, AM and Nasir, S and Bajwa, AA and Akbar, H and Ali, MM and Rashid, MI},
title = {A comparative study of the microbiomes of the ticks Rhipicephalus microplus and Hyalomma anatolicum.},
journal = {Parasite (Paris, France)},
volume = {31},
number = {},
pages = {74},
pmid = {39607975},
issn = {1776-1042},
support = {HEC-GCF-273//Higher Education Commission, Pakistan/ ; },
mesh = {Animals ; *Rhipicephalus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Ixodidae/microbiology ; *Microbiota ; Pakistan ; Phylogeny ; Symbiosis ; Female ; Gastrointestinal Microbiome ; Coxiella/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Hyalomma anatolicum and Rhipicephalus microplus are tick species that are important vectors of numerous pathogens affecting both humans and livestock. Endosymbionts, such as Coxiella-like endosymbionts (CLE), Francisella-like endosymbionts (FLE), and Candidatus Midichloria, play a crucial role in the physiology and vector competence of these ticks. In this study, we investigated the microbial composition of H. anatolicum and R. microplus from four geographically distinct regions of Pakistan to assess whether environmental differences influence their microbiomes. We analyzed the ticks' gut microbiome targeting the V3-V4 hypervariable region of 16S rRNA for Illumina 16S metagenome NGS sequencing and processed overall 144 ticks. Analysis of gut bacterial composition resulted in observation of 1200 R. microplus and 968 H. anatolicum unique amplicon sequencing variants (ASVs). Relative abundance, Alpha diversity (Shannon, Faith's phylogenetic distance) and beta diversity metrics (Bray-Curtis, Jaccard and UniFrac) were analyzed and revealed that H. anatolicum ticks have significantly unique and diverse microbial communities with Acinetobacter indicus and Francisella-like endosymbionts dominating as opposed to Candidatus Midichloria. Rhipicephalus microplus exhibited results consistent with the previous studies with no major changes in microbiome including Coxiella-like endosymbionts as the major contributor. These findings suggest that geographical and environmental factors play a significant role in shaping the tick microbiome, with potential consequences for disease transmission and tick survivability. Further research is needed to elucidate the functional roles of these microbial shifts and their impact on public health and livestock in affected regions.},
}

Animals
*Rhipicephalus/microbiology
*RNA, Ribosomal, 16S/genetics
*Ixodidae/microbiology
*Microbiota
Pakistan
Phylogeny
Symbiosis
Female
Gastrointestinal Microbiome
Coxiella/genetics/isolation & purification/classification
Bacteria/classification/genetics/isolation & purification

@article {pmid39607793,
year = {2024},
author = {Özdemir, A and Buyuktuncer, Z},
title = {Dietary legumes and gut microbiome: a comprehensive review.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/10408398.2024.2434725},
pmid = {39607793},
issn = {1549-7852},
abstract = {The gut microbiome plays a crucial role in human health, affecting metabolic, immune, and cognitive functions. While the impact of various dietary components on the microbiome is well-studied, the effect of legumes remains less explored. This review examines the influence of legume consumption on gut microbiome composition, diversity, and metabolite production, based on 10 human and 21 animal studies. Human studies showed mixed results, with some showing increased microbial diversity and others finding no significant changes. However, legume consumption was linked to increases in beneficial bacteria like Bifidobacterium and Faecalibacterium. Animal studies generally indicated enhanced microbial diversity and composition changes, though these varied by legume type and the host's health. Some studies highlighted legume-induced shifts in bacteria associated with better metabolic health. Overall, the review emphasizes the complexity of legume-microbiome interactions and the need for standardized methodologies and longitudinal studies. While legumes have the potential to positively affect the gut microbiome, the effects are nuanced and depend on context. Future research should investigate the long-term impacts of legume consumption on microbiome stability and its broader health implications, particularly for disease prevention and dietary strategies.},
}

@article {pmid39607629,
year = {2024},
author = {Chua, HC and Pham, S and Lombardi, DA and Hot, E and Mody, L},
title = {Patient Satisfaction Scale Following a Laxative for Antibiotic Washout Prior to Oral Microbiome Therapy.},
journal = {Advances in therapy},
volume = {},
number = {},
pages = {},
pmid = {39607629},
issn = {1865-8652},
abstract = {INTRODUCTION: Administration of fecal microbiota spores, live-brpk [Vowst Oral Spores (VOS)], an oral microbiome therapeutic approved for prevention of recurrent Clostridioides difficile infection in adults, requires antibiotic washout using a laxative prior to administration. Patient acceptability of the prerequisite laxative is important. This study assessed psychometric properties of the Antibiotic Washout Patient Satisfaction Scale (AWPSS) which was minimally modified from a previously validated patient satisfaction scale for bowel preparation prior to colonoscopy.

METHODS: Patients from the ECOSPOR IV trial who received a laxative preparation prior to oral administration of VOS and were administered the AWPSS were included. Reliability and construct validity of the AWPSS were evaluated.

RESULTS: AWPSS data were available for 110 patients; all completed all 6 items of the AWPSS, supporting its acceptability. Domain 1 mean/median transformed total scores of 105.9/100 [range (best-worst), 0-300] suggested that patients were satisfied with the laxative preparation; a Cronbach's alpha of 0.81 showed acceptable reliability. Almost all patients (97.3%) reported they were able to consume the entire laxative solution as instructed and would take it again if needed (95.5%). Higher satisfaction with the laxative preparation predicted higher acceptability of future use if needed (lower score) with mean/median of 101.7/100 and 195.0/200.00 for those who were willing or not willing to accept, respectively (P = 0.008).

CONCLUSIONS: AWPSS is a valid and reliable 6-item patient-reported outcome measure for use in patients requiring a laxative prior to oral microbiome therapy. AWPSS showed antibiotic washout was well tolerated and predicted that patients would be willing to consume the laxative in the future if needed.},
}

@article {pmid39607612,
year = {2024},
author = {Qasem, HH and El-Sayed, WM},
title = {The bacterial microbiome and cancer: development, diagnosis, treatment, and future directions.},
journal = {Clinical and experimental medicine},
volume = {25},
number = {1},
pages = {12},
pmid = {39607612},
issn = {1591-9528},
mesh = {Humans ; *Neoplasms/therapy/microbiology/diagnosis ; *Dysbiosis ; *Microbiota ; Bacteria/classification/genetics ; Probiotics/therapeutic use ; },
abstract = {The term "microbiome" refers to the collection of bacterial species that reside in the human body's tissues. Sometimes, it is used to refer to all microbial entities (bacteria, viruses, fungi, and others) which colonize the human body. It is now generally acknowledged that the microbiome plays a critical role in the host's physiological processes and general well-being. Changes in the structure and/or function of the microbiome (dysbiosis) are linked to the development of many diseases including cancer. The claim that because of their negatively charged membrane, cancer cells are more vulnerable to some bacteria than normal cells and that is how the link between these bacteria and cancer evolved has been refuted. Furthermore, the relationship between the microbiome and cancer is more evident in the emerging field of cancer immunotherapy. In this narrative review, we detailed the correlation between the presence/absence of specific bacterial species and the development, diagnosis, prognosis, and treatment of some types of cancer including colorectal, lung, breast, and prostate cancer. In addition, we discussed the mechanisms of microbiome-cancer interactions including genotoxin production, the role of free radicals, modification of signaling pathways in host cells, immune modulation, and modulation of drug metabolism by microbiome. Future directions and clinical application of microbiome in the early detection, prognosis, and treatment of cancer emphasizing on the role of fecal transplantation, probiotics, prebiotics, and microbiome biomarkers were also considered.},
}

Humans
*Neoplasms/therapy/microbiology/diagnosis
*Dysbiosis
*Microbiota
Bacteria/classification/genetics
Probiotics/therapeutic use

@article {pmid39607539,
year = {2024},
author = {Lv, JL and Bai, Y and Lv, YE and Chen, CC and Qin, XM and Du, GH and Zhou, YZ},
title = {Integrated colon microbiome and metabolomics to elucidate the antidepressant mechanisms of the Radix Bupleuri-Radix Paeoniae Alba herb pair.},
journal = {Metabolic brain disease},
volume = {40},
number = {1},
pages = {45},
pmid = {39607539},
issn = {1573-7365},
support = {202102130501010//Key Research and Development Program of Shanxi Province/ ; 202204051002011//The special fund for Science and Technology Innovation Teams of Shanxi Province/ ; 81673572//National Natural Science Foundation of China/ ; 2024-021//Research Project Supported by Shanxi Scholarship Council of China/ ; 202403021211150//Supported by Fundamental Research Program of Shanxi Province/ ; },
mesh = {Animals ; *Antidepressive Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Male ; Rats ; *Metabolomics ; *Paeonia ; *Depression/metabolism/drug therapy/microbiology ; *Rats, Sprague-Dawley ; Stress, Psychological/metabolism/drug therapy ; Bupleurum ; Drugs, Chinese Herbal/pharmacology/therapeutic use ; Colon/metabolism/drug effects/microbiology ; },
abstract = {Radix Bupleuri-Radix Paeoniae Alba herb pair (RB-RPA) is the fundamental medication combination of many classic antidepressant prescriptions, and RB-RPA's antidepressant effect is well established. For an extended period, the involvement of intestinal flora in the progression of depression has been widely acknowledged. However, it remains unclear whether RB-RPA could modulate intestinal microbiota disturbances and metabolic abnormalities induced by depression. The research explores the antidepressant mechanism of RB-RPA in chronic unpredictable mild stress (CUMS) rats in terms of intestinal flora and metabolites. We identified critical gut microbial species and metabolites associated with the antidepressant effects of RB-RPA using 16 S rRNA sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) metabolomics. And then, correlation analysis between critical microbiota and differential metabolites was conducted. The results demonstrate that RB-RPA significantly ameliorated depressive-like behavior in CUMS rats. RB-RPA improved intestinal flora disorders in depressed rats mainly by increasing the abundance of Lactobacillus (especially L. johnsonii), and ameliorated tryptophan synthesis and metabolism disorders in depressed rats and restored the levels of tryptophan and tryptophan microbial metabolites, such as indoleacrylic acid and 4-indoleacetaldehyde. Notably, correlation analysis showed that Lactobacillus had a significant positive correlation with tryptophan, indoleacrylic acid, and 4-indoleacetaldehyde. In conclusion, RB-RPA can improve the disorder of intestinal flora by increasing the abundance of Lactobacillus and improve the metabolic disorder of depressed rats by regulating tryptophan metabolism, thus exerting antidepressant effects.},
}

Animals
*Antidepressive Agents/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
Male
Rats
*Metabolomics
*Paeonia
*Depression/metabolism/drug therapy/microbiology
*Rats, Sprague-Dawley
Stress, Psychological/metabolism/drug therapy
Bupleurum
Drugs, Chinese Herbal/pharmacology/therapeutic use
Colon/metabolism/drug effects/microbiology

@article {pmid39607509,
year = {2024},
author = {Bahat, H and Paret, M and Uzan, A and Klainer, H and Sharon, E and Turjeman, S and Koren, O and Goldman, M and Youngster, I},
title = {Fecal microbiome composition in neonates with or without urinary tract infection.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {39607509},
issn = {1432-198X},
abstract = {BACKGROUND: Most infants with febrile urinary tract infection (UTI) do not have an underlying anatomical risk factor. Thus, other non-anatomical risk factors should be considered. Since the most common pathogens arise from the fecal microbiota, our aim was to investigate whether the gut microbiota composition differs between febrile infants younger than 2 months with or without UTI.

METHODS: In this prospective, case-control, pilot study, we performed 16S ribosomal ribonucleic acid amplicon sequencing to characterize gut microbiota of febrile neonates with and without UTI admitted to the pediatric ward at Shamir Medical Center between February 2019 and May 2021.

RESULTS: The study cohort included 42 febrile neonates: 17 with and 25 without febrile UTI. We found a significant difference in beta diversity (i.e. between-sample/study group similarity indices) between the UTI and non-UTI group (p = 0.016). There were also distinct differences in the relative abundance of the 20 most prevalent genera. Furthermore, several genera were significantly enriched in the UTI group, with others dominating the non-UTI group. Streptococci were underrepresented in the UTI group. There was no difference in alpha diversity (i.e. within-sample diversity/richness) between groups.

CONCLUSION: Febrile neonates with UTI have a different fecal microbiota composition (beta-diversity), but not alpha diversity, in comparison to febrile neonates without UTI. A larger study is warranted to confirm these findings and their potential applications.},
}

@article {pmid39607341,
year = {2024},
author = {Merk, LN and Shur, AS and Jena, S and Munoz, J and Brubaker, DK and Murray, RM and Green, LN},
title = {Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.3c00668},
pmid = {39607341},
issn = {2161-5063},
abstract = {Bacteria genetically engineered to execute defined therapeutic and diagnostic functions in physiological settings can be applied to colonize the human microbiome, providing in situ surveillance and conditional disease modulation. However, many engineered microbes can only respond to single-input environmental factors, limiting their tunability, precision, and effectiveness as living diagnostic and therapeutic systems. For engineering microbes to improve complex chronic disorders such as inflammatory bowel disease, the bacteria must respond to combinations of stimuli in the proper context and time. This work implements a previously characterized split activator AND logic gate in the probiotic Escherichia coli strain Nissle 1917 (EcN). Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, anhydrotetracycline (aTc), for manual control. We report 4-6 fold induction with a minimal leak when the two chemical signals are present. We model the AND gate dynamics using chemical reaction networks and tune parameters in silico to identify critical perturbations that affect our circuit's selectivity. Finally, we engineer the optimized AND gate to secrete a therapeutic anti-inflammatory cytokine IL-22 using the hemolysin secretion pathway in the probiotic E. coli strain. We used a germ-free transwell model of the human gut epithelium to show that our engineering bacteria produce similar host cytokine responses compared to recombinant cytokine. Our study presents a scalable workflow to engineer cytokine-secreting microbes driven by logical signal processing. It demonstrates the feasibility of IL-22 derived from probiotic EcN with minimal off-target effects in a gut epithelial context.},
}

@article {pmid39606796,
year = {2024},
author = {Wang, Z and Yang, S and Liu, L and Mao, A and Kan, H and Yu, F and Ma, X and Feng, L and Zhou, T},
title = {The gut microbiota-derived metabolite indole-3-propionic acid enhances leptin sensitivity by targeting STAT3 against diet-induced obesity.},
journal = {Clinical and translational medicine},
volume = {14},
number = {12},
pages = {e70053},
pmid = {39606796},
issn = {2001-1326},
support = {82470455//National Natural Science Foundation of China/ ; 82025005//National Natural Science Foundation of China/ ; 91939301//National Natural Science Foundation of China/ ; 81622007//National Natural Science Foundation of China/ ; },
mesh = {*Obesity/metabolism/drug therapy ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Leptin/metabolism ; Mice ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Obesity is associated with the gut microbiome. Here, we report that gut commensal Clostridia bacteria regulate host energy balance through the tryptophan-derived metabolite indole-3-propionic acid (IPA). IPA acts as an endogenous leptin sensitiser to counteract obesity. Mechanistically, IPA is secreted from the gut into the circulation, and then targets to the STAT3 in the hypothalamic appetite regulation centre, promoting its phosphorylation and nuclear translocation, which enhances the body's response to leptin, and regulates the balance between appetite and energy metabolism. The in vitro pull-down assays involving site-directed mutagenesis demonstrate that Trp623 in the SH2 domain is the key binding site for STAT3-IPA interaction. High-fat diet (HFD), rather than genetic factors, induces excessive secretion of antimicrobial peptides by Paneth cells, inhibiting the growth of Clostridia in the gut and resulting in decreased production of the beneficial metabolite IPA. IPA or Clostridium sporogenes supplement effectively controls weight gain, improves glucose metabolism, and reduces inflammation in DIO mice. IPA fails to achieve such effects in ob/ob mice, while exogenous leptin administration restores the therapeutic effect of IPA. Our study suggests that the IPA-based gut-brain axis regulates host metabolism, and supplementation with microbiome-derived IPA could be a promising intervention strategy for treating obesity.},
}

*Obesity/metabolism/drug therapy
Animals
*Gastrointestinal Microbiome/drug effects
*Leptin/metabolism
Mice
*STAT3 Transcription Factor/metabolism
*Indoles/pharmacology/metabolism
*Diet, High-Fat/adverse effects
Male
Mice, Inbred C57BL
Disease Models, Animal

@article {pmid39606663,
year = {2024},
author = {Özkan, S and Bay, V and Cömert Acar, M and Yalcın, S},
title = {Partial replacement of soybean with local alternative sources: effects on behavior, cecal microbiota, and intestinal histomorphometry of local chickens.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1463301},
pmid = {39606663},
issn = {2297-1769},
abstract = {Interest in partially replacing soybean meal in poultry diets with alternative protein sources such as agri-industrial by-products and black soldier fly (BSF, Hermetia illucens) has gained significant attention due to sustainability concerns. This study aimed to evaluate the effects of broiler diets in which soybean meal was partially substituted with agri-industrial by-products with or without BSF larvae meal, on the behavior, intestinal histomorphometry, and microbiome profile of a local broiler chicken strain. There were three dietary treatments. (1) A corn-soybean-based diet (Control), (2) a diet in which soybean was partly replaced (SPR) with local agri-industrial by-products, namely sunflower meal, brewers' dried grain, and wheat middlings, and (3) a diet in which BSF (5%) meal was added to SPR (SPR+BSF). Behavior was recorded on days 14, 35, and 49 at the pen level. On day 55, intestinal segments and cecal contents were collected from eight chickens per pen for histomorphometry and microbiome analysis. Dietary manipulations did not affect the behavior of broiler chickens (P > 0.05) suggesting that the experimental diets had no influence on behavior. A significant interaction between the intestinal segment and diets revealed that the SPR and SPR+BSF diets decreased duodenal villus height (VH) compared to the control diet (P < 0.05). However, this effect was not consistent across all of intestinal segments. Diet did not affect villus height to crypt depth ratio (VH/CD; P > 0.05), indicating no significant impact on the absorptive capacity of the digestive system. Firmicutes and Bacteroidetes were the dominant phyla in the cecal samples. Colidextribacter and Oscillibacter spp. were more abundant in chickens fed the SPR diet compared to those fed the control diet. The SPR+BSF diet resulted in higher abundance of Rikenella and Colidextribacter spp. compared to the control diet, while Desulfovibrio, Ruminococcus torques group, and Lachnoclostridium were more abundant in the ceca of birds fed the SPR diet than those fed SPR+BSF. In conclusion, replacement of soybean with agri-industrial by-products and BSF larvae meal could regulate the cecal microbiota composition without negatively affecting the behavior and intestinal histomorphometry of the local chickens.},
}

@article {pmid39606458,
year = {2024},
author = {Lozupone, C and O'Connor, J and Fouquier, J and Neff, C and Sterrett, J and Marden, T and Fiorillo, S and Siebert, J and Schneider, J and Nusbacher, N and Noe, A and Higgins, B and Higgins, J and Campbell, T and Palmer, B},
title = {Agrarian Diet Improves Metabolic Health in HIV-positive Men with Prevotella-Rich Microbiomes: Results from a Randomized Trial.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-5349309/v1},
pmid = {39606458},
issn = {2693-5015},
abstract = {This study aimed to assess the impact a high-fiber/low-fat agrarian diet (AD) on inflammation and metabolic outcomes in HIV positive men who have sex with men (MSM). Since the gut microbiome of MSM has been shown to have a striking resemblance to individuals in agrarian cultures, including being Prevotella-rich and Bacteroides-poor, we hypothesized that they would have particularly strong health benefits from consumption of a diet matched to their microbiome type. Sixty-six participants, including 36 HIV-positive MSM (HIV(+)MSM), 21 HIV-negative MSM, and 9 HIV negative men who have sex with women were randomized to either an AD or a high-fat western diet (WD) for four weeks. The AD reduced low-density lipoprotein cholesterol in HIV(+)MSM, with more significant reductions predicted by Prevotella-rich/Bacteroides-poor microbiomes at baseline. The AD also reduced T cell exhaustion and pro-inflammatory intermediate monocytes and altered host transcription in the colonic mucosa. Our findings suggest that tailoring diet interventions to baseline microbiome type can help promote metabolic health in HIV(+)MSM.},
}

@article {pmid39606371,
year = {2024},
author = {Jeong, S and Tollison, T and Brochu, H and Chou, H and Yu, T and Baghaie, P and Yount, KS and Darville, T and Peng, X and O'Connell, CM},
title = {Aptima Combo2-avoiding variants detected in cervical and endometrial specimens from a cohort of sexually active cisgender women during 16S microbiome profiling.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.13.24316066},
pmid = {39606371},
abstract = {BACKGROUND: Performance of a 16S rRNA analysis of the cervicovaginal microbiome of 220 participants recruited into the T Cell Response against Chlamydia (TRAC) cohort between February 2011 and August 2014 in Allegheny County, Pennsylvania USA surprisingly detected DNA encoding chlamydial 16S rRNA in samples from seven participants who had tested negatively for Chlamydia trachomatis (CT) and DNA encoding gonococcal 16S rRNA from five participants who had tested negatively for Neisseria gonorrhoeae (NG) infection with the Aptima Combo2 assay (Hologic).

METHODS: We used targeted PCR amplification followed by sequencing to characterize the chlamydial 23S rRNA locus and qPCR to detect gonococcal DNA in residual diagnostic swab eluates or DNA used to generate 16S rRNA libraries.

RESULTS: Discrepant specimens that contained chlamydial DNA carried a diagnostic-avoidant, G1526A variant in the 23S rRNA locus identical to variants previously detected in Finland, Denmark, and the UK. PCR validation of gonococcal DNA was confirmed for all participants who had tested negatively, with stochastic effects consistent with infection levels close to the limit of detection by the diagnostic assay.

CONCLUSIONS: These data indicate that this probe-avoidant CT mutant, and possibly others, were circulating in the northeastern US prior to their detection and characterization in 2019 and subsequently. Although infrequent, documentation of false negative results for CT indicates a need for clinicians to consider performance of a second test that uses alternate PCR probes if patients have persistent symptoms or have known contact to an infected sex partner and their initial NAAT is negative.},
}

@article {pmid39606341,
year = {2024},
author = {Scalzo, PL and Marshall, A and Soriano, S and Curry, K and Dulay, M and Hodics, T and Quigley, EM and Treangen, TJ and Piskorz, MM and Villapol, S},
title = {Gut microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.18.24317428},
pmid = {39606341},
abstract = {COVID-19 patients often exhibit altered immune responses and neuropsychiatric symptoms during hospitalization. However, the potential interactions with gut microbiome profiles have not been fully characterized. Here, COVID-19 disease severity was classified as low (27.4%), moderate (29.8%), and critical (42.8%). Fever (66.1%) and cough (55.6%) were common symptoms. Additionally, 27.3% reported somatic symptoms, 27.3% experienced anxiety, 39% had depressive symptoms, and 80.5% reported stress. Gut microbiome profiling was performed using full-length 16S rRNA gene sequencing. Elevated interleukin-6 levels were observed in the most severe cases, indicating systemic inflammation. Reduced gut bacterial diversity was more pronounced in women and obese patients and correlated with higher disease severity. The presence of the genus Mitsuokella was significantly associated with increased physical, stress, anxiety, and depressive symptoms, and Granulicatella with critically ill patients. These findings suggest a link between mental health status, systemic inflammation, and gut dysbiosis in COVID-19 patients, emphasizing the potential of microbiome-targeted therapies to improve recovery and reduce severe complications.},
}

@article {pmid39606148,
year = {2024},
author = {Xiao, L and Zhao, F},
title = {Exploring the frontier of microbiome biomarker discovery with artificial intelligence.},
journal = {National science review},
volume = {11},
number = {11},
pages = {nwae325},
pmid = {39606148},
issn = {2053-714X},
}

@article {pmid39606113,
year = {2024},
author = {Hanif, MS and Tayyab, M and Baillo, EH and Islam, MM and Islam, W and Li, X},
title = {Plant microbiome technology for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1500260},
pmid = {39606113},
issn = {1664-302X},
abstract = {Plants establish specific interactions with microorganisms, which are vital for promoting growth and resilience. Although advancements in microbiome modulation technologies show great potential for sustainable agriculture, several challenges have hindered the wider application of plant microbiomes in the field. These challenges may include inconsistent microbial colonization, competition with native microbiota, and environmental variability. Current strategies, while promising, often yield inconsistent results in real-world agricultural settings, highlighting the need for more refined approaches. Agricultural practices and plant genotypes significantly influence the composition and function of plant-associated microbiota. A data-driven strategy that incorporates genomic profiling, environmental assessments, and optimized delivery systems is essential for selecting effective microbial strains. Additionally, refining farming practices, such as crop rotation, intercropping, and reduced tillage, along with robust plant breeding programs, can greatly enhance crop health and productivity.},
}

@article {pmid39606112,
year = {2024},
author = {Skarlupka, JH and Cox, MS and Steinberger, AJ and Sbardellati, DL and McClure, JC and Bickhart, DM and Scheftgen, AJ and Zuniga-Chaves, I and Wolfe, LA and Paget, E and Skadron, C and Attipetty, N and Suen, G},
title = {Corrigendum: Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501270},
doi = {10.3389/fmicb.2024.1501270},
pmid = {39606112},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1466375.].},
}

@article {pmid39606108,
year = {2024},
author = {Liu, H and Zhang, Y and Li, H and Chen, S and Zhang, J and Ding, W},
title = {Characteristics of soil microbial community assembly patterns in fields with serious occurrence of tobacco Fusarium wilt disease.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1482952},
pmid = {39606108},
issn = {1664-302X},
abstract = {INTRODUCTION: Fusarium wilt disease (FWD) of tobacco is a destructive disease caused by Fusarium spp. in tobacco-growing regions worldwide. The Fusarium spp. infection may alter the composition and structure of the tobacco root microbial community; however, the relationship between these factors under large-scale geographical conditions in China remains underexplored.

METHODS: In the context of this investigation, soil samples from the rhizosphere of tobacco plants were procured from fields afflicted with FWD and those devoid of the disease in the Hanzhong region of Shaanxi province, as well as in the Sanmenxia and Nanyang regions of Henan province. These regions are recognized for the commercial cultivation of tobacco. The examination focused on discerning the influence of tobacco FWD on the composition and configuration of the rhizosphere microbial community, along with their co-occurrence patterns. This scrutiny was underpinned by targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of the 16S rRNA gene and the ITS1 region.

RESULTS: The amplicon data analyses showed that FWD influenced the microbial structure and composition of the tobacco rhizosphere soil. FWD had a greater impact on the microbiome of the tobacco fungal community than on the microbiome of the bacterial community. Healthy plants had the ability to recruit potential beneficial bacteria. Diseased plants were more susceptible to colonization by other pathogenic fungi, but they still had the capacity to recruit potential beneficial bacteria. The analysis of microbial intra- and inter-kingdom networks further indicated that FWD destabilized microbial networks. In the overall microbial interaction, microorganisms primarily interacted within their boundaries, but FWD increased the proportion of interactions occurring across boundaries. In addition, FWD could disrupt the interactions within microbial network modules.

DISCUSSION: This study provides evidence that FWD can cause changes in the composition and network of microbial communities, affecting the interactions among various microorganisms, including bacteria and fungi. These findings contribute to our understanding of how plant microbiomes change due to disease. Furthermore, they add to our knowledge of the mechanisms that govern the assembly and interactions of microbial communities under the influence of FWD.},
}

@article {pmid39606106,
year = {2024},
author = {Lu, Z and Zhang, T and Zhao, Y and Pang, Y and Guo, M and Zhu, X and Li, Y and Li, Z},
title = {The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1459773},
pmid = {39606106},
issn = {1664-302X},
abstract = {Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including AIF1L, ASS1, and QRFP were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between CCAR2, EGR3, GSTM3, and GPR61 genes and the abundance of microorganisms, such as Trueperella, Victivallis, and Erysipelatoclostridium. In addition, six microbial genera linked to growth and feed efficiency were identified as follows Lachnospiraceae_UCG-005, Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, Prevotella_1, Prevotella_9, and Veillonella. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.},
}

@article {pmid39605655,
year = {2024},
author = {O'Connor, LC and Kang, WK and Vo, P and Spinelli, JB and Alkema, MJ and Byrne, AB},
title = {Comamonas aquatica inhibits TIR-1/SARM1 induced axon degeneration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.20.622298},
pmid = {39605655},
issn = {2692-8205},
abstract = {Emerging evidence suggests the microbiome critically influences the onset and progression of neurodegenerative diseases; however, the identity of neuroprotective bacteria and the molecular mechanisms that respond within the host remain largely unknown. We took advantage of Caenorhabditis elegans' well characterized nervous system and ability to eat uni-bacterial diets to determine how metabolites and neuroprotective molecules from single species of bacteria suppress degeneration of motor neurons. We found Comamonas aquatica significantly protects against degeneration induced by overexpressing a key regulator of axon degeneration, TIR-1/SARM1. Genetic analyses and metabolomics reveal Comamonas protects against neurodegeneration by providing sufficient Vitamin B12 to activate METR-1/MTR methionine synthase in the intestine, which then lowers toxic levels of homocysteine in TIR-1-expressing animals. Defining a molecular pathway between Comamonas and neurodegeneration adds significantly to our understanding of gut-brain interactions and, given the prominent role of homocysteine in neurodegenerative disorders, reveals how such a bacterium could protect against disease.},
}

@article {pmid39605612,
year = {2024},
author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D},
title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.18.624180},
pmid = {39605612},
issn = {2692-8205},
abstract = {UNLABELLED: The continuingly decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal to identify microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here we propose a novel backward variable selection method based on the hyperdimensional computing paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.

AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the hyperdimensional computing paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.},
}

@article {pmid39605610,
year = {2024},
author = {Sterrett, JD and Quinn, KD and Doenges, KA and Nusbacher, NM and Levens, CL and Armstrong, ML and Reisdorph, RM and Smith, H and Saba, LM and Kuhn, KA and Lozupone, CA and Reisdorph, NA},
title = {Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.11.603097},
pmid = {39605610},
issn = {2692-8205},
abstract = {UNLABELLED: Studies have suggested that phytochemicals in green tea have systemic anti-inflammatory and neuroprotective effects. However, the mechanisms behind these effects are poorly understood, possibly due to differential metabolism of phytochemicals resulting from variation in gut microbiome composition. To unravel this complex relationship, our team utilized a novel combined microbiome analysis and metabolomics approach applied to low complexity microbiome (LCM) and human colonized (HU) gnotobiotic mice treated with an acute dose of powdered matcha green tea. A total of 20 LCM mice received 10 distinct human fecal slurries for an n=2 mice per human gut microbiome; 9 LCM mice remained un-colonized with human slurries throughout the experiment. We performed untargeted metabolomics on green tea and plasma to identify green tea compounds that were found in plasma of LCM and HU mice that had consumed green tea. 16S ribosomal RNA gene sequencing was performed on feces of all mice at study end to assess microbiome composition. We found multiple green tea compounds in plasma associated with microbiome presence and diversity (including acetylagmatine, lactiflorin, and aspartic acid negatively associated with diversity). Additionally, we detected strong associations between bioactive green tea compounds in plasma and specific gut bacteria, including associations between spiramycin and Gemmiger , and between wildforlide and Anaerorhabdus . Additionally, some of the physiologically relevant green tea compounds are likely derived from plant-associated microbes, highlighting the importance of considering foods and food products as meta-organisms. Overall, we describe a novel workflow for discovering relationships between individual food compounds and composition of the gut microbiome.

IMPORTANCE: Foods contain thousands of unique and biologically important compounds beyond the macro- and micro-nutrients listed on nutrition facts labels. In mammals, many of these compounds are metabolized by the community of microbes in the colon. These microbes may impact the thousands of biologically important compounds we consume; therefore, understanding microbial metabolism of food compounds will be important for understanding how foods impact health. We used metabolomics to track green tea compounds in plasma of mice with and without complex microbiomes. From this, we can start to recognize certain groups of green tea-derived compounds that are impacted by mammalian microbiomes. This research presents a novel technique for understanding microbial metabolism of food-derived compounds in the gut, which can be applied to other foods.},
}

@article {pmid39605587,
year = {2024},
author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD},
title = {The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.19.624359},
pmid = {39605587},
issn = {2692-8205},
abstract = {OBJECTIVES: Home-based hematopoietic stem cell transplantation (HCT) is a novel approach that has the potential to improve outcomes, however, the impact of transplant location on the gut microbiome remains uncharacterized. We hypothesized that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower antimicrobial resistance (AMR) gene abundance compared to those undergoing standard hospital HCT.

METHODS: We identified 28 patients enrolled in Phase II randomized trials of home (n=16) v. hospital (n=12) HCT at Duke and performed shotgun metagenomic sequencing of stools to compare taxonomic and AMR gene composition between groups. We performed a secondary analysis of patients from each group transplanted at an outpatient infusion clinic with those who underwent standard inpatient HCT ("outpatient" v. "inpatient").

RESULTS: No significant differences in duration of hospitalization were found in those randomized to home v. hospital HCT. Taxonomic and AMR gene α- and β-diversity were comparable. In contrast, secondary analyses demonstrated that patients from both home and hospital groups transplanted at an outpatient infusion clinic spent significantly less time in the hospital and demonstrated higher taxonomic α-diversity and differential β-diversity compared to standard inpatient HCT, although AMR gene α-diversity did not differ, and comparisons were confounded by both differences in transplant type and use of antibiotics.

CONCLUSIONS: Randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups.},
}

@article {pmid39605476,
year = {2024},
author = {Macadangdang, BR and Wang, Y and Woodward, C and Revilla, JI and Shaw, BM and Sasaninia, K and Makanani, SK and Berruto, C and Ahuja, U and Miller, JF},
title = {Targeted protein evolution in the gut microbiome by diversity-generating retroelements.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.15.621889},
pmid = {39605476},
issn = {2692-8205},
abstract = {Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of Type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, that some are highly active while others are tightly controlled, and that they preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2,700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are preferentially transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the roles of stochastic, targeted genome plasticity in shaping host-associated microbial communities.},
}

@article {pmid39605433,
year = {2024},
author = {Cortés-Martín, A and Buttimer, C and Maier, JL and Tobin, CA and Draper, LA and Ross, RP and Kleiner, M and Hill, C and Shkoporov, AN},
title = {Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.17.624012},
pmid = {39605433},
issn = {2692-8205},
abstract = {BACKGROUND: Bacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where bacteria employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies to overcome these defences. Among the most abundant phages in the gut are the crAss-like phages that infect members of the Bacteroidales, in particular Bacteroides . In this study, we explored some of the mechanisms enabling the co-existence of four phage-Bacteroidales host pairs in vitro using a multi-omics approach (transcriptomics, proteomics and metabolomics). These included three Bacteroides species paired with three crAss-like phages (Bacteroides intestinalis and ϕcrAss001, Bacteroides xylanisolvens and ϕcrAss002, and an acapsular mutant of Bacteroides thetaiotaomicron with DAC15), and Parabacteroides distasonis paired with the siphovirus ϕPDS1.

RESULTS: We show that phase variation of individual capsular polysaccharides (CPSs) is the primary mechanism promoting phage co-existence in Bacteroidales, but this is not the only strategy. Alternative resistance mechanisms, while potentially less efficient than CPS phase variation, can be activated to support bacterial survival by regulating gene expression and resulting in metabolic adaptations, particularly in amino acid degradation pathways. These mechanisms, also likely regulated by phase variation, enable bacterial populations to persist in the presence of phages, and vice versa . An acapsular variant of B. thetaiotaomicron demonstrated broader transcriptomic, proteomic, and metabolomic changes, supporting the involvement of additional resistance mechanisms beyond CPS variation.

CONCLUSIONS: This study advances our understanding of long-term phage-host interaction, offering insights into the long-term persistence of crAss-like phages and extending these observations to other phages, such as ϕPDS1. Knowledge of the complexities of phage-bacteria interactions is essential for designing effective phage therapies and improving human health through targeted microbiome interventions.},
}

@article {pmid39605394,
year = {2024},
author = {Kabonick, S and Verma, K and Modesto, JL and Pearce, VH and Winokur, KM and Groisman, EA and Townsend, GE},
title = {Hierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.13.623061},
pmid = {39605394},
issn = {2692-8205},
abstract = {Human dietary choices control the gut microbiome. Industrialized populations consume abundant glucose and fructose, resulting in microbe-dependent intestinal disorders. Simple sugars inhibit the carbohydrate utilization regulator (Cur), a transcription factor in the prominent gut bacterial phylum, Bacteroidetes . Cur encodes products necessary for carbohydrate utilization, host immunomodulation, and intestinal colonization. Here, we demonstrate how simple sugars decrease Cur activity in the mammalian gut. Our findings in two Bacteroides species show that ATP-dependent fructose-1,6-bisphosphate (FBP) synthesis is necessary for glucose or fructose to inhibit Cur, but dispensable for growth because of an essential pyrophosphate (PPi)-dependent enzyme. Furthermore, we show that ATP-dependent FBP synthesis is required to regulate Cur in the gut but does not contribute to fitness when cur is absent, indicating PPi is sufficient to drive glycolysis in these bacteria. Our findings reveal how sugar-rich diets inhibit Cur, thereby disrupting Bacteroides fitness and diminishing products that are beneficial to the host.},
}

@article {pmid39605370,
year = {2024},
author = {Sakamachi, Y and Wiley, E and Solis, A and Johnson, CG and Meng, X and Hussain, S and Lipinski, JH and O'Dwyer, DN and Randall, T and Malphurs, J and Papas, B and Wu, BG and Li, Y and Kugler, M and Mehta, S and Trempus, CS and Thomas, SY and Li, JL and Zhou, L and Karmaus, PW and Fessler, MB and McGrath, JA and Gibson, K and Kass, DJ and Gleiberman, A and Walts, A and Invernizzi, R and Molyneaux, PL and Yang, IV and Zhang, Y and Kaminski, N and Segal, LN and Schwartz, DA and Gudkov, AV and Garantziotis, S},
title = {Toll-Like-Receptor 5 protects against pulmonary fibrosis by reducing lung dysbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.30.591719},
pmid = {39605370},
issn = {2692-8205},
abstract = {UNLABELLED: Idiopathic pulmonary fibrosis (IPF) is a devastating pulmonary disease with no curative treatment other than lung transplantation. IPF results from maladaptive responses to lung epithelial injury, but the underlying mechanisms remain unclear. Here, we show that deficiency in the innate immune receptor, toll-like receptor 5 (TLR5), is associated with IPF in humans and with increased susceptibility to epithelial injury and experimental fibrosis in mice, while activation of lung epithelial TLR5 through a synthetic flagellin analogue protects from experimental fibrosis. Mechanistically, epithelial TLR5 activation induces antimicrobial gene expression and ameliorates dysbiosis after lung injury. In contrast, TLR5 deficiency in mice and IPF patients is associated with lung dysbiosis. Elimination of the microbiome in mice through antibiotics abolishes the protective effect of TLR5 and reconstitution of the microbiome rescues the observed phenotype. In aggregate, TLR5 deficiency is associated with IPF and dysbiosis in humans and in the murine model of pulmonary fibrosis. Furthermore, TLR5 protects against pulmonary fibrosis in mice and this protection is mediated by effects on the microbiome.

ONE-SENTENCE SUMMARY: Deficiency in the innate immune receptor TLR5 is a risk factor for pulmonary fibrosis, because TLR5 prevents microbial dysbiosis after lung injury.},
}

@article {pmid39605360,
year = {2024},
author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D},
title = {Longitudinal Microbiome-based Interpretable Machine Learning for Identification of Time-Varying Biomarkers in Early Prediction of Disease Outcomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.18.619118},
pmid = {39605360},
issn = {2692-8205},
abstract = {Information generated from longitudinally-sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g., metagenomics) poses analytical challenges. To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses: (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g., XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa but also offers improved prediction accuracy compared to existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. The identified critical early predictive time points are informative and aligned with clinical expectations.},
}

@article {pmid39605271,
year = {2024},
author = {Zhu, S and Teng, Z},
title = {[The characteristics of pharyngea microbiological in children with obstructive sleep apnea].},
journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery},
volume = {38},
number = {12},
pages = {1178-1182},
doi = {10.13201/j.issn.2096-7993.2024.12.017},
pmid = {39605271},
issn = {2096-7993},
mesh = {Humans ; *Sleep Apnea, Obstructive/microbiology ; *Microbiota ; Child ; *Pharynx/microbiology ; Male ; Female ; Prevotella/isolation & purification ; Haemophilus/isolation & purification ; Veillonella/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Proteobacteria/isolation & purification ; },
abstract = {Objective:This study aimed to explore the possible pathogenesis of OSA from the perspective of microbiology by evaluate the change in pharyngeal microbiome of OSA children, and provide new ideas for clinical prevention, diagnosis and treatment. Methods:Randomly enrolled 20 children with OSA as OSA group and 20 children without OSA as control group. The swallow swab of each children been collected. Using 16srDNA sequencing to investigate the characteristics of pharyngeal microbiome. Results:The α-diversity showed that the Chao1and Observe-Otus index has significantly increased in the OSA group, and the β-diversity was significantly different between the two groups. The relative abundance of Haemophilus（Proteobacteria） increased but that of Veillonella（member of Firmicutes） and Prevotella-7 and Prevotella（member of Bacteroidota） decreased in the OSA group compared to control group. Conclusion:The pharyngeal microbial richness are decreased significantly and composition are disrupted in children with OSA. This microbiome analysis provides a new understanding about the pathogenesis of OSA in children.},
}

Humans
*Sleep Apnea, Obstructive/microbiology
*Microbiota
Child
*Pharynx/microbiology
Male
Female
Prevotella/isolation & purification
Haemophilus/isolation & purification
Veillonella/isolation & purification
RNA, Ribosomal, 16S/genetics
Child, Preschool
Proteobacteria/isolation & purification

@article {pmid39605107,
year = {2024},
author = {Abdelwahab, SI and Taha, MME and Jerah, AA and Farasani, A and Abdullah, SM and Aljahdali, IA and Ibrahim, R and Oraibi, O and Oraibi, B and Alfaifi, HA and Alzahrani, AH and Babiker, YOH},
title = {Artificial intelligence and microbiome research: Evolution of hotspots, research trends, and thematic-based narrative review.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {70},
number = {10},
pages = {182-192},
doi = {10.14715/cmb/2024.70.10.24},
pmid = {39605107},
issn = {1165-158X},
mesh = {*Artificial Intelligence ; Humans ; *Microbiota/physiology ; Bibliometrics ; Machine Learning ; Biomedical Research/trends ; Gastrointestinal Microbiome/physiology ; },
abstract = {Artificial intelligence (AI) and microbiome have emerged in recent years as transformative fields with far-reaching implications for various biomedical domains. This paper presents a comprehensive bibliometric analysis examining the intersection of AI and the microbiome (AIM). The study aims to provide information on this interdisciplinary field's research landscape, trends, and emerging topics. Using a systematic approach, data-driven studies were extracted from the Scopus database on 23 November 2023 and analyzed using the VOSviewer and Bibliometrix applications. The regression coefficient of 0.94 and the yearly growth rate of 7.46% in AIM production indicate a consistent increase over time. Identification of essential contributors, organizations, and nations illuminated cooperative networks and research hotspots. The trend themes are the gut microbiome, disease prediction, machine learning, transfer learning, categorization, big data, artificial neural networks, chronic rhinosinusitis, epidemiology, COPD, and bronchoalveolar lavage. These hot issues in AIM reflect the present emphasis on research and developments in our knowledge of the microbiome's function in health, sickness, and individualized treatment. The findings give researchers, policymakers, and industry experts a thorough picture of the research environment and guide future paths in AIM's fascinating and promising subject.},
}

*Artificial Intelligence
Humans
*Microbiota/physiology
Bibliometrics
Machine Learning
Biomedical Research/trends
Gastrointestinal Microbiome/physiology

@article {pmid39605068,
year = {2024},
author = {Yue, C and Ma, X and Yang, W and Liu, Y and Yang, Z and Hou, R and Yan, X and Yang, M and Su, X and Liu, S},
title = {Characterization of Bacteroides fragilis from the vagina of a giant panda (Ailuropoda melanoleuca) with vaginitis.},
journal = {BMC veterinary research},
volume = {20},
number = {1},
pages = {528},
pmid = {39605068},
issn = {1746-6148},
mesh = {Female ; Animals ; *Ursidae/microbiology ; *Bacteroides fragilis/isolation & purification/genetics ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Vagina/microbiology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Vaginitis/veterinary/microbiology/drug therapy ; Bacteroides Infections/veterinary/microbiology/drug therapy ; Drug Resistance, Bacterial ; },
abstract = {BACKGROUND: Bacteroides fragilis is a prevalent anaerobic bacterium typically resides in the human vagina. It is known to potentially induce infections under specific conditions. Interestingly, there have been no previous reports of B. fragilis being isolated from the vagina of giant pandas.

CASE PRESENTATION: A novel strain of anaerobic bacteria was isolated from the vaginal tract of a giant panda exhibiting symptoms of vaginitis. This strain, designated as GPBF01, was identified as Bacteroides fragilis, a species commonly found in the vaginal microbiome of humans and other animals. After purifying of the single colony, a series of evaluations were conducted including morphological examination, physiological and biochemical identification, antibiotic resistance analysis, resistance genes detection, 16S rRNA sequence, and phylogenetic tree sequence analysis to investigate its biological characteristics. The findings indicated the presence of a predominant anaerobic bacterium, which was identified as B. fragilis and temporarily named GPBF01 with unique biological traits not previously.

CONCLUSIONS: This study is the first to report B. fragilis in the vaginal tract of giant pandas. The analysis of antibiotic resistance patterns among anaerobic bacteria, as conducted in this research, is critical for informing the selection of appropriate antimicrobial agents in the clinical treatment of vaginitis in this species. The findings of this report substantially enhance the scientific basis needed to understand the etiology and refine therapeutic approaches for vaginitis in giant pandas.},
}

Female
Animals
*Ursidae/microbiology
*Bacteroides fragilis/isolation & purification/genetics
*RNA, Ribosomal, 16S/genetics
*Phylogeny
*Vagina/microbiology
Anti-Bacterial Agents/therapeutic use/pharmacology
Vaginitis/veterinary/microbiology/drug therapy
Bacteroides Infections/veterinary/microbiology/drug therapy
Drug Resistance, Bacterial

@article {pmid39605008,
year = {2024},
author = {Bush, JR and Alfa, MJ},
title = {Consumption of resistant potato starch produces changes in gut microbiota that correlate with improvements in abnormal bowel symptoms: a secondary analysis of a clinical trial.},
journal = {BMC nutrition},
volume = {10},
number = {1},
pages = {152},
pmid = {39605008},
issn = {2055-0928},
abstract = {BACKGROUND: Studies have linked a lack of dietary fibre, including resistant starch (RS), to disease-associated changes in intestinal bacteria. Healthy people often report abnormal bowel symptoms (ABS), including bloating, constipation, abdominal pain, and diarrhea, however, connections between these symptoms and the gut microbiota are poorly understood. Determining correlations between ABS and taxonomic groups may provide predictive value for using prebiotics to mitigate ABS in combination with stool microbiome testing.

METHODS: Post hoc analysis of a three-arm randomized, double-blind, placebo-controlled clinical trial evaluating the effects of 3.5 g and 7 g resistant potato starch (RPS) doses or placebo was conducted. The study population (n = 70) were healthy adults aged 18-69 years old living in and around Guelph, ON. Participants evaluated their stools using the Bristol Stool Chart and also recorded any ABS daily. The presence of ABS was compared between treatment arms at baseline and changes in ABS were compared within treatment arms over 1- and 4-week periods. Pearson correlation analysis was used to identify significant relationships between changes in ABS and changes in bacterial taxa.

RESULTS: Abdominal pain, belching, bloating, constipation, diarrhea, gas, and feeling unwell were reported by participants at low levels at baseline. Neither RPS nor placebo had significant effects on mean ABS scores. However, we identified positive correlations between treatment-dependent changes in symptoms and changes in Granulicatella, Haemophilus, Lachnospira, Olsenella, Papillibacter, Turicibacter, unclassified Enterobacteriaceae, unclassified Fusobacteriaceae, unclassified Pasteurellaceae, and unclassified Gammaproteobacteria. We also identified negative correlations between treatment-dependent changes in symptoms and changes in Anaerotruncus, Dorea, RFN20, Victivallis, unclassified Coriobacteriaceae, and unclassified Oxalobacteraceae. These Pearson correlations were significant after correction for repeated testing. The mean relative abundance of these taxa did not change in response to treatment. Finally, macronutrient intake was unaffected by RPS or placebo treatments.

CONCLUSION: Changes in ABS can be positively or negatively correlated with changes in specific gut microbiota, creating opportunities for personalized microbiome-targeted interventions to resolve ABS.

TRIAL REGISTRATION: The trial was registered at ClinicalTrials.gov (NCT05242913) on February 16, 2022.},
}

@article {pmid39604724,
year = {2024},
author = {Knight, CG and Nicolitch, O and Griffiths, RI and Goodall, T and Jones, B and Weser, C and Langridge, H and Davison, J and Dellavalle, A and Eisenhauer, N and Gongalsky, KB and Hector, A and Jardine, E and Kardol, P and Maestre, FT and Schädler, M and Semchenko, M and Stevens, C and Tsiafouli, MΑ and Vilhelmsson, O and Wanek, W and de Vries, FT},
title = {Soil microbiomes show consistent and predictable responses to extreme events.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39604724},
issn = {1476-4687},
abstract = {Increasing extreme climatic events threaten the functioning of terrestrial ecosystems[1,2]. Because soil microbes govern key biogeochemical processes, understanding their response to climate extremes is crucial in predicting the consequences for ecosystem functioning[3,4]. Here we subjected soils from 30 grasslands across Europe to four contrasting extreme climatic events under common controlled conditions (drought, flood, freezing and heat), and compared the response of soil microbial communities and their functioning with those of undisturbed soils. Soil microbiomes exhibited a small, but highly consistent and phylogenetically conserved, response under the imposed extreme events. Heat treatment most strongly impacted soil microbiomes, enhancing dormancy and sporulation genes and decreasing metabolic versatility. Microbiome response to heat in particular could be predicted by local climatic conditions and soil properties, with soils that do not normally experience the extreme conditions being imposed being most vulnerable. Our results suggest that soil microbiomes from different climates share unified responses to extreme climatic events, but that predicting the extent of community change may require knowledge of the local microbiome. These findings advance our understanding of soil microbial responses to extreme events, and provide a first step for making general predictions about the impact of extreme climatic events on soil functioning.},
}

@article {pmid39604625,
year = {2024},
author = {Huelsmann, M and Schubert, OT and Ackermann, M},
title = {A framework for understanding collective microbiome metabolism.},
journal = {Nature microbiology},
volume = {9},
number = {12},
pages = {3097-3109},
pmid = {39604625},
issn = {2058-5276},
support = {180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 542389//Simons Foundation/ ; 542395//Simons Foundation/ ; 101023360//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; },
mesh = {*Microbiota/physiology ; *Bacteria/metabolism/genetics ; Proteome/metabolism ; Carbon Cycle ; Selection, Genetic ; Humans ; Metabolic Networks and Pathways ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each other by exchanging metabolic intermediates and cellular building blocks to achieve a collective metabolism. We currently lack a mechanistic framework to explain why microbiome members adopt partial metabolism and how metabolic functions are distributed among them. Here we argue that natural selection for proteome efficiency-that is, performing essential metabolic fluxes at a minimal protein investment-explains partial metabolism of microbiome members, which underpins the collective metabolism of microbiomes. Using the carbon cycle as an example, we discuss motifs of collective metabolism, the conditions under which these motifs increase the proteome efficiency of individuals and the metabolic interactions they result in. In summary, we propose a mechanistic framework for how collective metabolic functions emerge from selection on individuals.},
}

*Microbiota/physiology
*Bacteria/metabolism/genetics
Proteome/metabolism
Carbon Cycle
Selection, Genetic
Humans
Metabolic Networks and Pathways
Bacterial Proteins/metabolism/genetics

@article {pmid39604623,
year = {2024},
author = {Procházková, N and Laursen, MF and La Barbera, G and Tsekitsidi, E and Jørgensen, MS and Rasmussen, MA and Raes, J and Licht, TR and Dragsted, LO and Roager, HM},
title = {Gut physiology and environment explain variations in human gut microbiome composition and metabolism.},
journal = {Nature microbiology},
volume = {9},
number = {12},
pages = {3210-3225},
pmid = {39604623},
issn = {2058-5276},
support = {NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Adult ; Hydrogen-Ion Concentration ; Male ; Female ; Bacteria/classification/metabolism/genetics/isolation & purification ; Gastrointestinal Transit/physiology ; Young Adult ; Middle Aged ; Diet ; Fermentation ; Gastrointestinal Tract/microbiology/metabolism ; Methane/metabolism ; Healthy Volunteers ; },
abstract = {The human gut microbiome is highly personal. However, the contribution of gut physiology and environment to variations in the gut microbiome remains understudied. Here we performed an observational trial using multi-omics to profile microbiome composition and metabolism in 61 healthy adults for 9 consecutive days. We assessed day-to-day changes in gut environmental factors and measured whole-gut and segmental intestinal transit time and pH using a wireless motility capsule in a subset of 50 individuals. We observed substantial daily fluctuations, with intra-individual variations in gut microbiome and metabolism associated with changes in stool moisture and faecal pH, and inter-individual variations accounted for by whole-gut and segmental transit times and pH. Metabolites derived from microbial carbohydrate fermentation correlated negatively with the gut passage time and pH, while proteolytic metabolites and breath methane showed a positive correlation. Finally, we identified associations between segmental transit time/pH and coffee-, diet-, host- and microbial-derived metabolites. Our work suggests that gut physiology and environment are key to understanding the individuality of the human gut microbial composition and metabolism.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Feces/microbiology
Adult
Hydrogen-Ion Concentration
Male
Female
Bacteria/classification/metabolism/genetics/isolation & purification
Gastrointestinal Transit/physiology
Young Adult
Middle Aged
Diet
Fermentation
Gastrointestinal Tract/microbiology/metabolism
Methane/metabolism
Healthy Volunteers

@article {pmid39604606,
year = {2024},
author = {},
title = {Decoding ageing: Handan Melike Dönertaş on microbiomes, AI and improving lifespan and healthspan.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1579},
doi = {10.1038/s42003-024-07246-7},
pmid = {39604606},
issn = {2399-3642},
abstract = {Investigating the complexities of ageing through computational biology, Handan Melike Dönertaş shares her journey from evolutionary genomics research at Middle East Technical University to leading her own lab at the Leibniz Institute on Ageing. Her team is developing and applying computational approaches aiming to advance our understanding of the microbiome and ageing.},
}

@article {pmid39604530,
year = {2024},
author = {Shokoohi, E and Masoko, P},
title = {Microbiome of Xiphinema elongatum (Nematoda, Longidoridae), isolated from water berry.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29494},
pmid = {39604530},
issn = {2045-2322},
mesh = {Animals ; *Microbiota ; *Soil Microbiology ; South Africa ; Nematoda/microbiology ; Bacteria/classification/isolation & purification/genetics ; Soil/parasitology ; Fruit/microbiology/parasitology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The soil microbiome is crucial for the environment and significantly impacts the ecosystem. Understanding the microbiome and its interaction with soil microorganisms is essential for improving ecological and environmental strategies. In this study, Xiphinema elongatum nematodes were collected from water berry in Sovenga Hills, Limpopo Province, South Africa, and were analyzed their associated bacterial communities using metabarcoding analysis. The findings revealed that X. elongatum forms associations with a wide range of bacterial species. Among the most abundant species identified, we found Sphingomonas sp., a bacterial species commonly found in various habitats and primarily beneficial to plants, and Candidatus Xiphinematobacter, a bacterial species commonly found in nematode species of Xiphinema as an endosymbiont. The analysis using principal component analysis (PCA) revealed that the abundance of X. elongatum in the soil is inversely correlated with clay content (r = -0.52) and soil pH levels (r = -0.98), and directly correlated with soil sand content (r = 0.88). This study provides valuable insights into the bacterial species associated with plant-parasitic nematodes in trees in South Africa. It underscores the presence of various potentially detrimental and beneficial nematode-associated bacteria. The results could potentially influence the overall quality of the soil, leading to implications for the productivity and yield of fruit crops. Additionally, the results help us understand the interaction between bacteria and X. elongatum.},
}

Animals
*Microbiota
*Soil Microbiology
South Africa
Nematoda/microbiology
Bacteria/classification/isolation & purification/genetics
Soil/parasitology
Fruit/microbiology/parasitology
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid39604394,
year = {2024},
author = {Akiyama, S and Nishijima, S and Kojima, Y and Kimura, M and Ohsugi, M and Ueki, K and Mizokami, M and Hattori, M and Tsuchiya, K and Uemura, N and Kawai, T and Bork, P and Nagata, N},
title = {Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10291},
pmid = {39604394},
issn = {2041-1723},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/genetics/virology ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Male ; *Metagenomics/methods ; Female ; *Bacteriophages/genetics ; Adult ; Escherichia coli/genetics/metabolism ; Middle Aged ; Japan ; Fungi/genetics ; Bacteria/genetics/metabolism/classification ; Metagenome/genetics ; Saccharomyces cerevisiae/genetics ; Bifidobacterium/genetics ; Virome/genetics ; Enterococcus faecium/genetics/pathogenicity ; Fatty Acids, Volatile/metabolism ; Young Adult ; China ; Case-Control Studies ; },
abstract = {The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.},
}

Humans
*Colitis, Ulcerative/microbiology/genetics/virology
*Crohn Disease/microbiology
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
Male
*Metagenomics/methods
Female
*Bacteriophages/genetics
Adult
Escherichia coli/genetics/metabolism
Middle Aged
Japan
Fungi/genetics
Bacteria/genetics/metabolism/classification
Metagenome/genetics
Saccharomyces cerevisiae/genetics
Bifidobacterium/genetics
Virome/genetics
Enterococcus faecium/genetics/pathogenicity
Fatty Acids, Volatile/metabolism
Young Adult
China
Case-Control Studies

@article {pmid39604384,
year = {2024},
author = {Lima, HS and Mancine, N and Peruchi, GB and Francisco, CS and Wang, N and de Souza, RSC and Armanhi, JSL and Coletta-Filho, HD},
title = {Microbial community of cultivated and uncultivated citrus rhizosphere microbiota in Brazil.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1294},
pmid = {39604384},
issn = {2052-4463},
mesh = {*Citrus/microbiology ; *Microbiota ; Brazil ; *Rhizosphere ; *RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Bacteria/classification/genetics ; Plant Roots/microbiology ; },
abstract = {The rhizosphere microbiome is known to contain beneficial microorganisms that promote plant growth and increase tolerance to abiotic and biotic stresses. Understanding citrus microbiome diversity and the percentage of diversity that can be recovered in the laboratory is essential for developing innovative approaches to improve plant health and promote sustainable agricultural practices. However, information about the citrus root microbiome, especially in the context of exploring commercial citrus growing areas to identify beneficial plant growth-promoting rhizobacteria (PGPR), is scarce. Here, we present the microbiome data of healthy citrus trees sampled from geographical regions of São Paulo and Amazonas States, in Brazil. The resulting rhizosphere microbiome data comprise an average of 126,180 and 138,707 high-quality reads for the 16S rRNA V3-V4 and ITS1-5F regions, respectively. The taxonomic analysis of cultivated diversity revealed a total of 91 bacterial genera recovered in the laboratory. These data provide valuable information for understanding how the microbiome supports citrus plants in different environments and for developing new strategies to improve crop productivity by using PGPR.},
}

*Citrus/microbiology
*Microbiota
Brazil
*Rhizosphere
*RNA, Ribosomal, 16S/genetics
*Soil Microbiology
Bacteria/classification/genetics
Plant Roots/microbiology

@article {pmid39604327,
year = {2024},
author = {Saeed, H and Díaz, LA and Gil-Gómez, A and Burton, J and Bajaj, J and Romero-Gomez, M and Arrese, M and Arab, JP and Khan, MQ},
title = {Microbiome-Centered Therapies for the Management of Metabolic Dysfunction-Associated Steatotic Liver Disease.},
journal = {Clinical and molecular hepatology},
volume = {},
number = {},
pages = {},
doi = {10.3350/cmh.2024.0811},
pmid = {39604327},
issn = {2287-285X},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a significant global health issue, affecting over 30% of the population worldwide due to the rising prevalence of metabolic risk factors such as obesity and type 2 diabetes mellitus (T2DM). This spectrum of liver disease ranges from isolated steatosis to more severe forms such as steatohepatitis, fibrosis, and cirrhosis. Recent studies highlight the role of gut microbiota in MASLD pathogenesis, showing that dysbiosis significantly impacts metabolic health and the progression of liver disease. This review critically evaluates current microbiome-centered therapies in MASLD management, including prebiotics, probiotics, synbiotics, fecal microbiota transplantation (FMT), and emerging therapies such as engineered bacteria and bacteriophage therapy. We explore the scientific rationale, clinical evidence, and potential mechanisms by which these interventions influence MASLD. The gut-liver axis is crucial in MASLD, with notable changes in microbiome composition linked to disease progression. For instance, specific microbial profiles and reduced alpha diversity are associated with MASLD severity. Therapeutic strategies targeting the microbiome could modulate disease progression by improving gut permeability, reducing endotoxin-producing bacteria, and altering bile acid metabolism. Although promising, these therapies require further research to fully understand their mechanisms and optimize their efficacy. This review integrates findings from clinical trials and experimental studies, providing a comprehensive overview of microbiome-centered therapies' potential in managing MASLD. Future research should focus on personalized strategies, utilizing microbiome features, blood metabolites, and customized dietary interventions to enhance the effectiveness of these therapies.},
}

@article {pmid39603890,
year = {2024},
author = {Sutherland, DB and Kato, LM and Fagarasan, S},
title = {Breaking down IgA: Tomasiella immunophila enlightens microbiome-immune interactions.},
journal = {Trends in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.it.2024.11.003},
pmid = {39603890},
issn = {1471-4981},
abstract = {The recent discovery by Lu and colleagues of Tomasiella immunophila, a bacterium that degrades IgA, offers insights into microbial influences on mucosal immunity and evolutionary immune trade-offs. By modulating IgA titers, T. immunophila influences the dynamic interactions and balance between the host and pathogen. This has implications for immune health, microbiome research, and therapeutics.},
}

@article {pmid39603824,
year = {2024},
author = {Li, N and Wang, M and Liu, F and Wu, P and Wu, F and Xiao, H and Kang, Q and Li, Z and Yang, S and Wu, G and Tan, X and Yang, Q},
title = {Bioorthogonal Engineering of Bacterial Outer Membrane Vesicles for NIR-II Fluorescence Imaging-Guided Synergistic Enhanced Immunotherapy.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c04449},
pmid = {39603824},
issn = {1520-6882},
abstract = {The efficacy of immunotherapy in treating triple-negative breast cancer (TNBC) has been restricted due to its low immunogenicity and suppressive immune microenvironment. Bacterial outer membrane vesicles (OMVs) have emerged as innovative immunotherapeutic agents in antitumor therapy by stimulating the innate immune system, but intricate modifications and undesirable multiple dose administration severely hinder their utility. Herein, a two-step bacterial metabolic labeling technique was utilized for the bioorthogonal engineering of OMVs. At first, d-propargylglycine (DPG, an alkyne-containing d-amino acid) was introduced into the incubation process of probiotic Escherichia coli 1917 (Ecn) to produce DPG-functionalized OMVs, which were subsequently conjugated with azide-functionalized new indocyanine green (IR820) to yield OMV-DPG-IR820. The combination of phototherapy and immunostimulation of OMV-DPG-IR820 effectively arouses adaptive immune responses, causing maturation of dendritic cells, infiltration of T cells, repolarization of the M2 macrophage to the M1 macrophage, and upregulation of inflammatory factors. Remarkably, OMV-DPG-IR820 demonstrated tumor-targeting capabilities with guidance provided by near-infrared II (NIR-II) fluorescence imaging, leading to remarkable inhibition on both primary and distant tumors and preventing metastasis without causing noticeable adverse reactions. This study elucidates a sophisticated bioorthogonal engineering strategy for the design and production of functionalized OMVs and provides novel perspectives on the microbiome-mediated reversal of TNBC through a precise and efficient immunotherapy.},
}

@article {pmid39603712,
year = {2024},
author = {Arrington, HB and Lee, SG and Lee, JH and Covi, JA},
title = {Assessment of the cyst wall and surface microbiota in dormant embryos of the Antarctic calanoid copepod, Boeckella poppei.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70035},
pmid = {39603712},
issn = {1758-2229},
support = {PE24160//Korea Polar Research Institute (KOPRI)/ ; PM24030//Korea Polar Research Institute (KOPRI)/ ; 20200610//Korea Institute of Marine Science & Technology Promotion (KIMST)/ ; //Ministry of Oceans and Fisheries/ ; //National Science Foundation/ ; //National Science Foundation/ ; //College of Arts and Sciences, University of North Carolina at Wilmington/ ; },
mesh = {Animals ; *Copepoda/microbiology ; *Microbiota ; Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Embryo, Nonmammalian/microbiology ; Microscopy, Electron, Scanning ; Biofilms/growth & development ; Bacteria/genetics/classification/isolation & purification/metabolism ; Zooplankton/microbiology ; },
abstract = {Embryos of zooplankton from inland waters and estuaries can remain viable for years in an extreme state of metabolic suppression. How these embryos resist microbial attack with limited metabolic capacity for immune defence or repair is unknown. As a first step in evaluating resistance to microbial attack in dormant zooplankton, surface colonization of the Antarctic freshwater copepod, Boeckella poppei, was evaluated. Scanning electron micrographs demonstrate the outer two layers of a five-layered cyst wall in B. poppei fragment and create a complex environment for microbial colonization. By contrast, the third layer remains undamaged during years of embryo storage in native sediment. The absence of damage to the third layer indicates that it is resistant to degradation by microbial enzymes. Scanning electron microscopy and microbiome analysis using the 16S ribosomal subunit gene and internal transcribed spacer (ITS) region demonstrate the presence of a diverse microbial community on the embryo surface. Coverage of the embryos with microbial life varies from a sparse population with individual microbes to complete coverage by a thick biofilm. Extracellular polymeric substance binds debris and provides a structural element for the microbial community. Frequent observation of bacterial fission indicates that the biofilm is viable in stored sediments.},
}

Animals
*Copepoda/microbiology
*Microbiota
Antarctic Regions
RNA, Ribosomal, 16S/genetics
Embryo, Nonmammalian/microbiology
Microscopy, Electron, Scanning
Biofilms/growth & development
Bacteria/genetics/classification/isolation & purification/metabolism
Zooplankton/microbiology

@article {pmid39603509,
year = {2024},
author = {Shiraz, MG and Nielsen, J and Widmann, J and Chung, KHK and Davis, TP and Rasmussen, C and Scavenius, C and Enghild, JJ and Martin-Gallausiaux, C and Singh, Y and Javed, I and Otzen, DE},
title = {Young rat microbiota extracts strongly inhibit fibrillation of α-synuclein and protect neuroblastoma cells and zebrafish against α-synuclein toxicity.},
journal = {Molecules and cells},
volume = {},
number = {},
pages = {100161},
doi = {10.1016/j.mocell.2024.100161},
pmid = {39603509},
issn = {0219-1032},
abstract = {The clinical manifestations of Parkinson's Disease (PD) are driven by aggregation of α-Synuclein (α-Syn) in the brain. However, there is increasing evidence that PD may be initiated in the gut and thence spread to the brain, e.g. via the vagus nerve. Many studies link PD to changes in the gut microbiome, and bacterial amyloid has been shown to stimulate α-syn aggregation. Yet we are not aware of any studies reporting on a direct connection between microbiome components and α-Syn aggregation. Here we report that soluble extract from the gut microbiome of the rats, particularly young rats transgenic for PD, show a remarkably strong ability to inhibit in vitro α-Syn aggregation and keep it natively unfolded and monomeric. The active component(s) are heat-labile molecule(s) of around 30-100 kDa size which are neither nucleic acid nor lipid. Proteomic analysis identified several proteins whose concentrations in different rat samples correlated with the samples' anti-inhibitory activity, while a subsequent pulldown assay linked the protein chaperone DnaK with the inhibitory activity of young rat's microbiome, confirmed in subsequent in vitro assays. Remarkably, the microbiome extracts also protected neuroblastoma SH-SY5Y cells and zebrafish embryos against α-Syn toxicity. Our study sheds new light on the gut microbiome as a potential source of protection against PD and opens up for new microbiome-based therapeutic strategies.},
}

@article {pmid39603488,
year = {2024},
author = {Wang, Y and Wu, W and Zeng, F and Meng, X and Peng, M and Wang, J and Chen, Z and Liu, W},
title = {The role of kynurenine pathway metabolism mediated by exercise in the microbial-gut-brain axis in Alzheimer's disease.},
journal = {Experimental neurology},
volume = {384},
number = {},
pages = {115070},
doi = {10.1016/j.expneurol.2024.115070},
pmid = {39603488},
issn = {1090-2430},
abstract = {In recent years, the role of the microbiome-gut-brain axis in the pathogenesis of Alzheimer's disease (AD) has garnered increasing attention. Specifically, tryptophan metabolism via the kynurenine pathway (KP) plays a crucial regulatory role in this axis. This study reviews how exercise regulates the microbiome-gut-brain axis by influencing kynurenine pathway metabolism, thereby exerting resistance against AD. This paper also discusses how exercise positively impacts AD via the microbiome-gut-brain axis by modulating the endocrine, autonomic nervous, and immune systems. Although the specific mechanisms are not fully understood, research indicates that exercise may optimize tryptophan metabolism by promoting the growth of beneficial microbiota and inhibiting harmful microbiota, producing substances that are beneficial to the nervous system and combating AD. The aim of this review is to provide new perspectives and potential intervention strategies for the prevention and treatment of AD by exploring the links between exercise, KP and the gut-brain axis.},
}

@article {pmid39603393,
year = {2024},
author = {Chen, Z and Liu, S and Song, F and Hou, Z and Zhou, H and Fan, Y and Wang, R and Liu, Z},
title = {Integrated metabolome and microbiome strategy reveals the therapeutic effect of nervonic acid on Alzheimer's disease rats.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109813},
doi = {10.1016/j.jnutbio.2024.109813},
pmid = {39603393},
issn = {1873-4847},
abstract = {Alzheimer's disease (AD) is a complex neurodegenerative disease. Nervonic acid is a component of breast milk and is also found in fish oil and specific vegetable oils. Studies have shown that nervonic acid is essential for the development of the human nervous system. In this study, Morris water maze (MWM) test and pathological analysis showed that nervonic acid could improve cognitive deficits and brain nerve damage in AD rats. Then, through sequencing, we found that nervonic acid increased the abundance of beneficial bacteria such as Lactobacillus and Bacteroides, and decreased the abundance of Pseudomonadaceae_Pseudomonas. Not only that, nervonic acid also regulates the production of short-chain fatty acids (SCFA) and the levels of 29 fecal metabolites, and affects the metabolism of linoleic acid, α-linolenic acid, arachidonic acid, and sphingolipid. Finally, we verified the regulatory effect of nervonic acid on metabolic enzyme activity.},
}

@article {pmid39603332,
year = {2024},
author = {Tang, JW and Hau, CC and Tong, WM and Watt, RM and Yiu, CKY and Shum, KK},
title = {Alterations of oral microbiota in young children with autism: Unraveling potential biomarkers for early detection.},
journal = {Journal of dentistry},
volume = {152},
number = {},
pages = {105486},
doi = {10.1016/j.jdent.2024.105486},
pmid = {39603332},
issn = {1879-176X},
abstract = {OBJECTIVES: This study investigated the oral microbiota in young children with autism spectrum disorder (ASD) to determine possible alterations in microbial composition and identify potential biomarkers for early detection.

METHODS: Dental plaque samples from 25 children with ASD (aged 3-6 years; M = 4.79, SD = 0.83) and 30 age- and sex-matched typically developing (TD) children were analyzed using 16S rRNA sequencing.

RESULTS: The results showed lower bacterial diversity in children with ASD compared to controls, with distinct microbial compositions in the ASD and TD groups. Six discriminatory species (Microbacterium flavescens, Leptotrichia sp. HMT-212, Prevotella jejuni, Capnocytophaga leadbetteri, Leptotrichia sp. HMT-392, and Porphyromonas sp. HMT-278) were identified in the oral microbiota of ASD children, while five discriminatory species (Fusobacterium nucleatum subsp. polymorphum, Schaalia sp. HMT-180, Leptotrichia sp. HMT-498, Actinomyces gerencseriae, and Campylobacter concisus) were identified in TD controls. A model generated by random forest and leave-one-out cross-validation achieved an accuracy of 0.813. Receiver operating characteristic analysis yielded a sensitivity of 0.778, a specificity of 0.857, and an AUC (area under curve) of 0.937 (95 % CI: 0.82 - 1.00) for differentiating children with and without ASD.

CONCLUSION: The present study has unveiled significant disparities in the oral microbial composition between ASD and TD children.

SIGNIFICANCE: These findings contribute to understanding the microbiome-brain connection in ASD and its implications for early detection and management. Further research is needed to validate these oral bacterial biomarkers and explore their mechanistic association with ASD pathophysiology.},
}

@article {pmid39603245,
year = {2024},
author = {Pietrasanta, C and Carlosama, C and Lizier, M and Fornasa, G and Jost, TR and Carloni, S and Giugliano, S and Silvestri, A and Brescia, P and De Ponte Conti, B and Braga, D and Mihula, M and Morosi, L and Bernardinello, A and Ronchi, A and Martano, G and Mosca, F and Penna, G and Grassi, F and Pugni, L and Rescigno, M},
title = {Prenatal antibiotics reduce breast milk IgA and induce dysbiosis in mouse offspring, increasing neonatal susceptibility to bacterial sepsis.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.11.001},
pmid = {39603245},
issn = {1934-6069},
abstract = {Antibiotics (Abx) are administered to 20%-30% of pregnant women, but their effects on neonatal immune development are poorly understood. We show that newborn mice born to Abx-treated dams are more susceptible to late-onset sepsis. This susceptibility is linked to lower maternal breast milk immunoglobulin A (IgA), neonatal fecal IgA, and IgA coating of intestinal bacteria, thus causing the translocation of intestinal pathobionts. Weaned young adults born to Abx-treated mothers had reduced IgA+ plasma cells in the ileum and colon, fecal secretory IgA (SIgA), colonic CD4[+] T regulatory lymphocytes and T helper 17-like lymphocytes, and a less diverse fecal microbiome. However, treatment with apyrase, which restores SIgA secretion, prompted IgA production in breast milk and protected pups from sepsis. Additionally, breast milk from untreated mothers rescued the phenotypes of pups born to Abx-treated mothers. Our data highlight the impact of prenatal Abx on breast milk IgA and their long-term influence on intestinal mucosal immune function mediated by breastfeeding.},
}

@article {pmid39603188,
year = {2024},
author = {Xie, C and Liang, Q and Cheng, J and Yuan, Y and Xie, L and Ji, J},
title = {Transplantation of fecal microbiota from low to high residual feed intake chickens: Impacts on RFI, microbial community and metabolites profiles.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104567},
doi = {10.1016/j.psj.2024.104567},
pmid = {39603188},
issn = {1525-3171},
abstract = {Improving feed efficiency is vital to bolster profitability and sustainability in poultry production. Although several studies have established links between gut microbiota and feed efficiency, the direct effects remain unclear. In this study, two distinct lines of Huiyang bearded chickens, exhibiting significant differences in residual feed intake (RFI), were developed after 15 generations of selective breeding. Fecal microbiota transplantation (FMT) from low RFI (LRFI) chickens to high RFI (HRFI) chickens resulted in a reduction trend in RFI, decreasing from 5.65 to 4.49 in the HRFI recipient chickens (HFMT). Microbiota composition and functional profiles in LRFI and HFMT chickens formed a distinct cluster compared to HRFI chickens. Using 16S rDNA sequencing and RandomForest analysis, Slackia, Peptococcus, Blautia, and Dorea were identified as key microbial markers associated with feed efficiency. Additionally, untargeted metabolomics identified common differential metabolites between HFMT and LRFI vs. HRFI groups. Correlation analysis showed significant correlations between these microbial markers and differential metabolites. These findings provide a foundation for microbiome-based strategies to improve feed efficiency in poultry.},
}

@article {pmid39602985,
year = {2024},
author = {Gao, X and Chen, J and Yu, K and Bu, Y and Wang, L and Yu, X},
title = {Exposure to polypropylene microplastics induces the upregulation of protein digestion-associated genes and microbiome reorganization in the octocoral Junceella squamata.},
journal = {Marine pollution bulletin},
volume = {210},
number = {},
pages = {117331},
doi = {10.1016/j.marpolbul.2024.117331},
pmid = {39602985},
issn = {1879-3363},
abstract = {Microplastics, a new type of pollutants found in coral reefs, have attracted increasing attention. However, most of the current research focuses on the scleractinian corals and few reports on Octocorallia. To reveal the impact of microplastic exposure on Octocorallia, we analyzed the transcriptional response of the coral hosts Junceella squamata along with changes to the diversity and community structure of its symbiotic bacteria following exposure to polystyrene microplastics. These results suggest that the microplastics have adverse impacts on nutrient metabolism and absorption in J. squamata. The symbiotic bacteria of J. squamata exhibited a clear response after exposure to microplastics, which may also reflect an adaptation mechanism of corals, and help to maintain the physiological function of coral symbiotic function under the exposure of microplastics. This study has revealed the impact of microplastic exposure on J. squamata, providing new insights for coral protection against the background of increased microplastics pollution.},
}

@article {pmid39602306,
year = {2024},
author = {Pasolli, E and Mauriello, IE and Avagliano, M and Cavaliere, S and De Filippis, F and Ercolini, D},
title = {Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis.},
journal = {Cell reports},
volume = {43},
number = {12},
pages = {115027},
doi = {10.1016/j.celrep.2024.115027},
pmid = {39602306},
issn = {2211-1247},
abstract = {We performed a large-scale genome-wide analysis aiming to investigate the prevalence and strain-level diversity of Bifidobacteriaceae species in the human microbiome. We considered 9,528 publicly available human metagenomes and integrated them with 1,192 isolate genomes from different sources. The prevalence and abundance of Bifidobacteriaceae species in humans was linked to multiple host characteristics: they were reduced in older people and enriched in populations characterized by Westernized lifestyles with geography-specific patterns. Phylogenetic analysis highlighted 110 Bifidobacteriaceae species-level genome bins (SGBs), with 32 found in humans and 8 in food and probiotic sources. Functional annotation revealed a great diversity in carbohydrate-active enzyme families across these SGBs. We found potential subspecies for most of the SGBs prevalent in humans and identified patterns driven by age and geography. We provided evidence that strains used in probiotics were rarely identified in humans, with the only exception represented by Bifidobacterium animalis. We finally evaluated that the abundance of Bifidobacteriaceae species exhibited moderate and variable capabilities to predict health status in case-control studies.},
}

@article {pmid39602230,
year = {2024},
author = {Millot, M and Imbert, C and Pouget, C and Girardot, M and Mambu, L},
title = {Lichen and its Microbiome as an Untapped Source of Anti-biofilm Compounds.},
journal = {Chemistry & biodiversity},
volume = {},
number = {},
pages = {e202401557},
doi = {10.1002/cbdv.202401557},
pmid = {39602230},
issn = {1612-1880},
abstract = {Lichen substances have been firstly described in the 1870s and most of them have been evaluated for their activity on planktonic microorganisms (bacteria and fungi). More recently, microorganisms colonizing the lichen thallus have been isolated and identified giving access to a wild diversity of culturable microorganisms. The increasing research in lichens associated microbiome in recent years, has emphased a wide range of metabolites as a potential source of bioactive compounds. In parallel, humans are facing microbial resistance to conventional antimicrobial drugs. One of the reasons is the biofilm lifestyle of microorganisms. Indeed, the aggregation of microbial communities inside biofilms is now well-known and characterized and some possible ways to fight and destroy biofilms are identified (quorum sensing inhibitors,…). The present review aims to summarize the anti-biofilm potential of lichen metabolites and those from their associated microorganisms (bacteria and/or fungi). Are the metabolites isolated from lichens and their associated fungi displaying any anti-biofilm activity? This literature synthesis highlights the metabolites of interest as new anti-biofilm drugs and shows the lack of current biological research dealing with biofilm and lichen metabolites. Only two lichen metabolites, usnic acid and evernic acid, have been evaluated both as antifungal and antibacterial biofilm compounds.},
}

@article {pmid39602070,
year = {2024},
author = {Ehis-Eriakha, CB and Chikere, CB and Akaranta, O and Akemu, SE},
title = {A comparative assesment of biostimulants in microbiome-based ecorestoration of polycyclic aromatic hydrocarbon polluted soil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39602070},
issn = {1678-4405},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) pose severe environmental and public health risks due to their harmful and persistent nature. Therefore, developing sustainable and effective methods for PAH remediation is crucial. This study explores the biostimulation potential of various nutrient supplements in enhancing the metabolic activities of indigenous oleophilic bacteria to PAH degradation and removal. The physicochemical and microbiological characterization of the soil sample obtained from the aged crude oil spill site prior to bioremediation revealed the presence of PAH and other hydrocarbons, reduced nutrient availability as well as an appreciable population of PAH degrading bacteria such as strains of Pseudomonas, Enterobacter, Kosakonia and Staphylococcus. The polluted soil treatment was conducted in six microcosms representing each nutrient supplement: casmes-CM, cocodust-CCD and osmocote-OSM slow-release fertilizers, NPK 20:10:10, casmes + cow dung - CM + CD and a control (unamended soil). Each pot contained 4 kg of soil spiked with 4% Escravos crude oil to a final concentration of 989 mg/kg of PAH, respectively. All treatments enhanced the activity of the indigenous bacteria to promote PAH removal (> 50%) after 35 days although CM + CD had the highest biostimulation effect (B. E.) of 56% with 71.77% PAH attenuation followed by NPK treatment with B. E. of 54.9% and 70.4% PAH removal, respectively. The order of degradation of PAHs from lowest to highest is: control > casmes > osmocote > cocodust > NPK > CM + CD. First-order kinetic model revealed soil microcosm amended with CM + CD had a higher k value (0.0342 day-1) and lower t½ (18.48 day) and this was relatively followed by NPK treated soil. Biostimulation is an effective bioremediation approach to PAH degradation, however, a combined nutrient regimen in the presence of PAH-degrading microbes is more potent and eco-friendly in driving this process.},
}

@article {pmid39601988,
year = {2024},
author = {Rekadwad, BN and Shouche, YS and Jangid, K},
title = {Oil spill pollution and diversity analyses of resistant bacteria isolated from soil across the Arabian Sea and Bay of Bengal coastlines.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {12},
pages = {1265},
pmid = {39601988},
issn = {1573-2959},
mesh = {*Bacteria/classification/isolation & purification/genetics ; *Petroleum Pollution ; *Environmental Monitoring ; India ; *Soil Microbiology ; Biodiversity ; Bays/microbiology ; Drug Resistance, Bacterial ; },
abstract = {Pelagic transport causes oil pollution via international tanker routes in the open ocean across southern Asia and the Indian Territory. Nutrient-rich runoff from residential, commercial, and industrial wastes, oil tanker mishaps, and sailing flags have all resulted in pollution. The natural flow of ocean water from east to west dragged pollutants into Indian Territory. We have investigated that the severe deposition of oil spills and biohazardous wastes is causing faunal mortality. Microbiome analyses helped us understand the sample's microbial load. 16S amplicon metagenome analysis, followed by enumeration and confirmation using molecular methods, indicates the presence of diverse microbial profiles. The presence of non-native hydrocarbon- and AMR-resistant bacterial taxa, such as Brevundimonas, Staphylococcus spp., Mycolicibacterium, Spingomonas spp., Bacillus spp., Chitinophaga spp., Priestia spp., Domibacillus spp., Rossellomorea spp., and Acinetobacter spp., confirms the impacts of oil and urban pollution. This indicates that the coastal soil of Goa and Andhra Pradesh has hydrocarbon- and antibiotic-resistant bacteria, which confirms that the present pollution status and that high-traffic recreational activities put biodiversity and humans at risk of getting illnesses linked to antibiotic resistance.},
}

*Bacteria/classification/isolation & purification/genetics
*Petroleum Pollution
*Environmental Monitoring
India
*Soil Microbiology
Biodiversity
Bays/microbiology
Drug Resistance, Bacterial

@article {pmid39601776,
year = {2024},
author = {Mavros, CF and Bongers, M and Neergaard, FBF and Cusimano, F and Sun, Y and Kaufman, A and Richardson, M and Kammler, S and Kristensen, M and Sommer, MOA and Wang, HH},
title = {Bacteria Engineered to Produce Serotonin Modulate Host Intestinal Physiology.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.4c00453},
pmid = {39601776},
issn = {2161-5063},
abstract = {Bacteria in the gastrointestinal tract play a crucial role in intestinal motility, homeostasis, and dysfunction. Unraveling the mechanisms by which microbes impact the host poses many challenges due to the extensive array of metabolites produced or metabolized by bacteria in the gut. Here, we describe the engineering of a gut commensal bacterium, Escherichia coli Nissle 1917, to biosynthesize the human metabolite serotonin for examining the effects of microbially produced biogenic amines on host physiology. Upon oral administration to mice, our engineered bacteria reach the large intestine, where they produce serotonin. Mice treated with serotonin-producing bacteria exhibited biological changes in the gut at transcriptional and physiological levels. This work establishes a novel framework employing engineered bacteria to modulate luminal serotonin levels and suggests potential clinical applications of modified microbial therapeutics to address gut disorders in humans.},
}

@article {pmid39601521,
year = {2024},
author = {Atkinson, CGF and Kerns, KA and Hendrickson, EL and He, X and Bor, B and McLean, JS},
title = {Complete genome of Nanosynbacter sp. strain BB002, isolated and cultivated from a site of periodontal disease.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0063724},
doi = {10.1128/mra.00637-24},
pmid = {39601521},
issn = {2576-098X},
abstract = {Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris. As a member of the Saccharibacteria within the candidate phylum radiation group (CPR), its reduced genome facilitates the survival as an ultrasmall (<0.2 μm) epibiont.},
}

@article {pmid39601429,
year = {2024},
author = {Wang, Y and Wang, Y and Zhou, Y and Feng, Y and Sun, T and Xu, J},
title = {Tumor-related fungi and crosstalk with gut fungi in the tumor microenvironment.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2024.0240},
pmid = {39601429},
issn = {2095-3941},
support = {82373113 to XJ//National Natural Science Foundation of China/ ; 22-321-31-04 to ST//Shenyang Public Health R&D Special Project/ ; XLYC1907160 to XJ//Liaoning Revitalization Talents Program/ ; YXJL-2020-0941-0752 to ST//Beijing Medical Award Foundation/ ; CORP-239-N27 to CH//Beijing Medical Award Foundation/ ; 320.6750.2020-12-21//Wu Jieping Medical Foundation/ ; 320.6750.2020-6-30 to ST//Wu Jieping Medical Foundation/ ; 202229 to ST//Fundamental Research Funds for the Central Universities/ ; 202230 to XJ//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Most studies on the human gut microbiome have focused on the bacterial fraction rather than fungal biomics, which as resulted in an incomplete understanding of the fungal microbiome. Recent advances in microbiota detection and next-generation sequencing technology have boosted an increase in research on fungi. Symbiotic fungi have become increasingly influential in health and disease and modulate various physiologic functions within the host. Fungal infections can result in high morbidity and mortality rates and are life-threatening in some immunocompromised patients. In addition to bacterial dysbiosis, alterations in fungal communities are important and have been linked to many diseases, including asthma, mental illness, and various cancers. When investigating cancer it is imperative to consider the role of fungi alongside viruses and bacteria. This review examined the impact of intestinal fungi and peri-tumor fungi on tumorigenesis, cancer progression, and response to anticancer therapies. The review highlights the specific involvement of some fungal species in cancers include digestive tract tumors such as colorectal, pancreatic, liver, and gastric cancers, as well as non-digestive tract tumors such as lung, melanoma, breast, and ovarian cancers. Furthermore, fungal mechanisms of action, including fungus-host recognition and immune regulation, biofilm formation, toxin and metabolite production in the tumor microenvironment, and the complex effects of fungus-bacteria interactions on tumorigenesis and development, highlight the significance of potential biomarkers in cancer diagnosis and treatment.},
}

@article {pmid39601281,
year = {2024},
author = {Rios-Carlos, M and Cervantes-García, D and Córdova-Dávalos, LE and Bermúdez-Humarán, LG and Salinas, E},
title = {Unraveling the gut-skin axis in atopic dermatitis: exploiting insights for therapeutic strategies.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2430420},
doi = {10.1080/19490976.2024.2430420},
pmid = {39601281},
issn = {1949-0984},
mesh = {*Dermatitis, Atopic/microbiology/therapy/drug therapy ; Humans ; *Gastrointestinal Microbiome ; *Skin/microbiology ; *Probiotics/therapeutic use ; *Prebiotics/administration & dosage ; Animals ; Bacteria/metabolism/classification ; Fatty Acids, Volatile/metabolism ; },
abstract = {Gut microbiota exert functions of high importance in the intestine. Furthermore, there is increasing evidence for its role in immune regulation and maintenance of homeostasis in many physiological processes taking place in distant tissues. In particular, in this review, we explore the impact of metabolites produced by the gut microbiota on the development of atopic dermatitis (AD). Probiotics and prebiotics balance the microbiota and promote the generation of bacterial metabolites, such as short-chain fatty acids and tryptophan derivates, which promote the regulation of the exacerbated AD immune response through regulatory T cells and IL-10 and TGF-β cytokines. Metabolites also have a direct action on keratinocytes once they reach the bloodstream. Besides, probiotics decrease the levels of metabolites associated with AD onset, such as phenols. Understanding all these crosstalk processes between the gut and the skin reveals a number of possibilities, mainly through the manipulation of the gut microbiome, which may represent therapeutic strategies that can contribute to the standard treatments of AD patients to improve their quality of life.},
}

*Dermatitis, Atopic/microbiology/therapy/drug therapy
Humans
*Gastrointestinal Microbiome
*Skin/microbiology
*Probiotics/therapeutic use
*Prebiotics/administration & dosage
Animals
Bacteria/metabolism/classification
Fatty Acids, Volatile/metabolism

@article {pmid39601125,
year = {2024},
author = {Cao, H and Tian, Q and Chu, L and Wu, L and Gao, H and Gao, Q},
title = {Lycium ruthenicum Murray anthocyanin-driven neuroprotection modulates the gut microbiome and metabolome of MPTP-treated mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo01878h},
pmid = {39601125},
issn = {2042-650X},
abstract = {Emerging evidence suggests that Parkinson's disease (PD) is strongly associated with altered gut microbiota. The present study investigated the prophylactic effects of anthocyanins (ACNs) from Lycium ruthenicum Murray on Parkinson's disease based on microbiomics and metabolomics. In this study, sixty-six adult male C57BL/6J mice were randomized into the control group, model group, positive drug (Madopar) group, and low-, medium- and high-dose ACN groups. Behavioral experiments were conducted and pathological indicators were determined. Fresh feces were collected for microbiomic analysis using 16S rRNA sequencing. Urine and serum were analyzed by the UPLC-MS method for untargeted metabolomics. The results demonstrated that ACNs ameliorated 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced motor deficits, dopamine neuron death, and glial cell activation, while 100 mg kg[-1] and 200 mg kg[-1] ACNs were more neuroprotective than 50 mg kg[-1]. Mice with PD-like phenotypes have an altered gut microbiota composition, and ACNs may regulate this disorder by causing an increase in Firmicutes/Bacteroidota ratio and abundance of norank_f__Eubacterium_coprostanoligenes_group and a decrease in the abundance of norank_f__Muribaculaceae, Coriobacteriaceae_UCG-002 and Parvibacter. Furthermore, ACNs increased 14 urinary key metabolites such as DIMBOA-Glc and tauroursodeoxycholic acid, decreased N,N-dimethyllysine, and increased 12 serum key metabolites such as 1-methylguanine and 1-nitro-5-glutathionyl-6-hydroxy-5,6-dihydronaphthalene, and decreased lamivudine-monophosphate and 5-butyl-2- methylpyridine. The present study reveals that ACNs are protective against MPTP-induced PD in mice by modulating anti-inflammatory flora in the gut and endogenous metabolites in serum/urine, and the key mechanisms may be related to Coriobacteriaceae_UCG-002 and glycerophospholipid metabolic pathways. Our findings provide new insights into the pathogenesis and potential treatment of Parkinson's disease.},
}

@article {pmid39600755,
year = {2024},
author = {Castro-Vidal, ZA and Mathew, F and Ibrahim, AA and Shubhangi, F and Cherian, RR and Choi, HK and Begum, A and Ravula, HK and Giri, H},
title = {The Role of Gastrointestinal Dysbiosis and Fecal Transplantation in Various Neurocognitive Disorders.},
journal = {Cureus},
volume = {16},
number = {10},
pages = {e72451},
pmid = {39600755},
issn = {2168-8184},
abstract = {This review explores the critical role of the human microbiome in neurological and neurodegenerative disorders, focusing on gut-brain axis dysfunction caused by dysbiosis, an imbalance in gut bacteria. Dysbiosis has been linked to diseases such as Alzheimer's disease, Parkinson's disease (PD), multiple sclerosis (MS), and stroke. The gut microbiome influences the central nervous system (CNS) through signaling molecules, including short-chain fatty acids, neurotransmitters, and metabolites, impacting brain health and disease progression. Emerging therapies, such as fecal microbiota transplantation (FMT), have shown promise in restoring microbial balance and alleviating neurological symptoms, especially in Alzheimer's and PD. Additionally, nutritional interventions such as probiotics, prebiotics, and specialized diets are being investigated for their ability to modify gut microbiota and improve patient outcomes. This review highlights the therapeutic potential of gut microbiota modulation but emphasizes the need for further clinical trials to establish the safety and efficacy of these interventions in neurological and mental health disorders.},
}

@article {pmid39600698,
year = {2024},
author = {Liu, X and Li, B and Liang, L and Han, J and Mai, S and Liu, L},
title = {From microbes to medicine: harnessing the power of the microbiome in esophageal cancer.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1450927},
pmid = {39600698},
issn = {1664-3224},
mesh = {Humans ; *Esophageal Neoplasms/therapy/microbiology/immunology ; *Dysbiosis/therapy/microbiology ; *Gastrointestinal Microbiome/immunology ; Animals ; Probiotics/therapeutic use ; Microbiota/immunology ; },
abstract = {Esophageal cancer (EC) is a malignancy with a high incidence and poor prognosis, significantly influenced by dysbiosis in the esophageal, oral, and gut microbiota. This review provides an overview of the roles of microbiota dysbiosis in EC pathogenesis, emphasizing their impact on tumor progression, drug efficacy, biomarker discovery, and therapeutic interventions. Lifestyle factors like smoking, alcohol consumption, and betel nut use are major contributors to dysbiosis and EC development. Recent studies utilizing advanced sequencing have revealed complex interactions between microbiota dysbiosis and EC, with oral pathogens such as Porphyromonas gingivalis and Fusobacterium nucleatum promoting inflammation and suppressing immune responses, thereby driving carcinogenesis. Altered esophageal microbiota, characterized by reduced beneficial bacteria and increased pathogenic species, further exacerbate local inflammation and tumor growth. Gut microbiota dysbiosis also affects systemic immunity, influencing chemotherapy and immunotherapy efficacy, with certain bacteria enhancing or inhibiting treatment responses. Microbiota composition shows potential as a non-invasive biomarker for early detection, prognosis, and personalized therapy. Novel therapeutic strategies targeting the microbiota-such as probiotics, dietary modifications, and fecal microbiota transplantation-offer promising avenues to restore balance and improve treatment efficacy, potentially enhancing patient outcomes. Integrating microbiome-focused strategies into current therapeutic frameworks could improve EC management, reduce adverse effects, and enhance patient survival. These findings highlight the need for further research into microbiota-tumor interactions and microbial interventions to transform EC treatment and prevention, particularly in cases of late-stage diagnosis and poor treatment response.},
}

Humans
*Esophageal Neoplasms/therapy/microbiology/immunology
*Dysbiosis/therapy/microbiology
*Gastrointestinal Microbiome/immunology
Animals
Probiotics/therapeutic use
Microbiota/immunology

@article {pmid39600316,
year = {2024},
author = {Chen, S and Wang, C and Zou, X and Li, H and Yang, G and Su, X and Mo, Z},
title = {Multi-omics insights implicate the remodeling of the intestinal structure and microbiome in aging.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1450064},
pmid = {39600316},
issn = {1664-8021},
abstract = {BACKGROUND: Aging can impair the ability of elderly individuals to fight infections and trigger persistent systemic inflammation, a condition known as inflammaging. However, the mechanisms underlying the development of inflammaging remain unknown.

METHODS: We conducted 16S rRNA sequencing of intestinal contents from young and old C57BL/6J mice to elucidate changes in gut microbiota diversity and microbial community composition after aging. Aging-related differential bacterial taxa were then identified, and their abundance trends were validated in human samples. The variances in intestinal barrier function and circulating endotoxin between groups were also assessed. Furthermore, widely targeted metabolomics was conducted to characterize metabolic profiles after aging and to investigate the key metabolic pathways enriched by the differential metabolites.

RESULTS: Our findings demonstrated an increase in relative proportion of pathogenic bacteria with age, a trend also revealed in healthy populations of different age groups. Additionally, aging individuals exhibited reduced intestinal barrier function and increased circulating endotoxin levels. Widely targeted metabolomics revealed a significant increase in various secondary bile acid metabolites after aging, positively correlated with the relative abundance of several aging-related bacterial taxa. Furthermore, old group had lower levels of various anti-inflammatory or beneficial metabolites. Enrichment analysis identified the starch and sucrose metabolism pathway as potentially the most significantly impacted signaling pathway during aging.

CONCLUSION: This study aimed to provide insights into the complex interactions involved in organismal inflammaging through microbial multi-omics. These findings lay a solid foundation for future research aimed at identifying novel biomarkers for the clinical diagnosis of aging-related diseases or potential therapeutic targets.},
}

@article {pmid39600252,
year = {2024},
author = {Grupstra, CGB and Meyer-Kaiser, KS and Bennett, MJ and Andres, MO and Juszkiewicz, DJ and Fifer, JE and Da-Anoy, JP and Gomez-Campo, K and Martinez-Rugerio, I and Aichelman, HE and Huzar, AK and Hughes, AM and Rivera, HE and Davies, SW},
title = {Holobiont Traits Shape Climate Change Responses in Cryptic Coral Lineages.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17578},
doi = {10.1111/gcb.17578},
pmid = {39600252},
issn = {1365-2486},
support = {2048589//The National Science Foundation's Division of Ocean Sciences/ ; 2048678//The National Science Foundation's Division of Ocean Sciences/ ; },
mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Climate Change ; *Coral Reefs ; *Symbiosis ; Microbiota ; Dinoflagellida/physiology ; },
abstract = {As ocean warming threatens reefs worldwide, identifying corals with adaptations to higher temperatures is critical for conservation. Genetically distinct but morphologically similar (i.e. cryptic) coral populations can be specialized to extreme habitats and thrive under stressful conditions. These corals often associate with locally beneficial microbiota (Symbiodiniaceae photobionts and bacteria), obscuring the main drivers of thermal tolerance. Here, we leverage a holobiont (massive Porites) with high fidelity for C15 photobionts to investigate adaptive variation across classic ("typical" conditions) and extreme reefs characterized by higher temperatures and light attenuation. We uncovered three cryptic lineages that exhibit limited micro-morphological variation; one lineage dominated classic reefs (L1), one had more even distributions (L2), and a third was restricted to extreme reefs (L3). L1 and L2 were more closely related to populations ~4300 km away, suggesting that some lineages are widespread. All corals harbored Cladocopium C15 photobionts; L1 and L2 shared a photobiont pool that differed in composition between reef types, yet L3 mostly harbored unique photobiont strains not found in the other lineages. Assemblages of bacterial partners differed among reef types in lineage-specific ways, suggesting that lineages employ distinct microbiome regulation strategies. Analysis of light-harvesting capacity and thermal tolerance revealed adaptive variation underpinning survival in distinct habitats: L1 had the highest light absorption efficiency and lowest thermal tolerance, suggesting that it is a classic reef specialist. L3 had the lowest light absorption efficiency and the highest thermal tolerance, showing that it is an extreme reef specialist. L2 had intermediate light absorption efficiency and thermal tolerance, suggesting that is a generalist lineage. These findings reveal diverging holobiont strategies to cope with extreme conditions. Resolving coral lineages is key to understanding variation in thermal tolerance among coral populations, can strengthen our understanding of coral evolution and symbiosis, and support global conservation and restoration efforts.},
}

*Anthozoa/microbiology/physiology
Animals
*Climate Change
*Coral Reefs
*Symbiosis
Microbiota
Dinoflagellida/physiology

@article {pmid39600222,
year = {2024},
author = {Lu, SSM and Rutegård, M and Häggström, C and Gylfe, Å and Harlid, S and Van Guelpen, B},
title = {Prior antibiotics exposure is associated with an elevated risk of surgical site infections, including anastomotic leakage, after colon cancer but not rectal cancer surgery: A register-based study of 38,839 patients.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.35269},
pmid = {39600222},
issn = {1097-0215},
support = {RV-932777//Region Västerbotten/ ; LP 17-2154//the Lions Cancer Research Foundation in Northern Sweden/ ; //the Knut and Alice Wallenberg Foundation/ ; },
abstract = {Gut microbiota composition has been implicated in surgical site complications after colorectal cancer surgery. Antibiotics affect gut microbiota, but evidence for a role in surgical site complications is inconclusive. We aimed to investigate use of prescription antibiotics during the years before surgery in relation to the risk of surgical site infections, including anastomotic leakage, within 30 days after surgery. Cardiovascular/neurological complications and the urinary antiseptic methenamine hippurate, for which there is no clear link with the microbiota, were used as negative controls. We conducted a patient cohort study using complete population data from Swedish national registers between 2005 and 2020. The final study population comprised 26,527 colon cancer and 12,312 rectal cancer cases with a 4.5 year exposure window. In colon cancer patients, antibiotics use was associated with a higher risk of surgical site infections (adjusted odds ratio (aOR) for any versus no use = 1.20, 95% confidence interval (CI) 1.10-1.33) and anastomotic leakage in particular (aOR =1.19, 95% CI 1.03-1.36), both with dose-response relationships for increasing cumulative antibiotics use (Ptrend = <0.001 and Ptrend = 0.047, respectively). Conversely, associations in rectal cancer patients, as well as for the negative controls cardiovascular/neurological complications and methenamine hippurate, were null. In conclusion, prescription antibiotics use up to 4.5 years before colorectal cancer surgery is associated with a higher risk of surgical site infections, including anastomotic leakage, after colon cancer but not rectal cancer surgery. These findings support a role for antibiotics-induced intestinal dysbiosis in surgical site infections.},
}

@article {pmid39600051,
year = {2024},
author = {Rashad, S},
title = {Queuosine tRNA Modification: Connecting the Microbiome to the Translatome.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2400213},
doi = {10.1002/bies.202400213},
pmid = {39600051},
issn = {1521-1878},
support = {23H02741//Japan Society for the Promotion of Science/ ; },
abstract = {Transfer RNA (tRNA) modifications play an important role in regulating mRNA translation at the codon level. tRNA modifications can influence codon selection and optimality, thus shifting translation toward specific sets of mRNAs in a dynamic manner. Queuosine (Q) is a tRNA modification occurring at the wobble position. In eukaryotes, queuosine is synthesized by the tRNA-guanine trans-glycosylase (TGT) complex, which incorporates the nucleobase queuine (or Qbase) into guanine of the GUN anticodons. Queuine is sourced from gut bacteria and dietary intake. Q was recently shown to be critical for cellular responses to oxidative and mitochondrial stresses, as well as its potential role in neurodegenerative diseases and brain health. These unique features of Q provide an interesting insight into the regulation of mRNA translation by gut bacteria, and the potential health implications. In this review, Q biology is examined in the light of recent literature and nearly 4 decades of research. Q's role in neuropsychiatric diseases and cancer is highlighted and discussed. Given the recent interest in Q, and the new findings, more research is needed to fully comprehend its biological function and disease relevance, especially in neurobiology.},
}

@article {pmid39599889,
year = {2024},
author = {Meléndez-Vázquez, NM and Gomez-Manzano, C and Godoy-Vitorino, F},
title = {Oncolytic Virotherapies and Adjuvant Gut Microbiome Therapeutics to Enhance Efficacy Against Malignant Gliomas.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
pmid = {39599889},
issn = {1999-4915},
support = {2U54CA096297-16/BC/NCI NIH HHS/United States ; R25 GM061838/GM/NIGMS NIH HHS/United States ; 2U54MD007600/MD/NIMHD NIH HHS/United States ; R01CA256006/BC/NCI NIH HHS/United States ; },
mesh = {*Oncolytic Virotherapy/methods ; Humans ; *Gastrointestinal Microbiome ; *Oncolytic Viruses/genetics ; *Brain Neoplasms/therapy ; *Glioma/therapy ; Animals ; Immunotherapy/methods ; Glioblastoma/therapy ; Combined Modality Therapy ; },
abstract = {Glioblastoma (GBM) is the most prevalent malignant brain tumor. Current standard-of-care treatments offer limited benefits for patient survival. Virotherapy is emerging as a novel strategy to use oncolytic viruses (OVs) for the treatment of GBM. These engineered and non-engineered viruses infect and lyse cancer cells, causing tumor destruction without harming healthy cells. Recent advances in genetic modifications to OVs have helped improve their targeting capabilities and introduce therapeutic genes, broadening the therapeutic window and minimizing potential side effects. The efficacy of oncolytic virotherapy can be enhanced by combining it with other treatments such as immunotherapy, chemotherapy, or radiation. Recent studies suggest that manipulating the gut microbiome to enhance immune responses helps improve the therapeutic efficacy of the OVs. This narrative review intends to explore OVs and their role against solid tumors, especially GBM while emphasizing the latest technologies used to enhance and improve its therapeutic and clinical responses.},
}

*Oncolytic Virotherapy/methods
Humans
*Gastrointestinal Microbiome
*Oncolytic Viruses/genetics
*Brain Neoplasms/therapy
*Glioma/therapy
Animals
Immunotherapy/methods
Glioblastoma/therapy
Combined Modality Therapy

@article {pmid39599772,
year = {2024},
author = {Das, A and Gutkoska, J and Tadassa, Y and Jia, W},
title = {Enhanced Recovery and Detection of Highly Infectious Animal Disease Viruses by Virus Capture Using Nanotrap[®] Microbiome A Particles.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
pmid = {39599772},
issn = {1999-4915},
mesh = {Animals ; *Real-Time Polymerase Chain Reaction/methods ; Viruses/isolation & purification/genetics/classification ; Virus Diseases/diagnosis/veterinary/virology ; Sensitivity and Specificity ; Microbiota ; Cell Line ; },
abstract = {This study reports the use of Nanotrap[®] Microbiome A Particles (NMAPs) to capture and concentrate viruses from diluted suspensions to improve their recovery and sensitivity to detection by real-time PCR/RT-PCR (qPCR/RT-qPCR). Five highly infectious animal disease viruses including goatpox virus (GTPV), sheeppox virus (SPPV), lumpy skin disease virus (LSDV), peste des petits ruminants virus (PPRV), and African swine fever virus (ASFV) were used in this study. After capture, the viruses remained viable and recoverable by virus isolation (VI) using susceptible cell lines. To assess efficacy of recovery, the viruses were serially diluted in phosphate-buffered saline (PBS) or Eagle's Minimum Essential Medium (EMEM) and then subjected to virus capture using NMAPs. The NMAPs and the captured viruses were clarified on a magnetic stand, reconstituted in PBS or EMEM, and analyzed separately by VI and virus-specific qPCR/RT-qPCR. The PCR results showed up to a 100-fold increase in the sensitivity of detection of the viruses following virus capture compared to the untreated viruses from the same dilutions. Experimental and clinical samples were subjected to virus capture using NMAPs and analyzed by PCR to determine diagnostic sensitivity (DSe) that was comparable (100%) to that determined using untreated (-NMAPs) samples. NMAPs were also used to capture spiked viruses from EDTA whole blood (EWB). Virus capture from EWB was partially blocked, most likely by hemoglobin (HMB), which also binds NMAPs and outcompetes the viruses. The effect of HMB could be removed by either dilution (in PBS) or using HemogloBind™ (Biotech Support Group; Monmouth Junction, NJ, USA), which specifically binds and precipitates HMB. Enhanced recovery and detection of viruses using NMAPs can be applicable to other highly pathogenic animal viruses of agricultural importance.},
}

Animals
*Real-Time Polymerase Chain Reaction/methods
Viruses/isolation & purification/genetics/classification
Virus Diseases/diagnosis/veterinary/virology
Sensitivity and Specificity
Microbiota
Cell Line

@article {pmid39599756,
year = {2024},
author = {Horvath, A and Haller, R and Feldbacher, N and Habisch, H and Žukauskaitė, K and Madl, T and Stadlbauer, V},
title = {Probiotic Therapy of Gastrointestinal Symptoms During COVID-19 Infection: A Randomized, Double-Blind, Placebo-Controlled, Remote Study.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599756},
issn = {2072-6643},
support = {Project 3.23//Austrian Research Promotion Agency/ ; KLI 741//FWF Austrian Science Fund/ ; P28854//FWF Austrian Science Fund/ ; I3792//FWF Austrian Science Fund/ ; DOC-130//FWF Austrian Science Fund/ ; DK-MCD//FWF Austrian Science Fund/ ; W1226//FWF Austrian Science Fund/ ; 864690//Austrian Research Promotion Agency/ ; 870454//Austrian Research Promotion Agency/ ; //Integrative Metabolism Research Center Graz/ ; //Austrian Infrastructure Program 2016/2017/ ; //Styrian Government (Zukunftsfonds, doc.fund program)/ ; //City of Graz/ ; Flagship project//BioTechMed-Graz/ ; },
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Male ; *COVID-19/therapy ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Double-Blind Method ; *Feces/microbiology ; Adult ; *SARS-CoV-2 ; *Quality of Life ; Gastrointestinal Diseases/therapy/microbiology ; Aged ; Quarantine ; Telemedicine ; },
abstract = {BACKGROUND: The novel coronavirus (SARS-CoV-2) led to gastrointestinal manifestations in up to 50% of cases, with diarrhea being common, and probiotics have been suggested as a potential treatment.

AIM: This study aimed to assess changes in the microbiome and the effects of a multispecies probiotic in patients with COVID-19 in home quarantine through a fully remote telemedical approach.

METHODS: Thirty patients were randomized to receive either the Ecologic AAD probiotic (Winclove Probiotics, Amsterdam, The Netherlands), on the market as OMNi-BiOTiC 10 (Allergosan, Austria), or a placebo for 30 days in a 2:1 ratio. Respiratory and gastrointestinal symptoms were monitored in 2-10-day intervals via online surveys, and five stool samples were collected during the 30-day study period for microbiome and metabolomics analyses. Twenty-four healthy volunteers served as controls.

RESULTS: Of the 30 patients, 26 completed this study (10 placebo, 16 probiotic). Patients reported respiratory symptoms and a diminished gastrointestinal quality of life, both of which improved significantly during the study period, irrespective of the intervention. Compared to controls, infected patients showed significant alterations in the fecal microbiome (p = 0.002), including an increase in Bacteroidetes and decreases in Christensenellaceae, Ruminococcaceae, and Gammaproteobacteria, along with metabolomic changes. Probiotic treatment significantly modulated the patients' microbiome beta diversity (p = 0.001) and introduced the Enterococcus faecium W54 strain. Symptoms, COVID-19-related taxa, and the fecal metabolome were not affected by the intervention.

CONCLUSIONS: Patients with mild COVID-19 disease in home quarantine exhibited respiratory symptoms, a reduced gastrointestinal quality of life, and changes in the fecal microbiome and metabolome.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Male
*COVID-19/therapy
Female
*Gastrointestinal Microbiome
Middle Aged
Double-Blind Method
*Feces/microbiology
Adult
*SARS-CoV-2
*Quality of Life
Gastrointestinal Diseases/therapy/microbiology
Aged
Quarantine
Telemedicine

@article {pmid39599747,
year = {2024},
author = {Kajdas, AA and Żebrowska, A and Zalewska-Janowska, A and Czerwonogrodzka-Senczyna, A},
title = {The Role of Nutrition in the Pathogenesis and Treatment of Autoimmune Bullous Diseases-A Narrative Review.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599747},
issn = {2072-6643},
mesh = {Humans ; *Autoimmune Diseases/diet therapy ; *Skin Diseases, Vesiculobullous/diet therapy/therapy/drug therapy ; Diet ; Nutritional Status ; Dietary Supplements ; Pemphigus/therapy/diet therapy/drug therapy ; Female ; },
abstract = {Autoimmune bullous diseases (AIBDs) are a group of conditions marked by the formation of blisters and erosions on the skin and mucous membranes. It occurs in all age groups, slightly more often affecting women. Several factors may be linked to the development of AIBDs, with nutrition being one of them. The literature mentions various food products and food ingredients acting as disease modifiers. Given the complex relationship between bullous diseases and nutrition, the current literature on AIBDs has been reviewed, with an emphasis on the influence of dietary modifications, various diets, and the nutritional consequences of these conditions. This review summarizes the role of nutrition in the pathogenesis and treatment of the following AIBDs: (i) pemphigus, (ii) bullous pemphigoid and mucous membrane pemphigoid, (iii) dermatitis herpetiformis, and (iv) epidermolysis bullosa acquisita. Several nutrients and dietary factors have been studied for their potential roles in triggering or exacerbating AIBDs. The key nutrients and their potential impacts include thiols and bulb vegetables (Allium), phenols, tannic acid, tannins, phycocyanin, isothiocyanates, all trans-retinoic acids, cinnamic acid, and walnut antigens. Many patients with ABIDs may require supplementation, particularly of vitamin D and B3, calcium, potassium, zinc, selenium, and cobalt. In addition, various diets play an important role. A soft diet is recommended for individuals with issues in the oral cavity and/or esophagus, particularly for those who experience difficulties with biting or swallowing. This approach is commonly used in managing pemphigus. A high-protein, high-calcium diet, DASH (Dietary Approaches to Stop Hypertension), and the Mediterranean diet are utilized during long-term glucocorticoid therapy. However, in dermatitis herpetiformis it is advisable to follow a gluten-free diet and eliminate iodine from the diet. When it comes to herbal supplements, Algae (Spirulina platensis), Echinacea, and St. John's wort (Hyperitum perforatum) enhance the ABIDs, while Cassia fistula may be recommended in the treatment of erosions in pemphigus vulgaris. Fast foods enhance the development of ABIDs. However, the pathomechanism is not yet fully understood. Future researchers should more precisely define the relationships between nutrients and nutrition and blistering diseases by also looking at, i.e., genetic predispositions, microbiome differences, or exposure to stress.},
}

Humans
*Autoimmune Diseases/diet therapy
*Skin Diseases, Vesiculobullous/diet therapy/therapy/drug therapy
Diet
Nutritional Status
Dietary Supplements
Pemphigus/therapy/diet therapy/drug therapy
Female

@article {pmid39599742,
year = {2024},
author = {Al-Habsi, N and Al-Khalili, M and Haque, SA and Elias, M and Olqi, NA and Al Uraimi, T},
title = {Health Benefits of Prebiotics, Probiotics, Synbiotics, and Postbiotics.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599742},
issn = {2072-6643},
support = {(SR/AGR/Food/23/01)//His Majesty Trust Funds/ ; },
mesh = {Humans ; *Prebiotics/administration & dosage ; *Probiotics/administration & dosage ; *Synbiotics/administration & dosage ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Functional Food ; },
abstract = {The trillions of microbes that constitute the human gut microbiome play a crucial role in digestive health, immune response regulation, and psychological wellness. Maintaining gut microbiota is essential as metabolic diseases are associated with it. Functional food ingredients potentially improving gut health include prebiotics, probiotics, synbiotics, and postbiotics (PPSPs). While probiotics are living bacteria that provide health advantages when ingested sufficiently, prebiotics are non-digestible carbohydrates that support good gut bacteria. Synbiotics work together to improve immunity and intestinal health by combining probiotics and prebiotics. Postbiotics have also demonstrated numerous health advantages, such as bioactive molecules created during probiotic fermentation. According to a recent study, PPSPs can regulate the synthesis of metabolites, improve the integrity of the intestinal barrier, and change the gut microbiota composition to control metabolic illnesses. Additionally, the use of fecal microbiota transplantation (FMT) highlights the potential for restoring gut health through microbiota modulation, reinforcing the benefits of PPSPs in enhancing overall well-being. Research has shown that PPSPs provide several health benefits, such as improved immunological function, alleviation of symptoms associated with irritable bowel disease (IBD), decreased severity of allergies, and antibacterial and anti-inflammatory effects. Despite encouraging results, many unanswered questions remain about the scope of PPSPs' health advantages. Extensive research is required to fully realize the potential of these functional food components in enhancing human health and well-being. Effective therapeutic and prophylactic measures require further investigation into the roles of PPSPs, specifically their immune-system-modulating, cholesterol-lowering, antioxidant, and anti-inflammatory characteristics.},
}

Humans
*Prebiotics/administration & dosage
*Probiotics/administration & dosage
*Synbiotics/administration & dosage
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation
Functional Food

@article {pmid39599737,
year = {2024},
author = {Naghibi, M and Pont-Beltran, A and Lamelas, A and Llobregat, L and Martinez-Blanch, JF and Rojas, A and Álvarez, B and López Plaza, B and Arcos Castellanos, L and Chenoll, E and Vijayakumar, V and Day, R},
title = {Effect of Postbiotic Bifidobacterium longum CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599737},
issn = {2072-6643},
support = {TOLERA IDI-20170876//Spanish Ministry of Economy and Competitiveness, under the CDTI Project TOLERA IDI-20170876/ ; NA//Archer Daniels Midland (United States)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Double-Blind Method ; Pilot Projects ; Male ; Adult ; Female ; *Bifidobacterium longum ; *Probiotics/administration & dosage ; *Feces/microbiology ; Middle Aged ; Quality of Life ; Irritable Bowel Syndrome/microbiology/blood/therapy ; Young Adult ; Leukocyte L1 Antigen Complex/analysis/blood ; },
abstract = {OBJECTIVES: A randomised, double-blind, placebo-controlled pilot trial was conducted to assess the effect of heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) in healthy adults with mild to moderate digestive symptoms. A total of 60 participants were recruited and received either HT-ES1 or an identical placebo for 8 weeks with a further follow-up at week 10.

METHODS: This study monitored changes in the total Gastrointestinal Symptom Rating Scale for IBS score (GSRS-IBS), Irritable Bowel Syndrome Symptom Severity Scale (IBS-SSS), IBS Quality of Life index (IBS-QoL), gut microbiome using 16S rRNA sequencing, and the Visceral Sensitivity Index, as well as a range of biochemical markers, anthropometric parameters, and adverse events.

RESULTS: While minimal changes were observed in gastrointestinal (GI) symptoms, the HT-ES1 group showed a significant decrease in total and non-HDL cholesterol compared to the placebo. The intervention group also exhibited a significant increase in the abundance of the genera Faecalibacterium and Anaerobutyricum, both of which were positively correlated with butyrate concentrations. Faecal calprotectin significantly increased over time in the placebo group but remained stable in the HT-ES1 group.

CONCLUSIONS: Overall, these findings suggest that HT-ES1 may promote gut health by increasing butyrate-producing bacteria in the gut, maintaining normal levels of faecal calprotectin and reducing serum cholesterol.},
}

Humans
*Gastrointestinal Microbiome
Double-Blind Method
Pilot Projects
Male
Adult
Female
*Bifidobacterium longum
*Probiotics/administration & dosage
*Feces/microbiology
Middle Aged
Quality of Life
Irritable Bowel Syndrome/microbiology/blood/therapy
Young Adult
Leukocyte L1 Antigen Complex/analysis/blood

@article {pmid39599727,
year = {2024},
author = {Roth, MS and d'Aujourd'hui, M and Künstner, A and Hirose, M and Olbrich, M and Ibrahim, S and Hartmann, K and Roduit, C and Busch, H and Bellutti Enders, F},
title = {Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599727},
issn = {2072-6643},
mesh = {Humans ; *Immunoglobulin E/blood ; *Food Hypersensitivity/microbiology/immunology ; Female ; Male ; *Skin/microbiology/immunology ; *Gastrointestinal Microbiome ; Infant ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Microbiota ; Feces/microbiology ; Child, Preschool ; Dysbiosis/microbiology ; Bacteria/classification/immunology/genetics/isolation & purification ; },
abstract = {BACKGROUND/OBJECTIVES: The prevalence of food allergy (FA) in children is increasing. Dysbiosis of the microbiome has been linked to FA but needs to be better understood. We aimed to characterize the gut and skin microbiome of young food-allergic children over time and within different types of immunoglobulin E (IgE)-mediated FA.

METHODS: We studied 23 patients, as a pilot study of an ongoing prospective multicenter cohort study including children < 2y with newly diagnosed IgE-mediated FA. Samples (feces/skin swabs) were collected at enrollment and at 1-year follow-up and sequenced for the bacterial 16S rRNA gene (hypervariable v1-v2 region).

RESULTS: Gut and skin bacterial diversity was significantly higher in patients compared with controls and increased over time (beta test, Shannon diversity, p < 0.01). Within different types of IgE-mediated FA, bacterial diversity was similar. Community composition differed significantly over time and within IgE-mediated FA types (PERMANOVA: p < 0.01). Several significantly different genus abundances were revealed. We observed a positive correlation between high total IgE and a high abundance of the genus Collinsella in patients with a higher number of allergies/sensitizations (≥3), and patients with tree nut and/or peanut allergy.

CONCLUSIONS: This study revealed an increased bacterial diversity in children with FA compared with non-atopic children. Importantly, the gut and skin microbiome differed in their composition over time and within different types of IgE-mediated FA. These findings contribute to the understanding of microbiome changes in children with FA and indicate the potential of the genus Collinsella as a biomarker for tree nut and/or peanut allergy and possibly for allergy persistence.},
}

Humans
*Immunoglobulin E/blood
*Food Hypersensitivity/microbiology/immunology
Female
Male
*Skin/microbiology/immunology
*Gastrointestinal Microbiome
Infant
Prospective Studies
RNA, Ribosomal, 16S/genetics
Pilot Projects
Microbiota
Feces/microbiology
Child, Preschool
Dysbiosis/microbiology
Bacteria/classification/immunology/genetics/isolation & purification

@article {pmid39599721,
year = {2024},
author = {Ng, CYJ and Zhong, L and Ng, HS and Goh, KS and Zhao, Y},
title = {Managing Type 2 Diabetes Mellitus via the Regulation of Gut Microbiota: A Chinese Medicine Perspective.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599721},
issn = {2072-6643},
mesh = {*Diabetes Mellitus, Type 2/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Humans ; *Medicine, Chinese Traditional/methods ; *Drugs, Chinese Herbal/therapeutic use ; Akkermansia ; Acupuncture Therapy/methods ; Bifidobacterium ; Animals ; },
abstract = {Type 2 Diabetes Mellitus (T2DM) is a metabolic disorder characterized by insulin resistance and inadequate insulin production. Given the increased frequency of T2DM and the health issues it can cause, there is an increasing need to develop alternative T2DM management strategies. One such approach is Chinese Medicine (CM), a complementary therapy widely used in T2DM treatment. Given the emphasis on gut microbiota in current research, studying CM in the treatment of T2DM via gut microbiota modulation could be beneficial. Scope and approach: The use of various CM methods for managing T2DM via gut microbiota modulation is highlighted in this review. Following an introduction of the gut microbiota and its role in T2DM pathogenesis, we will review the potential interactions between gut microbiota and T2DM. Thereafter, we will review various CM treatment modalities that modulate gut microbiota and provide perspectives for future research. Key findings and discussion: In T2DM, Akkermansia, Bifidobacterium, and Firmicutes are examples of gut microbiota commonly imbalanced. Studies have shown that CM therapies can modulate gut microbiota, leading to beneficial effects such as reduced inflammation, improved metabolism, and improved immunity. Among these treatment modalities, Chinese Herbal Medicine and acupuncture are the most well-studied, and several in vivo studies have demonstrated their potential in managing T2DM by modulating gut microbiota. However, the underlying biomolecular mechanisms of actions are not well elucidated, which is a key area for future research. Future studies could also investigate alternate CM therapies such as moxibustion and CM exercises and conduct large-scale clinical trials to validate their effectiveness in treatment.},
}

*Diabetes Mellitus, Type 2/microbiology/therapy
*Gastrointestinal Microbiome/physiology
Humans
*Medicine, Chinese Traditional/methods
*Drugs, Chinese Herbal/therapeutic use
Akkermansia
Acupuncture Therapy/methods
Bifidobacterium
Animals

@article {pmid39599719,
year = {2024},
author = {Senaprom, S and Namjud, N and Ondee, T and Bumrungpert, A and Pongpirul, K},
title = {Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599719},
issn = {2072-6643},
support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; //The 90th Anniversary of Chulalongkorn University, Ratchadaphisek Somphot Fund/ ; //The Second Century Fund (C2F) for PhD Scholarship, Chulalongkorn University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Male ; Thailand ; Female ; Young Adult ; *Healthy Volunteers ; *Feces/microbiology ; Middle Aged ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; Dietary Sugars ; Southeast Asian People ; },
abstract = {BACKGROUND: The relationship between consuming Thai desserts-predominantly composed of carbohydrates-and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers.

METHODS: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi's Custard Cake (192 g, low-GI group, n = 10), Saraburi's Curry Puff (98 g, medium-GI group, n = 10), and Lampang's Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing.

RESULTS: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group.

CONCLUSIONS: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary.},
}

Humans
*Gastrointestinal Microbiome
Adult
Male
Thailand
Female
Young Adult
*Healthy Volunteers
*Feces/microbiology
Middle Aged
Adolescent
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics
Dietary Sugars
Southeast Asian People

@article {pmid39599707,
year = {2024},
author = {Farella, I and D'Amato, G and Orellana-Manzano, A and Segura, Y and Vitale, R and Clodoveo, ML and Corbo, F and Faienza, MF},
title = {"OMICS" in Human Milk: Focus on Biological Effects on Bone Homeostasis.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599707},
issn = {2072-6643},
mesh = {Humans ; *Milk, Human/chemistry ; *Homeostasis ; *Bone and Bones/metabolism ; Gastrointestinal Microbiome/physiology ; Proteomics/methods ; Bone Development/drug effects ; Infant ; Insulin-Like Growth Factor I/metabolism ; Metabolomics/methods ; Oligosaccharides/pharmacology ; MicroRNAs/metabolism ; Bone Density/drug effects ; },
abstract = {Human milk (HM) is a complex biofluid rich in nutrients and bioactive compounds essential for infant health. Recent advances in omics technologies-such as proteomics, metabolomics, and transcriptomics-have shed light on the influence of HM on bone development and health. This review discusses the impact of various HM components, including proteins, lipids, carbohydrates, and hormones, on bone metabolism and skeletal growth. Proteins like casein and whey promote calcium absorption and osteoblast differentiation, supporting bone mineralization. Long-chain polyunsaturated fatty acids like docosahexaenoic acid (DHA) contribute to bone health by modulating inflammatory pathways and regulating osteoclast activity. Additionally, human milk oligosaccharides (HMOs) act as prebiotics, improving gut health and calcium bioavailability while influencing bone mineralization. Hormones present in HM, such as insulin-like growth factor 1 (IGF-1), leptin, and adiponectin, have been linked to infant growth, body composition, and bone density. Research has shown that higher IGF-1 levels in breast milk are associated with increased weight gain, while leptin and adiponectin influence fat mass and bone metabolism. Emerging studies have also highlighted the role of microRNAs (miRNAs) in regulating key processes like adipogenesis and bone homeostasis. Furthermore, microbiome-focused techniques reveal HM's role in establishing a balanced infant gut microbiota, indirectly influencing bone development by enhancing nutrient absorption. Although current findings are promising, comprehensive longitudinal studies integrating omics approaches are needed to fully understand the intricate relationships among maternal diet, HM composition, and infant bone health. Bridging these gaps could offer novel dietary strategies to optimize skeletal health during infancy, advancing early-life nutrition science.},
}

Humans
*Milk, Human/chemistry
*Homeostasis
*Bone and Bones/metabolism
Gastrointestinal Microbiome/physiology
Proteomics/methods
Bone Development/drug effects
Infant
Insulin-Like Growth Factor I/metabolism
Metabolomics/methods
Oligosaccharides/pharmacology
MicroRNAs/metabolism
Bone Density/drug effects

@article {pmid39599702,
year = {2024},
author = {Ostrowska, M and Nowosad, K and Mikoluc, B and Szczerba, H and Komon-Janczara, E},
title = {Changes in the Gut and Oral Microbiome in Children with Phenylketonuria in the Context of Dietary Restrictions-A Preliminary Study.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599702},
issn = {2072-6643},
support = {VKT/MN-7/TŻ/21//University of Life Sciences in Lublin/ ; 2022/06/X/NZ9/00519//National Science Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Phenylketonurias/diet therapy/microbiology ; Child ; Male ; Female ; *Mouth/microbiology ; *RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Bacteria/classification/isolation & purification/genetics ; Microbiota ; Diet ; Case-Control Studies ; Phylogeny ; },
abstract = {BACKGROUND: Phenylketonuria (PKU) is a metabolic disorder that necessitates dietary restrictions, potentially impacting the composition of gut and oral microbiota. This study aimed to compare the microbiota composition between children with PKU and healthy controls.

METHODS: Using 16S rRNA gene sequencing, we analysed microbial communities at six phylogenetic levels.

RESULTS: Our findings revealed significant differences in the gut microbiota: Euryarchaeota was more abundant in controls (p = 0.01), while Bacilli and Lactobacillales were higher in PKU children (p = 0.019). Methanobacteriales were significantly elevated in controls (p = 0.01). At the genus and species levels, PKU children had higher Streptococcus and Eubacterium dolichum (p = 0.019, p = 0.015), whereas controls had more Barnesiella, Coprococcus, and Faecalibacterium prausnitzii (p = 0.014, p = 0.019, p = 0.014). In the oral microbiota, control children exhibited significantly higher Bacteroidetes (p = 0.032), while PKU children had increased Bacilli and Betaproteobacteria (p = 0.0079, p = 0.016). Streptococcus and Neisseria were more prevalent in PKU (p = 0.0079, p = 0.016).

CONCLUSIONS: These results suggest that PKU and its dietary management significantly alter the gut and oral microbiota composition. Understanding these microbial shifts could have implications for managing PKU and improving patient outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Phenylketonurias/diet therapy/microbiology
Child
Male
Female
*Mouth/microbiology
*RNA, Ribosomal, 16S/genetics
Child, Preschool
Bacteria/classification/isolation & purification/genetics
Microbiota
Diet
Case-Control Studies
Phylogeny

@article {pmid39599673,
year = {2024},
author = {Lorefice, L and Zoledziewska, M},
title = {Propionic Acid Impact on Multiple Sclerosis: Evidence and Challenges.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599673},
issn = {2072-6643},
mesh = {*Multiple Sclerosis/drug therapy ; Humans ; *Propionates/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Animals ; Dietary Supplements ; },
abstract = {Accumulating evidence suggests that multiple sclerosis (MS) is an environmentally influenced disorder with contributions from life-time exposure to factors including Epstein-Barr virus infection or shifts in microbiome, diet and lifestyle. One suggested factor is a deficiency in propionic acid, a short-chain fatty acid produced by gut bacteria that may contribute to the disease pathology both in animal models and in human cases of MS. Propionate appears to exert beneficial effects on the immune, peripheral and central nervous systems of people with MS (pwMS), showing immunoregulatory, neuroprotective and neurogenerative effects. These functions are crucial, given that MS is characterized by immune-mediated damage of myelin in the central nervous system. Accordingly, propionate supplementation or a modulated increase in its levels through the microbiome and diet may help counteract the pro-inflammatory state in MS by directly regulating immune system and/or by decreasing permeability of gut barrier and blood-brain barrier. This could potentially improve outcomes when used with immune-modulating therapy. However, while its broad effects are promising, further large clinical trials are necessary to evaluate its efficacy and safety in pwMS and clarify its role as a complementary therapeutic strategy. This review provides a comprehensive analysis of the evidence, challenges and limitations concerning propionic acid supplementation in MS.},
}

*Multiple Sclerosis/drug therapy
Humans
*Propionates/therapeutic use
*Gastrointestinal Microbiome/drug effects
Animals
Dietary Supplements

@article {pmid39599626,
year = {2024},
author = {Horvath, A and Habisch, H and Prietl, B and Pfeifer, V and Balazs, I and Kovacs, G and Foris, V and John, N and Kleinschek, D and Feldbacher, N and Grønbæk, H and Møller, HJ and Žukauskaitė, K and Madl, T and Stadlbauer, V},
title = {Alteration of the Gut-Lung Axis After Severe COVID-19 Infection and Modulation Through Probiotics: A Randomized, Controlled Pilot Study.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599626},
issn = {2072-6643},
support = {Project 3.23//Austrian Research Promotion Agency/ ; KLI 741//FWF Austrian Science Fund/ ; P28854//FWF Austrian Science Fund/ ; I3792//FWF Austrian Science Fund/ ; DOC-130//FWF Austrian Science Fund/ ; DK-MCD//FWF Austrian Science Fund/ ; W1226//FWF Austrian Science Fund/ ; 864690//Austrian Research Promotion Agency/ ; 870454//Austrian Research Promotion Agency/ ; //Integrative Metabolism Research Center Graz/ ; //Austrian Infrastructure Program 2016/2017/ ; //Styrian Government (Zukunftsfonds, doc. fund program)/ ; //City of Graz/ ; Flagship project//BioTechMed-Graz/ ; },
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Pilot Projects ; *COVID-19/therapy ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Lung ; *SARS-CoV-2 ; Aged ; Metabolome ; Adult ; Feces/microbiology ; Biomarkers/blood ; Severity of Illness Index ; },
abstract = {BACKGROUND: The gut-lung axis could be a potential therapeutic target for improving post-acute COVID-19 symptoms, and probiotics have been proposed as possible modulators.

AIM: We conducted a pilot study to understand alterations in the gut-lung axis and to explore the effects of a probiotic in post-acute COVID-19 disease.

METHODS: We included patients after severe COVID-19 disease (sCOV, n = 21) in a randomized, placebo-controlled trial to test the effect of a probiotic (Pro-Vi 5, Institute Allergosan, Graz, Austria) in a six-month intervention and used patients after mild disease (mCOV, n = 10) as controls, to compare the intestinal microbiome, metabolome, and patient-reported outcomes and biomarkers along the gut-lung axis at baseline and throughout probiotic intervention.

RESULTS: Compared to mCOV patients, sCOV patients showed lower microbial richness, which was significantly improved by probiotic intervention. A reorganization of Ruminococcaceae and Lachnospiraceae taxa was observed in sCOV patients but remained unaffected by the intervention. Serum metabolome showed a dysregulation of lipoproteins in accordance with higher BMI and comorbidities in sCOV patients. HDL and LDL fractions/components were temporarily decreased in the probiotic group. Stool metabolome was altered at baseline in sCOV patients and an increase in L-DOPA after 3 months and butyrate after 6 months of intervention could be observed. Probiotics partially improved reduced quality of life and modulated altered immune responses in sCOV patients. Increased intestinal permeability at baseline remained unaffected.

CONCLUSION: The study provides evidence of long-term alterations of the gut-lung axis after severe COVID-19 infection and suggests that probiotics can modulate the biomarkers of the gut-lung axis.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Pilot Projects
*COVID-19/therapy
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Lung
*SARS-CoV-2
Aged
Metabolome
Adult
Feces/microbiology
Biomarkers/blood
Severity of Illness Index

@article {pmid39599625,
year = {2024},
author = {Inoue, R and Hosomi, K and Park, J and Sakaue, H and Yumioka, H and Kamitani, H and Kinugasa, Y and Harano, K and Syauki, AY and Doi, M and Kageyama, S and Yamamoto, K and Mizuguchi, K and Kunisawa, J and Irie, Y},
title = {Clinical Phenotypes Associated with the Gut Microbiome in Older Japanese People with Care Needs in a Nursing Home.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599625},
issn = {2072-6643},
support = {22ae0121035s0102, 22gm1010006h0004, 22ae0121042h0002, 22ae0121035s0102//Japan Agency for Medical Research and Development/ ; 20AC5004//Ministry of Health and Welfare of Japan and Public/Private R&D Investment Strategic Expan-sion Progra/ ; 21K11730//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Nursing Homes ; *Gastrointestinal Microbiome ; Male ; Female ; Aged, 80 and over ; Aged ; *Phenotype ; Japan ; *Frailty ; *Nutritional Status ; Frail Elderly ; Dementia/microbiology ; Homes for the Aged ; Geriatric Assessment/methods ; Asian People ; East Asian People ; },
abstract = {BACKGROUND: Frailty increases the risk of needing nursing care and significantly affects the life and functional prognosis of older individuals. Early detection and tailored interventions are crucial for maintaining and enhancing their life functions. Recognizing distinct clinical phenotypes is essential for devising appropriate interventions. This study aimed to explore diverse frailty phenotypes, focusing on poor nutrition in older Japanese individuals through observational research.

METHODS: Twenty-one nursing home residents underwent a comprehensive survey covering physical, blood, dietary, cardiac, cognitive, nutritional, nursing care, frailty, agitated behavior, and gut microbiome assessments (high-throughput 16S rRNA gene sequencing). Using clustering analysis with 239 survey items (excluding gut microbiome), participants were classified into subgroups based on clinical phenotypes, and group characteristics were compared through analysis.

RESULTS: Individuals with moderate or severe frailty and suspected dementia formed subgroups with distinct clinical phenotypes based on nutritional, defecation, and nursing care statuses. The gut microbiome significantly varied among these groups (p = 0.007), indicating its correlation with changes in clinical phenotype. Nutritional status differences suggested poor nutrition as a differentiating factor in the core clinical phenotype.

CONCLUSIONS: This study proposes that the gut microbiome differs based on the clinical phenotype of Japanese older individuals with frailty, and targeted interventions addressing the gut microbiome may contribute to preventing frailty in this population.},
}

Humans
*Nursing Homes
*Gastrointestinal Microbiome
Male
Female
Aged, 80 and over
Aged
*Phenotype
Japan
*Frailty
*Nutritional Status
Frail Elderly
Dementia/microbiology
Homes for the Aged
Geriatric Assessment/methods
Asian People
East Asian People

@article {pmid39599623,
year = {2024},
author = {Yang, J and Ou, W and Lin, G and Wang, Y and Chen, D and Zeng, Z and Chen, Z and Lu, X and Wu, A and Lin, C and Liang, Y},
title = {PAMK Ameliorates Non-Alcoholic Steatohepatitis and Associated Anxiety/Depression-like Behaviors Through Restoring Gut Microbiota and Metabolites in Mice.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599623},
issn = {2072-6643},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; Mice ; *Depression ; *Anxiety ; Male ; *Atractylodes/chemistry ; *Disease Models, Animal ; *Polysaccharides/pharmacology ; *Behavior, Animal/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Drugs, Chinese Herbal/pharmacology ; Diet, Western/adverse effects ; },
abstract = {OBJECTIVES: Long-term Western diet-induced non-alcoholic steatohepatitis (NASH) can lead to liver cirrhosis and NASH-associated hepatocellular carcinoma, which are end-stage liver diseases. Meanwhile, NASH is associated with mental burden and worsens as the disease progresses. Atractylodes Macrocephala Koidz (AMK) is one of the main ingredients of Shenling Baizhu San, and the effect of Polysaccharide from AMK ameliorates (PAMK), as an important medicinal ingredient of AMK, on NASH and associated anxiety/depression-like behaviors is still unclear.

METHODS: This study investigated the protective effect of PAMK on NASH and associated anxiety/depression-like behaviors through a Western diet-induced NASH mice model.

RESULTS: showed that PAMK decreased the concentrations of liver TC, TG, and serum AST and ALT, improving glucose tolerance, and reducing liver steatosis and fibrosis. Moreover, the expression of liver IL-6, IL-1β, TNF-α, IL-18 and MCP-1 could be reduced by PAMK significantly. Additionally, PAMK decreased anxiety/depression-like behaviors and expression of IL-6, IL-1β, TNF-α, and MCP-1 in the hippocampus. 16S rRNA gene sequencing revealed that PAMK diminished the Firmicutes/Bacteroidetes ratio and abundance of Faecalibaculum_rodentium, and increased the abundance of Muribaculaceae. This might be related to gene abundance of Pentose, the glucuronate interconversions pathway and carbohydrate enzymes (GH1, GH4). Serum metabolomics suggested that PC (18:5e/2:0), PC (16:2e/2:0), Lysopc 20:4, PC (16:0/2:0), and LPC 19:0 upregulated significantly after PAMK intervention, together with the enrichment of carbon metabolism and Citrate cycle pathways specially.

CONCLUSIONS: PAMK as a potential prebiotic ameliorated NASH and associated anxiety/depression-like behaviors in mice, probably by regulating Faecalibaculum_rodentium, carbohydrate enzymes and lipid metabolites.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Non-alcoholic Fatty Liver Disease/metabolism
Mice
*Depression
*Anxiety
Male
*Atractylodes/chemistry
*Disease Models, Animal
*Polysaccharides/pharmacology
*Behavior, Animal/drug effects
Mice, Inbred C57BL
Liver/metabolism/drug effects
Drugs, Chinese Herbal/pharmacology
Diet, Western/adverse effects

@article {pmid39599583,
year = {2024},
author = {De La Barrera, S and De La Barrera, B and Legault, MA and Gamache, I and Manousaki, D},
title = {Association Between Circulating Vitamin K Levels, Gut Microbiome, and Type 1 Diabetes: A Mendelian Randomization Study.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
pmid = {39599583},
issn = {2072-6643},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Diabetes Mellitus, Type 1/microbiology/blood/genetics ; *Gastrointestinal Microbiome ; *Vitamin K/blood ; *Genome-Wide Association Study ; Male ; Female ; Polymorphism, Single Nucleotide ; Risk Factors ; },
abstract = {BACKGROUND/OBJECTIVES: Nutritional deficiencies have been proposed as possible etiological causes for autoimmune diseases, among which type 1 diabetes (T1D). Vitamin K (VK) has potentially positive effects on type 2 diabetes, but its role on T1D in humans remains largely unknown. We aimed to examine the presence of a causal association between VK and T1D using a Mendelian randomization (MR) approach.

METHODS: Genetic variants from a genome-wide association study (GWAS) for VK (N = 2138 Europeans) were used as instruments in our two-sample MR study to investigate whether circulating VK levels are causally associated with the risk of T1D in a large European T1D GWAS cohort (18,942 cases/520,580 controls). Through a multivariable MR (MVMR), the effects of both VK and specific gut microbiota on T1D were investigated given that the gut microbiome synthesizes VK.

RESULTS: We found that changes in levels of circulating VK did not affect T1D risk in our univariate two-sample MR, but this study had limited power to detect small effects of VK (OR for T1D of less than 0.8). However, our MVMR indicated a suggestive association of VK with the risk of T1D adjusting for two different gut microbiome populations.

CONCLUSIONS: In conclusion, VK levels are unlikely to significantly affect the risk of T1D, but small effects cannot be excluded, and the role of gut microbiome in this association should be further investigated.},
}

Humans
*Mendelian Randomization Analysis
*Diabetes Mellitus, Type 1/microbiology/blood/genetics
*Gastrointestinal Microbiome
*Vitamin K/blood
*Genome-Wide Association Study
Male
Female
Polymorphism, Single Nucleotide
Risk Factors

@article {pmid39599558,
year = {2024},
author = {Druszczynska, M and Sadowska, B and Kulesza, J and Gąsienica-Gliwa, N and Kulesza, E and Fol, M},
title = {The Intriguing Connection Between the Gut and Lung Microbiomes.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39599558},
issn = {2076-0817},
abstract = {Recent advances in microbiome research have uncovered a dynamic and complex connection between the gut and lungs, known as the gut-lung axis. This bidirectional communication network plays a critical role in modulating immune responses and maintaining respiratory health. Mediated by immune interactions, metabolic byproducts, and microbial communities in both organs, this axis demonstrates how gut-derived signals, such as metabolites and immune modulators, can reach the lung tissue via systemic circulation, influencing respiratory function and disease susceptibility. To explore the implications of this connection, we conducted a systematic review of studies published between 2001 and 2024 (with as much as nearly 60% covering the period 2020-2024), using keywords such as "gut-lung axis", "microbiome", "respiratory disease", and "immune signaling". Studies were selected based on their relevance to gut-lung communication mechanisms, the impact of dysbiosis, and the role of the gut microbiota in respiratory diseases. This review provides a comprehensive overview of the gut-lung microbiome axis, emphasizing its importance in regulating inflammatory and immune responses linked to respiratory health. Understanding this intricate pathway opens new avenues for microbiota-targeted therapeutic strategies, which could offer promising interventions for respiratory diseases like asthma, chronic obstructive pulmonary disease, and even infections. The insights gained through this research underscore the potential of the gut-lung axis as a novel target for preventative and therapeutic approaches in respiratory medicine, with implications for enhancing both gut and lung health.},
}

@article {pmid39599549,
year = {2024},
author = {Du, C and Zhang, Y and Zhang, H and Zhang, H and Liu, J and Shen, N},
title = {Bibliometric Analysis of Research Trends and Prospective Directions of Lung Microbiome.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39599549},
issn = {2076-0817},
support = {2022YFC2303200//National Key Research and Development Program of China/ ; No. 010071//Beijing Key Clinical Specialty Funding/ ; No.82202415//National Natural Science Foundation of China/ ; },
abstract = {The lung microbiome has emerged as a pivotal area of research in human health. Despite the increasing number of publications, there is a lack of research that comprehensively and objectively presents the current status of lung microbiome-related studies. Thus, this study aims to address this gap by examining over two decades of publications through bibliometric analysis. The original bibliographic data of this study were obtained from the Web of Science Core Collection, focusing on publications from 2003 to 2023. The analysis included the data extraction and examination of authors, affiliations, countries, institutions, abstracts, keywords, references, publication dates, journals, citations, H-indexes, and journal impact factors. A total of 845 publications were identified, showing an increasing trend in both publications and citations over the years, particularly in the last decade. The analysis highlighted the most productive authors, institutions, and countries/regions, and identified potential partners for interested researchers. Co-citation analysis revealed that lung microbiome- and infectious/pulmonary disease-related studies are at the forefront of the field. The hotspots and frontiers of the lung microbiome field have progressed from basic composition to exploring specific mechanisms and the clinical value of diseases. In conclusion, this study provides a comprehensive overview of the current research status and trends in the field of the lung microbiome over the past two decades and highlights the areas that need more attention and research efforts. It offers valuable insights for researchers and institutions and identifies key hotspots and frontiers, which can serve as references for related researchers and future research.},
}

@article {pmid39599495,
year = {2024},
author = {Mousavi, A and Thaker, KN and Ackerman, JE and Diaz, N and Martin, R and Tipton, CD and Tallman, N and Henao, LM and Nassiri, N and Veale, J and Ackerman, AL and Scotland, KB},
title = {Exploring Condition-Specific Variability in the Ureteral Stent Microbiome.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39599495},
issn = {2076-0817},
support = {N/A//Urology Care Foundation Medical Student Fellowship Grant/ ; N/A//Viola Hyde Surgical Research Scholarship/ ; N/A//UCLA Innovation Award/ ; },
abstract = {(1) Background: Indwelling ureteral stents are commonly used urological devices to maintain ureteral patency, yet they have been associated with complications such as infections. Some studies have shown that bacteria adhere to and create an antimicrobial-resistant biofilm on stents. One factor that may impact biofilm formation is the original condition informing stent placement, such as kidney stones and renal allografts. Both kidney stones and renal allografts are independently associated with infection, yet the differential stent microbiomes of these populations remain poorly characterized. Our objective was to characterize these microbiomes in order to inform urological health practice and help prevent ureteral stent-associated infections. (2) Methods: Stents were collected from kidney stone and renal transplant recipients undergoing routine cystoscopic stent removal. Microbial DNA was extracted from stents and analyzed using 16S Next Generation Sequencing. Descriptive statistics, alpha diversity, and beta diversity methods were used for statistical analysis. (3) Results: The microbiome of ureteral stents in kidney stone and transplant patients is composed of unique species, each with different biofilm-forming abilities. (4) Conclusions: Our findings demonstrate that the microbiome of stents differs based on preceding condition. It is important to conduct future studies that explore this microbiome further to understand what type of stent-associated infection someone may develop based on their initial condition.},
}

@article {pmid39598705,
year = {2024},
author = {Gościniak, A and Lainé, E and Cielecka-Piontek, J},
title = {How Do Cyclodextrins and Dextrans Affect the Gut Microbiome? Review of Prebiotic Activity.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {22},
pages = {},
pmid = {39598705},
issn = {1420-3049},
support = {Preludium BIS (2020/39/O/NZ7/03441)//National Science Center/ ; },
mesh = {*Prebiotics ; *Gastrointestinal Microbiome/drug effects ; *Cyclodextrins/pharmacology/chemistry ; Humans ; Animals ; Fatty Acids, Volatile/metabolism ; Bacteria/drug effects/metabolism ; },
abstract = {The modulation of the gut microbiome through dietary components has garnered significant attention for its potential health benefits. Prebiotics, non-digestible food ingredients that promote the growth of beneficial gut bacteria, play a crucial role in maintaining gut health, enhancing immune function, and potentially preventing various metabolic and inflammatory disorders. This review explores the prebiotic activity of cyclodextrins and dextrans, focusing on their ability to influence gut microbiota composition and function. Both cyclodextrins and dextrans have demonstrated the capacity to promote the growth of beneficial bacterial populations, while also impacting short-chain fatty acid production, crucial for gut health.},
}

*Prebiotics
*Gastrointestinal Microbiome/drug effects
*Cyclodextrins/pharmacology/chemistry
Humans
Animals
Fatty Acids, Volatile/metabolism
Bacteria/drug effects/metabolism

@article {pmid39598283,
year = {2024},
author = {Mederle, AL and Dima, M and Stoicescu, ER and Căpăstraru, BF and Levai, CM and Hațegan, OA and Maghiari, AL},
title = {Impact of Gut Microbiome Interventions on Glucose and Lipid Metabolism in Metabolic Diseases: A Systematic Review and Meta-Analysis.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {39598283},
issn = {2075-1729},
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a key player in metabolic health, influencing glucose and lipid metabolism through various mechanisms. However, the efficacy of gut microbiota-targeted interventions, such as probiotics, prebiotics, fecal microbiota transplantation (FMT), and diet-based treatments, remains unclear for specific metabolic outcomes. In this study, the aim was to evaluate the impact of these interventions on the glucose and lipid parameters in individuals with metabolic diseases such as diabetes mellitus (DM), obesity, and metabolic syndrome.

METHODS: This systematic review and meta-analysis included 41 randomized controlled trials that investigated the effects of gut microbiota-targeted treatments on metabolic parameters such as fasting glucose, glycated hemoglobin (HbA1c), homeostatic model assessment for insulin resistance (HOMA-IR), total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides. A comprehensive search was conducted using databases like PubMed, Google Scholar, and Scopus, focusing on interventions targeting the gut microbiota. A meta-analysis was performed using random-effects models, with effect sizes calculated for each outcome. Risk of bias was assessed using the Cochrane Risk of Bias tool.

RESULTS: Gut microbiota-targeted interventions significantly reduced fasting glucose, HbA1c, HOMA-IR, total cholesterol, LDL-C, and triglycerides, with moderate heterogeneity observed across studies. The interventions also led to modest increases in HDL-C levels. Probiotic and synbiotic interventions showed the most consistent benefits in improving both glucose and lipid profiles, while FMT yielded mixed results. Short-term interventions showed rapid microbial shifts but less pronounced metabolic improvements, whereas longer-term interventions had more substantial metabolic benefits.

CONCLUSIONS: In this study, it is demonstrated that gut microbiota-targeted interventions can improve key metabolic outcomes, offering a potential therapeutic strategy for managing metabolic diseases. However, the effectiveness of these interventions varies depending on the type, duration, and population characteristics, highlighting the need for further long-term studies to assess the sustained effects of microbiota modulation on metabolic health.},
}

@article {pmid39598237,
year = {2024},
author = {Min, M and Tarmaster, A and Bodemer, A and Sivamani, RK},
title = {The Influence of a Plant-Based Diet on Skin Health: Inflammatory Skin Diseases, Skin Healing, and Plant-Based Sources of Micro- and Macro-Nutrients.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {39598237},
issn = {2075-1729},
abstract = {Dietary patterns have been shown to worsen or alleviate several dermatological diseases. A well-balanced, plant-based diet is known to have anti-inflammatory, probiotic, and antioxidant properties, along with weight loss-promoting effects. Moreover, a plant-based diet has a low glycemic load, improving metabolic disease. Due to these qualities, plant-based diets may have beneficial effects on inflammatory skin conditions. In this review, we aim to discuss the possible mechanisms by which a plant-based diet reduces disease severity in psoriasis, acne, hidradenitis suppurativa, and atopic dermatitis. We also aim to clarify how a plant-based diet may influence skin healing and identify sources of vitamins, nutrients, fatty acids, and protein in a well-balanced, plant-based diet. We performed a literature search on PubMed/MEDLINE databases with the following keywords: "plant-based" OR "vegan" OR "vegetarian" OR "meat" OR "diet" AND "psoriasis" OR "hidradenitis suppurativa" OR "acne" OR "atopic dermatitis" OR "skin healing" OR "dermatology". Our findings demonstrate that plant-based foods may improve inflammatory skin diseases by supporting the gut microbiome, exerting anti-inflammatory effects, providing barrier support, and improving glycemic control. With the proper education, there is an abundance of plant-based food sources or supplements that contain riboflavin, vitamin B12, vitamin A, omega-3 fatty acids, and protein, thereby ameliorating the risk of nutritional deficiencies. Thus, a plant-based diet may have therapeutic potential in dermatology. In spite of the evidence available, there is a paucity of clinical studies focusing specifically on plant-based diets and dermatologic conditions and further investigation is warranted.},
}

@article {pmid39598196,
year = {2024},
author = {Shalmon, G and Ibrahim, R and Israel-Elgali, I and Grad, M and Shlayem, R and Shapira, G and Shomron, N and Youngster, I and Scheinowitz, M},
title = {Gut Microbiota Composition Positively Correlates with Sports Performance in Competitive Non-Professional Female and Male Runners.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {39598196},
issn = {2075-1729},
abstract = {There is still a pressing need for further investigation to bridge the gap in understanding the differences in gut microbiota composition between female runners and their male counterparts. We aimed to determine the gut microbiota composition in competitive non-professional female and male runners and to correlate the gut bacteria to performance. Our study included 40 subjects, of which 22 were runners (13 males and 9 females) and 18 control subjects (9 males and 9 females, representing the general population who perform light physical activity with a weekly running volume of ≤5 km per week). Fecal specimens were collected and analyzed for taxonomic profiling to compare species' relative abundances between males and females based on the results of 16SrRNA analysis. Bacterial alpha and beta diversity were assessed to determine the differences in microbial composition between runners and controls, and between sexes. Each participant underwent a maximal oxygen consumption test and a time-to-exhaustion test at 85% of the measured VO2max. Blood lactate was collected every 5 min during the tests. Bacterial alpha diversity showed a significant difference (p = 0.04) between runners and controls. Taxonomic analysis of gut microbiota composition showed a lower Enterobacteriaceae abundance and a higher Methanosphaera abundance in runners compared with the control group. Ten different bacteria (Methanosphaera, Mitsuokella, Prevotellaceae, Megamonas, Rothia, Oscillospira, Bacteroides, Odoribacter, Blautia massiliensis, Butyricicoccus_pullicaecorum) were positively correlated with exercise (VO2max, lactate blood levels, time to exhaustion, and weekly training volume). We found no significant differences in the gut microbiota composition between male and female runners. Gut microbiota composition positively correlates with sports performance in competitive non-professional female and male runners, and female runners show similar gut microbiome diversity to male runners.},
}

@article {pmid39598083,
year = {2024},
author = {Neiroukh, D and Hajdarpasic, A and Ayhan, C and Sultan, S and Soliman, O},
title = {Gut Microbial Taxonomy and Its Role as a Biomarker in Aortic Diseases: A Systematic Review and Future Perspectives.},
journal = {Journal of clinical medicine},
volume = {13},
number = {22},
pages = {},
pmid = {39598083},
issn = {2077-0383},
abstract = {Background/Objectives: Evidence of the association between the gut microbiome and cardiovascular diseases has accumulated. An imbalance or dysbiosis of this system has been shown to play a role in the pathogenesis of cardiovascular events, including aortic diseases. We aimed to elucidate the findings of the gut microbial taxonomy associated with aortic diseases and their subtypes. Furthermore, we sought to investigate whether gut microbiome dysbiosis can be used as a biomarker for aortic disease detection and to identify which species can be disease-specific. Methods: A systematic search was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines for original research papers on gut microbiome composition in patients with aortic disease, using patients without aortic disease as the control (i.e., healthy controls). The databases PubMed, Scopus, Cochrane, and Web of Science were used by employing the medical subject headings (MeSH) terms "aortic diseases", "microbiome"," microbiota", and "taxa" before August 2024. We extracted the study characteristics, study population, and gut microbiome in aortic disease, including microbiota taxa diversity and abundance, regardless of taxa level. The National Institutes of Health (NIH) Quality Assessment Tool was used to assess study quality. Data were synthesized narratively to address the heterogeneity of the studies. Results: In this review, twelve studies that have identified gut microbial species and their potential impact on aortic disease pathogenesis were included. The studies showed the phyla dominance of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Euryarchaeota in aortic disease patients. We also included the taxa sequencing methods and those used to extract the microorganisms. Aortic diseases were categorized into Takayasu's arteritis, giant cell arteritis, aortic aneurysm, and aortic dissection. Aortic disease patients had a higher rate of dysbiosis when compared to the healthy control groups, with significantly different microbiome composition. Conclusions: Patients with aortic disease exhibit a distinct difference between their gut microbiota composition and that of the healthy controls, which suggests a potential biomarker role of gut dysbiosis. Further exploration of the microbiome and its metagenome interface can help identify its role in aortic disease pathogenesis in depth, generating future therapeutic options. However, a unified methodology is required to identify potential microbial biomarkers in cardiovascular and cardiometabolic diseases.},
}

@article {pmid39598069,
year = {2024},
author = {Marfil-Cantón, M and Prados-Carmona, A and Cebolla-Verdugo, M and Husein-ElAhmed, H and Campos, F and Ruiz-Villaverde, R},
title = {Anti-OX40 Biological Therapies in the Treatment of Atopic Dermatitis: A Comprehensive Review.},
journal = {Journal of clinical medicine},
volume = {13},
number = {22},
pages = {},
pmid = {39598069},
issn = {2077-0383},
abstract = {Introduction. Atopic dermatitis (AD) is the most prevalent inflammatory dermatological disorder, affecting a significant percentage of the global population. This chronic disease has a multifactorial and intricate pathogenesis, influenced by genetic predisposition, skin barrier dysfunction, immune dysregulation, neuroimmune mechanisms, and alterations in the skin microbiome, among other factors. Methods. The treatment of AD has faced significant clinical challenges due to the ineffectiveness of conventional therapies. However, recent advances in understanding its pathophysiology have led to the introduction of new therapeutic options. Recently, the OX40 receptor has been identified as a key factor in the development of AD. Recent studies have demonstrated that blocking the OX40 ligand with monoclonal antibodies significantly and sustainably improves the signs and symptoms of moderate to severe AD. Results. A comprehensive review of the available literature on anti-OX40 treatments in atopic dermatitis that evaluates their mechanism of action, their clinical efficacy, and the prospects of this promising therapeutic option for improving AD management is provided. Conclusions. Anti-OX40 and anti-OX40L blockers are a promising therapeutic alternative for the management of moderate-severe atopic dermatitis. Prospective analytical studies are needed to determine whether this new therapeutic target represents a qualitative advance in modifying the progression of the disease.},
}

@article {pmid39598018,
year = {2024},
author = {Marchlewicz, M and Sagan, P and Grabowska, M and Kiedrowicz, M and Kruk, J and Gill, K and Piasecka, M and Duchnik, E},
title = {The Role of Vitamin D3 Deficiency and Colonization of the Oral Mucosa by Candida Yeast-like Fungi in the Pathomechanism of Psoriasis.},
journal = {Journal of clinical medicine},
volume = {13},
number = {22},
pages = {},
pmid = {39598018},
issn = {2077-0383},
support = {WNoZ-324/S/2024//Pomeranian Medical University/ ; },
abstract = {Psoriasis is a chronic inflammatory skin disease with complex pathogenesis and variable severity. Performed studies have indicated the impact of vitamin D3 deficiency on the pathogenesis of psoriasis and its severity. However, there is no clear evidence of the influence of the mucosal microbiome on the onset and progression of psoriasis. This review aims to present the current evidence on the role of vitamin D3 and colonization of the oral mucosa by Candida yeast-like fungi in the pathogenesis of psoriasis. Candida albicans is a common yeast that can colonize the skin and mucosal surfaces, particularly in individuals with weakened immune systems or compromised skin barriers. In psoriasis, the skin's barrier function is disrupted, potentially making patients more susceptible to fungal infections such as Candida. Since patients with psoriasis are at increased risk of metabolic syndrome, they may experience the vicious circle effect in which chronic inflammation leads to obesity. Vitamin D3 deficiency is also associated with microbiological imbalance, which may promote excessive growth of Candida fungi. Under normal conditions, the intestinal and oral microflora support the immune system. Vitamin D3 deficiency, however, leads to disruption of this balance, which allows Candida to overgrow and develop infections.},
}

@article {pmid39597764,
year = {2024},
author = {Zobrist, Y and Doulberis, M and Biedermann, L and Leventhal, GE and Rogler, G},
title = {Anthocyanin-Rich Extract Mitigates the Contribution of the Pathobiont Genus Haemophilus in Mild-to-Moderate Ulcerative Colitis Patients.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597764},
issn = {2076-2607},
support = {33IC30_166844/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Anthocyanins (ACs) have been shown to elicit anti-inflammatory and antioxidant effects in animal models of ulcerative colitis (UC). Furthermore, we previously observed in a double-blind randomized trial in UC patients that biochemical disease activity tended to be lower in patients that were exposed to AC. Here, we report on the changes in the fecal microbiome composition in these patients upon AC exposure. UC patients received a 3 g daily dose of an AC-rich bilberry extract (ACRE) for eight weeks. We determined the microbiome composition in longitudinal stool samples from 24 patients and quantified the degree of change over time. We also correlated the relative abundances of individual microbial taxa at different timepoints to fecal concentrations of calprotectin, a proxy for inflammation. Microbiome composition did not change over time as a result of the intervention, in terms of both alpha and beta diversity. However, before the intervention, the abundance of Haemophilus parainfluenzae was positively correlated with fecal calprotectin concentrations, and this correlation persisted in placebo-treated subjects throughout the study. In contrast, the correlation between H. parainfluenzae and calprotectin vanished in ACRE-treated subjects, while the relative abundance of H. parainfluenzae did not change. Our results suggest that ACRE treatment mitigates the contribution of H. parainfluenzae to inflammation. Further research is warranted to better comprehend the role of microbial composition in response to medical therapy including AC-rich extract in UC patients.},
}

@article {pmid39597757,
year = {2024},
author = {Duffy, HR and Ashton, NN and Blair, A and Hooper, N and Stulce, P and Williams, DL},
title = {Regulatory Standard for Determining Preoperative Skin Preparation Efficacy Underreports True Dermal Bioburden in a Porcine Model.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597757},
issn = {2076-2607},
support = {2139322//National Science Foundation/ ; NA//L.S. Peery Foundation (Department of Orthopeadics, University of Utah)/ ; },
abstract = {Medical device companies and regulatory bodies rely on a nondestructive bacterial sampling technique specified by the American Society for Testing and Materials (ASTM E1173-15) to test preoperative skin preparations (PSPs). Despite the widespread use of PSPs, opportunistic skin-flora pathogens remain the most significant contributor to surgical site infections, suggesting that the ASTM testing standard may be underreporting true dermal bioburden. We hypothesized that ASTM E1173-15 may fail to capture deep skin-dwelling flora. To test this hypothesis, we applied ASTM E1173-15 and a full-thickness skin sampling technique, which we established previously through application to the backs of seven pigs (Yorkshire/Landrace hybrid) following a clinically used PSP (4% chlorhexidine gluconate). The results showed that samples quantified using the full-thickness skin method consistently cultured more bacteria than the ASTM standard, which principally targeted surface-dwelling bacteria. Following PSP, the ASTM standard yielded 1.05 ± 0.24 log10 CFU/cm[2], while the full-thickness tissue method resulted in 3.24 ± 0.24 log10 CFU/cm[2], more than a 2 log10 difference (p < 0.001). Immunofluorescence images corroborated the data, showing that Staphylococcus epidermidis was present in deep skin regions with or without PSP treatment. Outcomes suggested that a full-thickness sampling technique may better evaluate PSP technologies as it resolves bioburdens dwelling in deeper skin regions.},
}

@article {pmid39597740,
year = {2024},
author = {Taufer, CR and da Silva, J and Rampelotto, PH},
title = {In Silico Analysis of Probiotic Bacteria Changes Across COVID-19 Severity Stages.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597740},
issn = {2076-2607},
support = {88887.513461/2020-00//CAPES/ ; },
abstract = {The gut microbiota plays a crucial role in modulating the immune response during COVID-19, with several studies reporting significant alterations in specific bacterial genera, including Akkermansia, Bacteroides, Bifidobacterium, Faecalibacterium, Lactobacillus, Oscillospira, and Ruminococcus. These genera are symbionts of the gut microbiota and contribute to host health. However, comparing results across studies is challenging due to differences in analysis methods and reference databases. We screened 16S rRNA raw datasets available in public databases on COVID-19, focusing on the V3-V4 region of the bacterial genome. In total, seven studies were included. All samples underwent the same bioinformatics pipeline, evaluating the differential abundance of these seven bacterial genera at each level of severity. The reanalysis identified significant changes in differential abundance. Bifidobacterium emerged as a potential biomarker of disease severity and a therapeutic target. Bacteroides presented a complex pattern, possibly related to disease-associated inflammation or opportunistic pathogen growth. Lactobacillus showed significant changes in abundance across the COVID-19 stages. On the other hand, Akkermansia and Faecalibacterium did not show significant differences, while Oscillospira and Ruminococcus produced statistically significant results but with limited relevance to COVID-19 severity. Our findings reveal new insights into the differential abundance of key bacterial genera in COVID-19, particularly Bifidobacterium and Bacteroides.},
}

@article {pmid39597739,
year = {2024},
author = {Sun, X and Liu, Y and He, L and Kuang, Z and Dai, S and Hua, L and Jiang, Q and Wei, T and Ye, P and Zeng, H},
title = {Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597739},
issn = {2076-2607},
support = {2023NSFSC1262//the Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; CARS-21-21//National Chinese Medicinal Materials Technology System/ ; 2022ZZCX078//Sichuan Provincial Finance Independent Innovation Project/ ; },
abstract = {Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.},
}

@article {pmid39597729,
year = {2024},
author = {Alexandrescu, L and Suceveanu, AP and Stanigut, AM and Tofolean, DE and Axelerad, AD and Iordache, IE and Herlo, A and Nelson Twakor, A and Nicoara, AD and Tocia, C and Dumitru, A and Dumitru, E and Condur, LM and Aftenie, CF and Tofolean, IT},
title = {Intestinal Insights: The Gut Microbiome's Role in Atherosclerotic Disease: A Narrative Review.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597729},
issn = {2076-2607},
abstract = {Recent advances have highlighted the gut microbiota as a significant contributor to the development and progression of atherosclerosis, which is an inflammatory cardiovascular disease (CVD) characterized by plaque buildup within arterial walls. The gut microbiota, consisting of a diverse collection of microorganisms, impacts the host's metabolism, immune responses, and lipid processing, all of which contribute to atherosclerosis. This review explores the complex mechanisms through which gut dysbiosis promotes atherogenesis. We emphasize the potential of integrating microbiota modulation with traditional cardiovascular care, offering a holistic approach to managing atherosclerosis. Important pathways involve the translocation of inflammatory microbial components, modulation of lipid metabolism through metabolites such as trimethylamine-N-oxide (TMAO), and the production of short-chain fatty acids (SCFAs) that influence vascular health. Studies reveal distinct microbial profiles in atherosclerosis patients, with increased pathogenic bacteria (Megamonas, Veillonella, Streptococcus) and reduced anti-inflammatory genera (Bifidobacterium, Roseburia), highlighting the potential of these profiles as biomarkers and therapeutic targets. Probiotics are live microorganisms that have health benefits on the host. Prebiotics are non-digestible dietary fibers that stimulate the growth and activity of beneficial gut bacteria. Interventions targeting microbiota, such as probiotics, prebiotics, dietary modifications, and faecal microbiota transplantation (FMT), present effective approaches for restoring microbial equilibrium and justifying cardiovascular risk. Future research should focus on longitudinal, multi-omics studies to clarify causal links and refine therapeutic applications.},
}