@article {pmid38670070,
year = {2024},
author = {Wong, CC and Yu, J},
title = {Mapping the pancancer metastasis tumor microbiome.},
journal = {Cell},
volume = {187},
number = {9},
pages = {2126-2128},
doi = {10.1016/j.cell.2024.03.040},
pmid = {38670070},
issn = {1097-4172},
mesh = {Humans ; *Microbiota ; *Neoplasm Metastasis ; Neoplasms/pathology/microbiology ; },
abstract = {The landscape of the intratumoral microbiome in tumor metastases is largely unchartered. In this issue of Cell, Voest et al. profiled the tumor metastasis-associated microbiome in a pancancer cohort of 4,160 biopsies from 26 cancer types. This dataset offers a useful resource for understanding the role of the microbiome in metastatic cancers.},
}

Humans
*Microbiota
*Neoplasm Metastasis
Neoplasms/pathology/microbiology

@article {pmid38670037,
year = {2024},
author = {Wen, X and Xu, J and Wang, Y and Yang, X and Peng, G and Li, S and Ma, B and Zou, Y and Liao, X and Wang, Y and Worrich, A and Wu, Y},
title = {Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system.},
journal = {Microbiological research},
volume = {284},
number = {},
pages = {127734},
doi = {10.1016/j.micres.2024.127734},
pmid = {38670037},
issn = {1618-0623},
abstract = {The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10[-3] copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.},
}

@article {pmid38669694,
year = {2024},
author = {Ho, CC and Gilbert, MB and Urtecho, G and Lee, H and Drew, DA and Klempner, SJ and Cho, JS and Ryan, TJ and Rustgi, N and Lee, H and Lee, J and Caraballo, A and Magicheva-Gupta, MV and Rios, C and Shin, AE and Tseng, YY and Davis, JL and Chung, DC and Chan, AT and Wang, HH and Ryeom, S},
title = {Stool protein mass spectrometry identifies biomarkers for the early detection of diffuse-type gastric cancer.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1158/1940-6207.CAPR-23-0449},
pmid = {38669694},
issn = {1940-6215},
abstract = {There is a high unmet need for early detection approaches for diffuse gastric cancer (DGC). We examined whether the stool proteome of mouse models of GC or individuals with hereditary diffuse GC (HDGC) have utility as biomarkers for early detection. Proteomic mass spectrometry of stool from a genetically engineered mouse model driven by oncogenic KrasG12D and loss of p53 and Cdh1 in gastric parietal cells (known as TCON mice) identified differentially abundant proteins compared to littermate controls. Immunoblot assays validated a panel of proteins including actinin alpha 4 (ACTN4), N-acylsphingosine amidohydrolase 2 (ASAH2), dipeptidyl peptidase 4 (DPP4), and valosin-containing protein (VCP) as enriched in TCON stool compared to littermate control stool. Immunofluorescence analysis of these proteins in TCON stomach sections revealed increased protein expression as compared to littermate controls. Proteomic mass spectrometry of stool obtained from HDGC patients with CDH1 mutations identified increased expression of ASAH2, DPP4, VCP, lactotransferrin (LTF), and tropomyosin-2 (TPM2) relative to stool from healthy sex and age-matched donors. Chemical inhibition of ASAH2 using C6-urea ceramide was toxic to GC cell lines and patient derived-GC organoids. This toxicity was reversed by adding downstream products of the S1P synthesis pathway, suggesting a dependency on ASAH2 activity in GC. An exploratory analysis of the HDGC stool microbiome identified features which correlated with patient tumors. Here we provide evidence supporting the potential of analyzing stool biomarkers for the early detection of DGC.},
}

@article {pmid38669258,
year = {2024},
author = {Zeber-Lubecka, N and Kulecka, M and Dabrowska, M and Baginska-Drabiuk, K and Glowienka-Stodolak, M and Nowakowski, A and Slabuszewska-Jozwiak, A and Bednorz, B and Jędrzejewska, I and Piasecka, M and Pawelec, J and Wojciechowska-Lampka, E and Ostrowski, J},
title = {Cervical microbiota dysbiosis associated with high-risk Human Papillomavirus infection.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0302270},
doi = {10.1371/journal.pone.0302270},
pmid = {38669258},
issn = {1932-6203},
mesh = {Humans ; Female ; *Papillomavirus Infections/virology/microbiology/complications ; *Dysbiosis/microbiology/virology ; *Microbiota ; Adult ; *Cervix Uteri/microbiology/virology ; *Lactobacillus/isolation & purification/genetics ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Uterine Cervical Neoplasms/microbiology/virology ; Human papillomavirus 16/genetics/isolation & purification ; Case-Control Studies ; Human papillomavirus 18/genetics/isolation & purification ; Uterine Cervical Dysplasia/microbiology/virology ; },
abstract = {High-risk Human Papillomavirus (HR-HPV) genotypes, specifically HPV16 and HPV18, pose a significant risk for the development of cervical intraepithelial neoplasia and cervical cancer. In the multifaceted cervical microenvironment, consisting of immune cells and diverse microbiota, Lactobacillus emerges as a pivotal factor, wielding significant influence in both stabilizing and disrupting the microbiome of the reproductive tract. To analyze the distinction between the cervical microbiota and Lactobacillus-dominant/non-dominant status of HR-HPV and non-infected healthy women, sixty-nine cervical swab samples were analyzed, included 44 with HR-HPV infection and healthy controls. All samples were recruited from Human Papillomavirus-based cervical cancer screening program and subjected to 16s rRNA sequencing analysis. Alpha and beta diversity analyses reveal no significant differences in the cervical microbiota of HR-HPV-infected women, including 16 and 18 HPV genotypes, and those with squamous intraepithelial lesion (SIL), compared to a control group. In this study we identified significantly lower abundance of Lactobacillus mucosae in women with HR-HPV infection compared to the control group. Furthermore, changes in bacterial diversity were noted in Lactobacillus non-dominant (LND) samples compared to Lactobacillus-dominant (LD) in both HR-HPV-infected and control groups. LND samples in HR-HPV-infected women exhibited a cervical dysbiotic state, characterized by Lactobacillus deficiency. In turn, the LD HR-HPV group showed an overrepresentation of Lactobacillus helveticus. In summary, our study highlighted the distinctive roles of L. mucosae and L. helveticus in HR-HPV infections, signaling a need for further research to demonstrate potential clinical implications of cervical microbiota dysbiosis.},
}

Humans
Female
*Papillomavirus Infections/virology/microbiology/complications
*Dysbiosis/microbiology/virology
*Microbiota
Adult
*Cervix Uteri/microbiology/virology
*Lactobacillus/isolation & purification/genetics
*RNA, Ribosomal, 16S/genetics
Middle Aged
Uterine Cervical Neoplasms/microbiology/virology
Human papillomavirus 16/genetics/isolation & purification
Case-Control Studies
Human papillomavirus 18/genetics/isolation & purification
Uterine Cervical Dysplasia/microbiology/virology

@article {pmid38669216,
year = {2024},
author = {Wagner, MR},
title = {Identifying causes and consequences of rhizosphere microbiome heritability.},
journal = {PLoS biology},
volume = {22},
number = {4},
pages = {e3002604},
pmid = {38669216},
issn = {1545-7885},
mesh = {*Rhizosphere ; *Microbiota/genetics ; *Hordeum/microbiology/genetics ; Soil Microbiology ; Genotype ; Bacteria/genetics/classification ; Plant Roots/microbiology/genetics ; },
abstract = {Host genotype affects microbiome composition in many plants, but the mechanisms and implications of this phenomenon are understudied. New work in PLOS Biology illustrates how host genotype leads to differential gene expression and fitness in bacteria of the barley rhizosphere.},
}

*Rhizosphere
*Microbiota/genetics
*Hordeum/microbiology/genetics
Soil Microbiology
Genotype
Bacteria/genetics/classification
Plant Roots/microbiology/genetics

@article {pmid38669195,
year = {2024},
author = {Sengupta, S and Pabbaraja, S and Mehta, G},
title = {Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery.},
journal = {Organic & biomolecular chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4ob00236a},
pmid = {38669195},
issn = {1477-0539},
abstract = {Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.},
}

@article {pmid38668956,
year = {2024},
author = {Puga, MI and Poza-Carrión, C and Martinez-Hevia, I and Perez-Liens, L and Paz-Ares, J},
title = {Recent advances in research on phosphate starvation signaling in plants.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {38668956},
issn = {1618-0860},
abstract = {Phosphorus is indispensable for plant growth and development, with its status crucial for determining crop productivity. Plants have evolved various biochemical, morphological, and developmental responses to thrive under conditions of low P availability, as inorganic phosphate (Pi), the primary form of P uptake, is often insoluble in soils. Over the past 25 years, extensive research has focused on understanding these responses, collectively forming the Pi starvation response system. This effort has not only expanded our knowledge of strategies to cope with Pi starvation (PS) but also confirmed their adaptive significance. Moreover, it has identified and characterized numerous components of the intricate regulatory network governing P homeostasis. This review emphasizes recent advances in PS signaling, particularly highlighting the physiological importance of local PS signaling in inhibiting primary root growth and uncovering the role of TORC1 signaling in this process. Additionally, advancements in understanding shoot-root Pi allocation and a novel technique for studying Pi distribution in plants are discussed. Furthermore, emerging data on the regulation of plant-microorganism interactions by the PS regulatory system, crosstalk between the signaling pathways of phosphate starvation, phytohormones and immunity, and recent studies on natural variation in Pi homeostasis are addressed.},
}

@article {pmid38668878,
year = {2024},
author = {Farfour, E and Vasse, M and Vallée, A},
title = {Oligella spp.: A systematic review on an uncommon urinary pathogen.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38668878},
issn = {1435-4373},
abstract = {BACKGROUND: Oligella is an uncommon Gram-negative coccobacillus that was first thought to belong to the urogenital tract. The genus Oligella comprises two species that were recovered from various samples worldwide.

METHODS: We perform a systematic review focusing on Oligella microbiological characteristics, habitat, role in Human microbiome and infection, and antimicrobial susceptibility.

RESULTS: In humans, Oligella is mainly found as part of the microbiome of individuals with predisposing conditions. Oligella were also associated with invasive infections in patients with underlying diseases. Nevertheless, their prevalence remains to determine. Oligella culture requires up to 48 h on agar media in vitro, while urinary samples are usually incubated for 24 h. Consequently, microbiologists should be prompt to prolong the incubation of agar media when the direct examination showed Gram-negative coccobacilli. Oligella is accurately identified using MALDI-TOF mass spectrometry, but biochemical methods often provided inconsistent results. Specific guidelines for antimicrobial susceptibility testing of Oligella lack but the incubation could require up to 48 h of incubation. In contrast to O. urethralis, which is susceptible to third-generation cephalosporin, O. ureolytica is likely resistant to numerous antimicrobials. Genectic determinants of resistance were identified for beta-lactams and aminoglycosides.

CONCLUSION: Oligella is an uncommon pathogen that can be underrecognized. Microbiologists should be prompt to prolong the incubation of agar media plated with urines when the direct examination showed Gram-negative coccobacilli. Carbapenems should probably be given for the empirical treatment.},
}

@article {pmid38668783,
year = {2024},
author = {Shamjana, U and Vasu, DA and Hembrom, PS and Nayak, K and Grace, T},
title = {The role of insect gut microbiota in host fitness, detoxification and nutrient supplementation.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {71},
pmid = {38668783},
issn = {1572-9699},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Insecta/microbiology ; *Symbiosis ; Nutrients/metabolism ; Metagenomics ; Host Microbial Interactions ; Inactivation, Metabolic ; Bacteria/classification/genetics/metabolism ; },
abstract = {Insects are incredibly diverse, ubiquitous and have successfully flourished out of the dynamic and often unpredictable nature of evolutionary processes. The resident microbiome has accompanied the physical and biological adaptations that enable their continued survival and proliferation in a wide array of environments. The host insect and microbiome's bidirectional relationship exhibits their capability to influence each other's physiology, behavior and characteristics. Insects are reported to rely directly on the microbial community to break down complex food, adapt to nutrient-deficit environments, protect themselves from natural adversaries and control the expression of social behavior. High-throughput metagenomic approaches have enhanced the potential for determining the abundance, composition, diversity and functional activities of microbial fauna associated with insect hosts, enabling in-depth investigation into insect-microbe interactions. We undertook a review of some of the major advances in the field of metagenomics, focusing on insect-microbe interaction, diversity and composition of resident microbiota, the functional capability of endosymbionts and discussions on different symbiotic relationships. The review aims to be a valuable resource on insect gut symbiotic microbiota by providing a comprehensive understanding of how insect gut symbionts systematically perform a range of functions, viz., insecticide degradation, nutritional support and immune fitness. A thorough understanding of manipulating specific gut symbionts may aid in developing advanced insect-associated research to attain health and design strategies for pest management.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Insecta/microbiology
*Symbiosis
Nutrients/metabolism
Metagenomics
Host Microbial Interactions
Inactivation, Metabolic
Bacteria/classification/genetics/metabolism

@article {pmid38668709,
year = {2024},
author = {Mehdipour, A and Fateh, R and Fuladvand, F and Aghaali, M and Keykha, E and Hadilou, M},
title = {Association between sleep pattern, salivary cariogenic bacteria and fungi populations, pH and buffering capacity in children: A comparative study.},
journal = {Dental and medical problems},
volume = {61},
number = {2},
pages = {217-224},
doi = {10.17219/dmp/167411},
pmid = {38668709},
issn = {2300-9020},
mesh = {Humans ; Child ; *Saliva/microbiology/chemistry ; Hydrogen-Ion Concentration ; Cross-Sectional Studies ; Female ; Male ; *Dental Caries/microbiology ; Streptococcus mutans/isolation & purification ; Candida albicans/isolation & purification ; Buffers ; Lactobacillus/isolation & purification ; Sleep/physiology ; },
abstract = {BACKGROUND: Sleep quality has a significant impact on a child's health and is linked to oral and systemic diseases. It affects the circadian rhythm, which plays a crucial role in regulating the balance of the endocrine and hormonal systems. Current research has focused on exploring its role in the development of caries, which is influenced by inherent oral factors such as the composition of the oral microbiome and pH levels.

OBJECTIVES: This study aimed to investigate the relationship between bacterial population, pH, and buffering properties of saliva and sleep patterns in 8- to 12-year-old children.

MATERIAL AND METHODS: This cross-sectional study was conducted on 85 elementary school children aged 8-12 years. After obtaining written consent, non-stimulating saliva samples were collected using the spitting method. The participants' sleep pattern information was obtained with the use of the Persian version of the Children's Sleep Habits Questionnaire (CSHQ). Based on the results of the CSHQ, the participants were divided into 2 groups: those with appropriate sleep patterns; and those with inappropriate sleep patterns. The study compared the bacterial population of Streptococcus mutans, Lactobacillus spp. and Candida albicans, as well as the buffering capacity and pH of the saliva between the 2 groups. The statistical analysis employed the χ2 test, the independent samples t-test and Spearman's correlation.

RESULTS: The group with inappropriate sleep patterns had significantly lower pH and buffering capacity (p < 0.001) and significantly higher colony counts of Lactobacillus and S. mutans (p < 0.001 and p = 0.012, respectively). There was no association between C. albicans and sleep patterns (p = 0.121).

CONCLUSIONS: Inappropriate sleep patterns increase the population of caries-causing bacteria and reduce salivary pH and buffering capacity. This can be a significant factor in the development of dental caries in children aged 8-12 years.},
}

Humans
Child
*Saliva/microbiology/chemistry
Hydrogen-Ion Concentration
Cross-Sectional Studies
Female
Male
*Dental Caries/microbiology
Streptococcus mutans/isolation & purification
Candida albicans/isolation & purification
Buffers
Lactobacillus/isolation & purification
Sleep/physiology

@article {pmid38668434,
year = {2024},
author = {Chow, L and Flaherty, E and Pezzanite, L and Williams, M and Dow, S and Wotman, K},
title = {Impact of Equine Ocular Surface Squamous Neoplasia on Interactions between Ocular Transcriptome and Microbiome.},
journal = {Veterinary sciences},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/vetsci11040167},
pmid = {38668434},
issn = {2306-7381},
support = {N/a//Colorado State University Young Investigator Grant in Companion Animal Studies/ ; },
abstract = {Ocular surface squamous neoplasia (OSSN) represents the most common conjunctival tumor in horses and frequently results in vision loss and surgical removal of the affected globe. Multiple etiologic factors have been identified as contributing to OSSN progression, including solar radiation exposure, genetic mutations, and a lack of periocular pigmentation. Response to conventional treatments has been highly variable, though our recent work indicates that these tumors are highly responsive to local immunotherapy. In the present study, we extended our investigation of OSSN in horses to better understand how the ocular transcriptome responds to the presence of the tumor and how the ocular surface microbiome may also be altered by the presence of cancer. Therefore, we collected swabs from the ventral conjunctival fornix from 22 eyes in this study (11 with cytologically or histologically confirmed OSSN and 11 healthy eyes from the same horses) and performed RNA sequencing and 16S microbial sequencing using the same samples. Microbial 16s DNA sequencing and bulk RNA sequencing were both conducted using an Illumina-based platform. In eyes with OSSN, we observed significantly upregulated expression of genes and pathways associated with inflammation, particularly interferon. Microbial diversity was significantly reduced in conjunctival swabs from horses with OSSN. We also performed interactome analysis and found that three bacterial taxa (Actinobacillus, Helcococcus and Parvimona) had significant correlations with more than 100 upregulated genes in samples from animals with OSSN. These findings highlight the inflammatory nature of OSSN in horses and provide important new insights into how the host ocular surface interacts with certain microbial populations. These findings suggest new strategies for the management of OSSN in horses, which may entail immunotherapy in combination with ocular surface probiotics or prebiotics to help normalize ocular cell and microbe interactions.},
}

@article {pmid38668367,
year = {2024},
author = {Bajic, D and Wiens, F and Wintergerst, E and Deyaert, S and Baudot, A and Abbeele, PVD},
title = {HMOs Impact the Gut Microbiome of Children and Adults Starting from Low Predicted Daily Doses.},
journal = {Metabolites},
volume = {14},
number = {4},
pages = {},
pmid = {38668367},
issn = {2218-1989},
abstract = {Recent studies suggest that the dietary intake of human milk oligosaccharides (HMOs) provides health benefits from infancy up to adulthood. Thus far, beneficial changes in the adult gut microbiome have been observed at oral doses of 5-20 g/day of HMOs. Efficacy of lower doses has rarely been tested. We assessed four HMO molecular species-2'Fucosyllactose (2'FL), Lacto-N-neotetraose (LNnT), 3'Sialyllactose (3'SL), and 6'Sialyllactose (6'SL)-at predicted doses from 0.3 to 5 g/day for 6-year-old children and adults (n = 6 each), using ex vivo SIFR[®] technology (Cryptobiotix, Ghent, Belgium). This technology employing bioreactor fermentation on fecal samples enables us to investigate microbial fermentation products that are intractable in vivo given their rapid absorption/consumption in the human gut. We found that HMOs significantly increased short-chain fatty acids (SCFAs), acetate, propionate (in children/adults), and butyrate (in adults) from predicted doses of 0.3-0.5 g/day onwards, with stronger effects as dosing increased. The fermentation of 6'SL had the greatest effect on propionate, LNnT most strongly increased butyrate, and 2'FL and 3'SL most strongly increased acetate. An untargeted metabolomic analysis revealed that HMOs enhanced immune-related metabolites beyond SCFAs, such as aromatic lactic acids (indole-3-lactic acid/3-phenyllactic acid) and 2-hydroxyisocaproic acid, as well as gut-brain-axis-related metabolites (γ-aminobutyric acid/3-hydroxybutyric acid/acetylcholine) and vitamins. The effects of low doses of HMOs potentially originate from the highly specific stimulation of keystone species belonging to, for example, the Bifidobacteriaceae family, which had already significantly increased at doses of only 0.5 g/day LNnT (adults) and 1 g/day 2'FL (children/adults).},
}

@article {pmid38668317,
year = {2024},
author = {Shen, W and Zhao, M and Xu, W and Shi, X and Ren, F and Tu, P and Gao, N and Shan, J and Gao, B},
title = {Sex-Specific Effects of Polystyrene Microplastic and Lead(II) Co-Exposure on the Gut Microbiome and Fecal Metabolome in C57BL/6 Mice.},
journal = {Metabolites},
volume = {14},
number = {4},
pages = {},
pmid = {38668317},
issn = {2218-1989},
support = {42107459//National Natural Science Foundation of China/ ; },
abstract = {The wide spread of microplastics has fueled growing public health concern globally. Due to their porous structure and large surface area, microplastics can serve as carriers for other environmental pollutants, including heavy metals. Although the toxic effects of microplastics or heavy metals have been reported previously, investigations into the sex-differential health effects of combined exposure to microplastics and heavy metals are lacking. In the present study, the effects of polystyrene microplastics and lead(II) co-exposure on the gut microbiome, intestinal permeability, and fecal metabolome were examined in both male and female mice. Combined exposure of polystyrene microplastics and lead(II) increased intestinal permeability in both male and female mice. Sex-specific responses to the co-exposure were found in gut bacteria, fungi, microbial metabolic pathways, microbial genes encoding antibiotic resistance and virulence factors, as well as fecal metabolic profiles. In particular, Shannon and Simpson indices of gut bacteria were reduced by the co-exposure only in female mice. A total of 34 and 13 fecal metabolites were altered in the co-exposure group in female and male mice, respectively, among which only three metabolites were shared by both sexes. These sex-specific responses to the co-exposure need to be taken into consideration when investigating the combined toxic effects of microplastics and heavy metals on the gut microbiota.},
}

@article {pmid38668232,
year = {2024},
author = {Liu, A and Garrett, S and Hong, W and Zhang, J},
title = {Staphylococcus aureus Infections and Human Intestinal Microbiota.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/pathogens13040276},
pmid = {38668232},
issn = {2076-0817},
abstract = {Staphylococcus aureus (S. aureus) is a common pathogen that can cause many human diseases, such as skin infection, food poisoning, endocarditis, and sepsis. These diseases can be minor infections or life-threatening, requiring complex medical management resulting in substantial healthcare costs. Meanwhile, as the critically ignored "organ," the intestinal microbiome greatly impacts physiological health, not only in gastrointestinal diseases but also in disorders beyond the gut. However, the correlation between S. aureus infection and intestinal microbial homeostasis is largely unknown. Here, we summarized the recent progress in understanding S. aureus infections and their interactions with the microbiome in the intestine. These summarizations will help us understand the mechanisms behind these infections and crosstalk and the challenges we are facing now, which could contribute to preventing S. aureus infections, effective treatment investigation, and vaccine development.},
}

@article {pmid38668046,
year = {2024},
author = {Capella, MP and Esfahani, K},
title = {A Review of Practice-Changing Therapies in Oncology in the Era of Personalized Medicine.},
journal = {Current oncology (Toronto, Ont.)},
volume = {31},
number = {4},
pages = {1913-1919},
pmid = {38668046},
issn = {1718-7729},
mesh = {Humans ; *Precision Medicine/methods ; *Neoplasms/therapy ; *Medical Oncology/methods/trends ; },
abstract = {In the past decade, a lot of insight was gathered into the composition of the host and tumor factors that promote oncogenesis and treatment resistance. This in turn has led to the ingenious design of multiple new classes of drugs, which have now become the new standards of care in cancer therapy. These include novel antibody-drug conjugates, chimeric antigen receptor T cell therapies (CAR-T), and bispecific T cell engagers (BitTE). Certain host factors, such as the microbiome composition, are also emerging not only as biomarkers for the response and toxicity to anti-cancer therapies but also as potentially useful tools to modulate anti-tumor responses. The field is slowly moving away from one-size-fits-all treatment options to personalized treatments tailored to the host and tumor. This commentary aims to cover the basic concepts associated with these emerging therapies and the promises and challenges to fight cancer.},
}

Humans
*Precision Medicine/methods
*Neoplasms/therapy
*Medical Oncology/methods/trends

@article {pmid38668025,
year = {2024},
author = {Parga, A and Pose-Rodríguez, JM and Muras, A and Baus-Domínguez, M and Otero-Casal, P and Ortega-Quintana, ML and Torres-Lagares, D and Otero, A},
title = {Do Concurrent Peri-Implantitis and Periodontitis Share Their Microbiotas? A Pilot Study.},
journal = {Dentistry journal},
volume = {12},
number = {4},
pages = {},
pmid = {38668025},
issn = {2304-6767},
support = {ED6481B-2023/117//Xunta de Galicia/ ; },
abstract = {The microbial compositions from concurrent peri-implant and periodontal lesions were compared, since the results reported in the literature on the etiological relationship between these oral pathologies are contradictory. Microbial compositions from nine patients were evaluated using Illumina MiSeq sequencing of 16S rRNA gene amplicons and Principal Components Analysis. Comparisons between the use of curettes or paper points as collection methods and between bacterial composition in both pathologies were performed. Paper points allowed the recovery of a higher number of bacterial genera. A higher bacterial diversity was found in peri-implantitis compared to periodontal samples from the same patient, while a greater number of operational taxonomic units (OTUs) were present in the corresponding periodontal samples. A higher abundance of oral pathogens, such as Porphyromonas or Treponema, was found in peri-implantitis sites. The opposite trend was observed for Aggregatibacter abundance, which was higher in periodontal than in peri-implantitis lesions, suggesting that both oral pathologies could be considered different but related diseases. Although the analysis of a higher number of samples would be needed, the differences regarding the microbial composition provide a basis for further understating the pathogenesis of peri-implant infections.},
}

@article {pmid38667474,
year = {2024},
author = {Ju, HM and Ahn, YW and Ok, SM and Jeong, SH and Na, HS and Chung, J},
title = {Microbial Profiles in Oral Lichen Planus: Comparisons with Healthy Controls and Erosive vs. Non-Erosive Subtypes.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {38667474},
issn = {2075-4418},
support = {NRF-2017M3A9B6062021//National Research Foundation of Korea/ ; },
abstract = {Recent studies have begun exploring the potential involvement of microbiota in the pathogenesis of oral lichen planus (OLP), yet comprehensive investigations remain limited. Hence, this study aimed to compare the microbial profiles in saliva samples obtained from patients with OLP against those from healthy controls (HC), along with a comparison between erosive (E) and non-erosive (NE) OLP patients. Saliva samples were collected from 60 OLP patients (E: n = 25, NE: n = 35) and 30 HC individuals. Analysis revealed no significant differences in alpha diversity, as assessed by the Chao1 and Shannon index, across the three groups. However, Bray-Curtis distance analysis indicated a significant disparity in microbiome composition distribution between HC and E-OLP, as well as HC and NE-OLP groups. The six most abundant phyla observed across the groups were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria, and Saccharibacteria (TM7). Notably, OLP groups exhibited a higher prevalence of Bacteroidetes. Prevotella emerged as the predominant genus in the OLP groups, while Capnocytophaga showed a relatively higher prevalence in E-OLP compared to NE-OLP. This study's findings indicate a notable difference in microbiota composition between HC and patients with OLP. Additionally, differences in the microbiome were identified between the E-OLP and NE-OLP groups. The increase in the proportion of certain bacterial species in the oral microbiome suggests that they may exacerbate the inflammatory response and act as antigens for OLP.},
}

@article {pmid38667404,
year = {2024},
author = {Cai, Z and Zhao, X and Qian, Y and Zhang, K and Guo, S and Kan, Y and Wang, Y and Ayra-Pardo, C and Li, D},
title = {Transcriptomic and Metatranscriptomic Analyses Provide New Insights into the Response of the Pea Aphid Acyrthosiphon pisum (Hemiptera: Aphididae) to Acetamiprid.},
journal = {Insects},
volume = {15},
number = {4},
pages = {},
pmid = {38667404},
issn = {2075-4450},
support = {31970480//National Natural Science Foundation of China/ ; 212300410063//Natural Science Foundation of Henan province/ ; 231111111000//Key Research Project of Henan Province/ ; },
abstract = {Acetamiprid is a broad-spectrum neonicotinoid insecticide used in agriculture to control aphids. While recent studies have documented resistance to acetamiprid in several aphid species, the underlying mechanisms are still not fully understood. In this study, we analyzed the transcriptome and metatranscriptome of a laboratory strain of the pea aphid, Acyrthosiphon pisum (Harris, 1776), with reduced susceptibility to acetamiprid after nine generations of exposure to identify candidate genes and the microbiome involved in the adaptation process. Sequencing of the transcriptome of both selected (RS) and non-selected (SS) strains allowed the identification of 14,858 genes and 4938 new transcripts. Most of the differentially expressed genes were associated with catalytic activities and metabolic pathways involving carbon and fatty acids. Specifically, alcohol-forming fatty acyl-CoA reductase (FAR) and acyl-CoA synthetase (ACSF2), both involved in the synthesis of epidermal wax layer components, were significantly upregulated in RS, suggesting that adaptation to acetamiprid involves the synthesis of a thicker protective layer. Metatranscriptomic analyses revealed subtle shifts in the microbiome of RS. These results contribute to a deeper understanding of acetamiprid adaptation by the pea aphid and provide new insights for aphid control strategies.},
}

@article {pmid38667044,
year = {2024},
author = {Lardenoije, CMJG and van Riel, SJJM and Peters, LJF and Wassen, MMLH and Cremers, NAJ},
title = {Medical-Grade Honey as a Potential New Therapy for Bacterial Vaginosis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/antibiotics13040368},
pmid = {38667044},
issn = {2079-6382},
abstract = {The prevalence of bacterial vaginosis (BV) among women of reproductive age is 29%. BV arises from a vaginal imbalance marked by reduced levels of lactic acid-producing lactobacilli and an overgrowth of pathogenic anaerobes. The multifactorial nature of BV's pathogenesis complicates its treatment. Current antibiotic therapy exhibits a recurrence rate of about 60% within a year. Recurrence can be caused by antibiotic treatment failure (e.g., due to antimicrobial resistance), the persistence of residual infections (e.g., due to biofilm formation), and re-infection. Because of the high recurrence rates, alternative therapies are required. Medical-grade honey (MGH), known for its antimicrobial and wound healing properties in wound care, emerges as a potential novel therapy for BV. MGH exerts broad-spectrum antimicrobial activity, employing multiple mechanisms to eliminate the risk of resistance. For example, the low pH of MGH and the production of hydrogen peroxide benefit the microbiota and helps restore the natural vaginal balance. This is supported by in vitro studies demonstrating that MGH has an antibacterial effect on several pathogenic bacteria involved in the pathophysiology of BV, while lactobacilli and the vaginal microenvironment can be positively affected. In contrast to antibiotics, MGH exerts anti-biofilm activity, affects the microbiome as pre- and probiotic, and modulates the vaginal microenvironment through its anti-inflammatory, anti-oxidative, physicochemical, and immunomodulatory properties. More clinical research is required to confirm the positive effect of MGH on BV and to investigate the long-term cure rate.},
}

@article {pmid38667028,
year = {2024},
author = {Junaid, M and Lu, H and Din, AU and Yu, B and Liu, Y and Li, Y and Liu, K and Yan, J and Qi, Z},
title = {Deciphering Microbiome, Transcriptome, and Metabolic Interactions in the Presence of Probiotic Lactobacillus acidophilus against Salmonella Typhimurium in a Murine Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38667028},
issn = {2079-6382},
support = {31660713, 81903168//National Natural Science Foundation of China/ ; 20212014//The Nanning Science and Technology base Project/ ; 20210035, 20220026//The Project of Bama Country for Talents in Science and Technology/ ; },
abstract = {Salmonella enterica serovar Typhimurium (S. Typhimurium), a foodborne pathogen that poses significant public health risks to humans and animals, presents a formidable challenge due to its antibiotic resistance. This study explores the potential of Lactobacillus acidophilus (L. acidophilus 1.3251) probiotics as an alternative strategy to combat antibiotic resistance associated with S. Typhimurium infection. In this investigation, twenty-four BALB/c mice were assigned to four groups: a non-infected, non-treated group (CNG); an infected, non-treated group (CPG); a group fed with L. acidophilus but not infected (LAG); and a group fed with L. acidophilus and challenged with Salmonella (LAST). The results revealed a reduction in Salmonella levels in the feces of mice, along with restored weight and improved overall health in the LAST compared to the CPG. The feeding of L. acidophilus was found to downregulate pro-inflammatory cytokine mRNA induced by Salmonella while upregulating anti-inflammatory cytokines. Additionally, it influenced the expression of mRNA transcript, encoding tight junction protein, oxidative stress-induced enzymes, and apoptosis-related mRNA expression. Furthermore, the LEfSe analysis demonstrated a significant shift in the abundance of critical commensal genera in the LAST, essential for maintaining gut homeostasis, metabolic reactions, anti-inflammatory responses, and butyrate production. Transcriptomic analysis revealed 2173 upregulated and 506 downregulated differentially expressed genes (DEGs) in the LAST vs. the CPG. Functional analysis of these DEGs highlighted their involvement in immunity, metabolism, and cellular development. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis indicated their role in tumor necrosis factor (TNF), mitogen-activated protein kinase (MAPK), chemokine, Forkhead box O (FOXO), and transforming growth factor (TGF-β) signaling pathway. Moreover, the fecal metabolomic analysis identified 929 differential metabolites, with enrichment observed in valine, leucine, isoleucine, taurine, glycine, and other metabolites. These findings suggest that supplementation with L. acidophilus promotes the growth of beneficial commensal genera while mitigating Salmonella-induced intestinal disruption by modulating immunity, gut homeostasis, gut barrier integrity, and metabolism.},
}

@article {pmid38667016,
year = {2024},
author = {Twomey, E and O'Connor, PM and Coffey, A and Kiste, M and Guinane, CM and Hill, C and Field, D and Begley, M},
title = {Inhibition of Clinical MRSA Isolates by Coagulase Negative Staphylococci of Human Origin.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38667016},
issn = {2079-6382},
abstract = {Staphylococcus aureus is frequently highlighted as a priority for novel drug research due to its pathogenicity and ability to develop antibiotic resistance. Coagulase-negative staphylococci (CoNS) are resident flora of the skin and nares. Previous studies have confirmed their ability to kill and prevent colonization by S. aureus through the production of bioactive substances. This study screened a bank of 37 CoNS for their ability to inhibit the growth of methicillin-resistant S. aureus (MRSA). Deferred antagonism assays, growth curves, and antibiofilm testing performed with the cell-free supernatant derived from overnight CoNS cultures indicated antimicrobial and antibiofilm effects against MRSA indicators. Whole genome sequencing and BAGEL4 analysis of 11 CoNS isolates shortlisted for the inhibitory effects they displayed against MRSA led to the identification of two strains possessing complete putative bacteriocin operons. The operons were predicted to encode a nukacin variant and a novel epilancin variant. From this point, strains Staphylococcus hominis C14 and Staphylococcus epidermidis C33 became the focus of the investigation. Through HPLC, a peptide identical to previously characterized nukacin KQU-131 and a novel epilancin variant were isolated from cultures of C14 and C33, respectively. Mass spectrometry confirmed the presence of each peptide in the active fractions. Spot-on-lawn assays demonstrated both bacteriocins could inhibit the growth of an MRSA indicator. The identification of natural products with clinically relevant activity is important in today's climate of escalating antimicrobial resistance and a depleting antibiotic pipeline. These findings also highlight the prospective role CoNS may play as a source of bioactive substances with activity against critical pathogens.},
}

@article {pmid38666993,
year = {2024},
author = {Olson, S and Welton, L and Jahansouz, C},
title = {Perioperative Considerations for the Surgical Treatment of Crohn's Disease with Discussion on Surgical Antibiotics Practices and Impact on the Gut Microbiome.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38666993},
issn = {2079-6382},
abstract = {Crohn's disease, a chronic inflammatory process of the gastrointestinal tract defined by flares and periods of remission, is increasing in incidence. Despite advances in multimodal medical therapy, disease progression often necessitates multiple operations with high morbidity. The inability to treat Crohn's disease successfully is likely in part because the etiopathogenesis is not completely understood; however, recent research suggests the gut microbiome plays a critical role. How traditional perioperative management, including bowel preparation and preoperative antibiotics, further changes the microbiome and affects outcomes is not well described, especially in Crohn's patients, who are unique given their immunosuppression and baseline dysbiosis. This paper aims to outline current knowledge regarding perioperative management of Crohn's disease, the evolving role of gut dysbiosis, and how the microbiome can guide perioperative considerations with special attention to perioperative antibiotics as well as treatment of Mycobacterium avium subspecies paratuberculosis. In conclusion, dysbiosis is common in Crohn's patients and may be exacerbated by malnutrition, steroids, narcotic use, diarrhea, and perioperative antibiotics. Dysbiosis is also a major risk factor for anastomotic leak, and special consideration should be given to limiting factors that further perturb the gut microbiota in the perioperative period.},
}

@article {pmid38666955,
year = {2024},
author = {Bilski, K and Żeber-Lubecka, N and Kulecka, M and Dąbrowska, M and Bałabas, A and Ostrowski, J and Dobruch, A and Dobruch, J},
title = {Microbiome Sex-Related Diversity in Non-Muscle-Invasive Urothelial Bladder Cancer.},
journal = {Current issues in molecular biology},
volume = {46},
number = {4},
pages = {3595-3609},
pmid = {38666955},
issn = {1467-3045},
support = {2019/33/B/NZ5/02447//National Science Center/ ; },
abstract = {Sex-specific discrepancies in bladder cancer (BCa) are reported, and new studies imply that microbiome may partially explain the diversity. We aim to provide characterization of the bladder microbiome in both sexes diagnosed with non-muscle-invasive BCa with specific insight into cancer grade. In our study, 16S rRNA next-generation sequencing was performed on midstream urine, bladder tumor sample, and healthy-appearing bladder mucosa. Bacterial DNA was isolated using QIAamp Viral RNA Mini Kit. Metagenomic analysis was performed using hypervariable fragments of the 16S rRNA gene on Ion Torrent Personal Genome Machine platform. Of 41 sample triplets, 2153 taxa were discovered: 1739 in tumor samples, 1801 in healthy-appearing bladder mucosa and 1370 in midstream urine. Women were found to have smaller taxa richness in Chao1 index than men (p = 0.03). In comparison to low-grade tumors, patients with high-grade lesions had lower bacterial diversity and richness in urine. Significant differences between sexes in relative abundance of communities at family level were only observed in high-grade tumors.},
}

@article {pmid38666797,
year = {2024},
author = {Llorenç-Vicedo, A and Lluesma Gomez, M and Zeising, O and Kleiner, T and Freitag, J and Martinez-Hernandez, F and Wilhelms, F and Martinez-Garcia, M},
title = {New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0007324},
doi = {10.1128/msphere.00073-24},
pmid = {38666797},
issn = {2379-5042},
abstract = {UNLABELLED: The signs of climate change are undeniable, and the impact of these changes on ecosystem function heavily depends on the response of microbes that underpin the food web. Antarctic ice shelf is a massive mass of floating ice that extends from the continent into the ocean, exerting a profound influence on global carbon cycles. Beneath Antarctic ice shelves, marine ice stores valuable genetic information, where marine microbial communities before the industrial revolution are archived. Here, in this proof-of-concept, by employing a combination of single-cell technologiesand metagenomics, we have been able to sequence frozen microbial DNA (≈300 years old) stored in the marine ice core B15 collected from the Filchnner-Ronne Ice Shelf. Metagenomic data indicated that Proteobacteria and Thaumarchaeota (e.g., Nitrosopumilus spp.), followed by Actinobacteria (e.g., Actinomarinales), were abundant. Remarkably, our data allow us to "travel to the past" and calibrate genomic and genetic evolutionary changes for ecologically relevant microbes and functions, such as Nitrosopumilus spp., preserved in the marine ice (≈300 years old) with those collected recently in seawater under an ice shelf (year 2017). The evolutionary divergence for the ammonia monooxygenase gene amoA involved in chemolithoautotrophy was about 0.88 amino acid and 2.8 nucleotide substitution rate per 100 sites in a century, while the accumulated rate of genomic SNPs was 2,467 per 1 Mb of genome and 100 years. Whether these evolutionary changes remained constant over the last 300 years or accelerated during post-industrial periods remains an open question that will be further elucidated.

IMPORTANCE: Several efforts have been undertaken to predict the response of microbes under climate change, mainly based on short-term microcosm experiments under forced conditions. A common concern is that manipulative experiments cannot properly simulate the response of microbes to climate change, which is a long-term evolutionary process. In this proof-of-concept study with a limited sample size, we demonstrate a novel approach yet to be fully explored in science for accessing genetic information from putative past marine microbes preserved under Antarctic ice shelves before the industrial revolution. This potentially allows us estimating evolutionary changes as exemplified in our study. We advocate for gathering a more comprehensive Antarctic marine ice core data sets across various periods and sites. Such a data set would enable the establishment of a robust baseline, facilitating a better assessment of the potential effects of climate change on key genetic signatures of microbes.},
}

@article {pmid38666794,
year = {2024},
author = {Zaher, A and Elsaygh, J and Peterson, SJ and Weisberg, IS and Parikh, MA and Frishman, WH},
title = {The Interplay of Microbiome Dysbiosis and Cardiovascular Disease.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000000701},
pmid = {38666794},
issn = {1538-4683},
abstract = {The intricate ecosystem of the mammalian gut, which hosts a diverse microbiome, plays a vital role in various physiological functions. Trillions of bacteria within the gut contribute to host metabolism, immune modulation, energy homeostasis, and more. Emerging research highlights the gut microbiota's significant impact on cardiovascular diseases (CVDs), with intestinal dysbiosis identified as a risk factor for conditions such as obesity and diabetes, both linked to atherosclerosis. Chronic inflammation, pivotal in atherosclerosis, is influenced by the gut microbiome, where microbial signals, such as lipopolysaccharides, can translocate from the gut to trigger inflammatory responses. Diet has major effects on the gut microbiota, with the Western diet, rich in saturated fats, contributing to dysbiosis and elevated cardiovascular risks. Probiotics and prebiotics offer therapeutic potential in CVD management. Probiotics, or live microorganisms, exhibit antioxidant, anti-inflammatory, and cholesterol-lowering effects. Probiotics are most effective when given with prebiotics, with the former acting on the latter as substrate. Understanding the dynamic interplay between diet, gut microbiota, and CVD provides insights into preventive and therapeutic strategies.},
}

@article {pmid38666460,
year = {2024},
author = {Campbell, A and Bae, J and Hein, M and Hillis, SL and Rebeck, ON and Rakel, BA and Grice, E and Gardner, SE},
title = {The heterogeneous wound microbiome varies with wound care pain, dressing type, and inflammatory gene expression.},
journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/wrr.13184},
pmid = {38666460},
issn = {1524-475X},
support = {R01NR015639/NR/NINR NIH HHS/United States ; R01NR015642/NR/NINR NIH HHS/United States ; UL1TR002537/TR/NCATS NIH HHS/United States ; },
abstract = {Wound dressing changes are essential procedures for wound management. However, ~50% of patients experience severe pain during these procedures despite the availability of analgesic medications, indicating a need for novel therapeutics that address underlying causes of pain. Along with other clinical factors, wound pathogens and inflammatory immune responses have previously been implicated in wound pain. To test whether these factors could contribute to severe pain during wound dressing changes, we conducted an exploratory, cross-sectional analysis of patient-reported pain, inflammatory immune responses, and wound microbiome composition in 445 wounds at the time of a study dressing change. We profiled the bacterial composition of 406 wounds using 16S ribosomal RNA amplicon sequencing and quantified gene expression of 13 inflammatory markers in wound fluid using quantitative real-time polymerase chain reaction (qPCR). Neither inflammatory gene expression nor clinically observed inflammation were associated with severe pain, but Corynebacterium and Streptococcus were of lower relative abundance in wounds of patients reporting severe pain than those reporting little or no pain. Wound microbiome composition differed by wound location, and correlated with six of the inflammatory markers, including complement receptor C5AR1, pro-inflammatory cytokine interleukin (IL)1β, chemokine IL-8, matrix metalloproteinase MMP2, and the antimicrobial peptide encoding cathelicidin antimicrobial peptide. Interestingly, we found a relationship between the wound microbiome and vacuum-assisted wound closure (VAC). These findings identify preliminary, associative relationships between wound microbiota and host factors which motivate future investigation into the directional relationships between wound care pain, wound closure technologies, and the wound microbiome.},
}

@article {pmid38666261,
year = {2024},
author = {Li, M and Kopylova, E and Mao, J and Namkoong, J and Sanders, J and Wu, J},
title = {Microbiome and lipidomic analysis reveal the interplay between skin bacteria and lipids in a cohort study.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1383656},
pmid = {38666261},
issn = {1664-302X},
abstract = {Human skin acts as a protective barrier between the body and the external environment. Skin microbiome and intercellular lipids in the stratum corneum (SC) are essential for maintaining skin barrier function. However, the interplay between skin bacteria and the lipids is not fully understood. In this study, we characterized the skin microbiome and SC lipid profiles from the forearm and face in a cohort of 57 healthy participants. 16S rRNA gene sequencing showed the skin microbial composition is significantly different between body locations and genders. Female forearm samples have the highest microbial diversity. The relative abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium tuberculostearicum, Finegoldia magna, and Moraxellaceae sp. are significantly higher in the forearm than the face. The predictive functional analysis of 16S rRNA gene sequencing by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and ANCOM-BC showed different bacterial metabolic pathway profiles between body locations or genders, and identified 271 differential pathways, including arginine and polyamine biosynthesis, chorismate biosynthesis pathways, which are more abundant in the female forearm, and sulfur oxidation pathway, which is more abundant in the male face. The SC lipid profiles differ between the body locations as well. Total free fatty acids (FFA), cholesterol sulfate and sphingosine are more abundant in the face. Dihydro-/6-hydroxy/phyto-ceramides are more abundant in the forearm. The correlation analysis of 16S rRNA gene sequencing and lipids revealed novel interplay between the bacteria and skin lipids. Shannon entropy and S. hominis negatively correlated with FFA, cholesterol sulfate and sphingosine; while positively correlated with dihydro-/6-hydroxy/phyto-ceramides. The correlation of predictive pathway profiles and lipids identified pathways involved in amino acids metabolism, carbohydrates degradation, aromatic compounds metabolism and fatty acid degradation metabolism are positively correlated with dihydro-/6-hydroxy/phyto-ceramides and negatively correlated with FFA, cholesterol sulfate and sphingosine. This study provides insights on the potential correlation between skin microbiome and lipids.},
}

@article {pmid38666257,
year = {2024},
author = {Wang, Z and Xu, L and Lu, X and Wang, R and Han, J and Yan, A},
title = {The endophytic microbiome response patterns of Juglans regia to two pathogenic fungi.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1378273},
pmid = {38666257},
issn = {1664-302X},
abstract = {The endophytic microbial community reassembles to participate in plant immune balance when the host plants are stressed by pathogens. However, it remains unclear whether this assembly is pathogen-specific and how regulatory pathways are coordinated in multi-pathogens. In order to investigate the effects of infection with Colletotrichum gloeosporioides (Cg treatment) and Fusarium proliferatum (Fp treatment) on walnut leaf endophytic microbiome in their assembly, co-occurrence pattern, and on comprehensive chemical function of the internal environment of leaf, an interaction system of the walnut-pathogenic fungi was constructed using seed embryo tissue culture technology. The study showed differences in the assembly of endophytic microbial communities in walnut trees across three groups (control group, Ck; Cg; Fp) after Cg and Fp treatments. Despite changes in relative abundances, the dominant communities in phyla and genera remained comparable during the infection of the two pathogens. Endophyte fungi were more sensitive to the pathogen challenge than endophyte bacteria. Both promoted the enrichment of beneficial bacteria such as Bacillus and Pseudomonas, changed the modularity of the community, and reduced the stability and complexity of the endophyte community. Pathogenic fungi infection mainly affects the metabolism of porphyrin and chlorophyll, purine metabolism, phenylpropane metabolism, and amino acid metabolism. However, there was no significant difference in the secondary metabolites for the different susceptible plants. By screening endogenous antagonistic bacteria, we further verified that Pseudomonas psychrotolerans and Bacillus subtilis had inhibitory effects on the two pathogenic fungi and participated in the interaction between the leaves and pathogenic fungi. The antibacterial substances may be 1-methylnaphthalene, 1,3-butadiene, 2,3-butanediol, and toluene aldehyde.},
}

@article {pmid38666212,
year = {2024},
author = {Pujolassos, M and Susín, A and Calle, ML},
title = {Microbiome compositional data analysis for survival studies.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {2},
pages = {lqae038},
pmid = {38666212},
issn = {2631-9268},
abstract = {The growing interest in studying the relationship between the human microbiome and our health has also extended to time-to-event studies where researchers explore the connection between the microbiome and the occurrence of a specific event of interest. The analysis of microbiome obtained through high throughput sequencing techniques requires the use of specialized Compositional Data Analysis (CoDA) methods designed to accommodate its compositional nature. There is a limited availability of statistical tools for microbiome analysis that incorporate CoDA, and this is even more pronounced in the context of survival analysis. To fill this methodological gap, we present coda4microbiome for survival studies, a new methodology for the identification of microbial signatures in time-to-event studies. The algorithm implements an elastic-net penalized Cox regression model adapted to compositional covariates. We illustrate coda4microbiome algorithm for survival studies with a case study about the time to develop type 1 diabetes for non-obese diabetic mice. Our algorithm identified a bacterial signature composed of 21 genera associated with diabetes development. coda4microbiome for survival studies is integrated in the R package coda4microbiome as an extension of the existing functions for cross-sectional and longitudinal studies.},
}

@article {pmid38666051,
year = {2024},
author = {Kicic-Starcevich, E and Hancock, DG and Iosifidis, T and Agudelo-Romero, P and Caparros-Martin, JA and Karpievitch, YV and Silva, D and Turkovic, L and Le Souef, PN and Bosco, A and Martino, DJ and Kicic, A and Prescott, SL and Stick, SM},
title = {Airway epithelium respiratory illnesses and allergy (AERIAL) birth cohort: study protocol.},
journal = {Frontiers in allergy},
volume = {5},
number = {},
pages = {1349741},
pmid = {38666051},
issn = {2673-6101},
abstract = {INTRODUCTION: Recurrent wheezing disorders including asthma are complex and heterogeneous diseases that affect up to 30% of all children, contributing to a major burden on children, their families, and global healthcare systems. It is now recognized that a dysfunctional airway epithelium plays a central role in the pathogenesis of recurrent wheeze, although the underlying mechanisms are still not fully understood. This prospective birth cohort aims to bridge this knowledge gap by investigating the influence of intrinsic epithelial dysfunction on the risk for developing respiratory disorders and the modulation of this risk by maternal morbidities, in utero exposures, and respiratory exposures in the first year of life.

METHODS: The Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) study is nested within the ORIGINS Project and will monitor 400 infants from birth to 5 years. The primary outcome of the AERIAL study will be the identification of epithelial endotypes and exposure variables that influence the development of recurrent wheezing, asthma, and allergic sensitisation. Nasal respiratory epithelium at birth to 6 weeks, 1, 3, and 5 years will be analysed by bulk RNA-seq and DNA methylation sequencing. Maternal morbidities and in utero exposures will be identified on maternal history and their effects measured through transcriptomic and epigenetic analyses of the amnion and newborn epithelium. Exposures within the first year of life will be identified based on infant medical history as well as on background and symptomatic nasal sampling for viral PCR and microbiome analysis. Daily temperatures and symptoms recorded in a study-specific Smartphone App will be used to identify symptomatic respiratory illnesses.

DISCUSSION: The AERIAL study will provide a comprehensive longitudinal assessment of factors influencing the association between epithelial dysfunction and respiratory morbidity in early life, and hopefully identify novel targets for diagnosis and early intervention.},
}

@article {pmid38665319,
year = {2024},
author = {Ganesan, A and Kumar, G and Gauthaman, J and Lakshmi, KC and Kumbalaparambil, YA},
title = {Exploring the Relationship between Psychoneuroimmunology and Oral Diseases: A Comprehensive Review and Analysis.},
journal = {Journal of lifestyle medicine},
volume = {14},
number = {1},
pages = {13-19},
pmid = {38665319},
issn = {2234-8549},
abstract = {The relationship between psychoneuroimmunology (PNI) and oral health has recently garnered increasing attention due to the intricate interaction among psychological factors, the nervous system, immune responses, and oral diseases. This comprehensive review aims to elucidate the multifaceted connections between PNI and various oral conditions and conduct an in-depth analysis. Psychological factors, such as stress, anxiety, and depression, have been linked to oral microbiome alterations and immune function and the development and progression of oral diseases, such as periodontal disorders, oral ulcers, and temporomandibular disorders. Conversely, oral health conditions, particularly chronic periodontitis, have been associated with systemic inflammation, affecting mental health and overall well-being through neuroendocrine-immune pathways. Moreover, neural mechanisms, including the brain-gut axis and the autonomic nervous system, significantly influenced oral health through immune modulation and inflammatory responses. Understanding these complex interactions has implications for therapeutic interventions that target both psychological well-being and oral health outcomes. This review synthesizes current research findings from various disciplines, including immunology, neuroscience, dentistry, and psychology, to offer a comprehensive understanding of the bidirectional relationship between PNI and oral diseases. The implications of these interactions on treatment strategies, preventive measures, and interdisciplinary approaches underscore the need for integrated healthcare models that address psychological and oral health aspects to improve outcomes and quality of life in patients.},
}

@article {pmid38665315,
year = {2024},
author = {Ismail, A and Yogarajah, A and Falconer, JL and Dworakowski, R and Watson, S and Breeze, J and Gunning, M and Khan, H and Hussain, A and Howard, JP and Cheong, P and Shah, M and Nibali, L and Sousa, V},
title = {Insights into microorganisms, associated factors, and the oral microbiome in infective endocarditis patients.},
journal = {Frontiers in oral health},
volume = {5},
number = {},
pages = {1270492},
pmid = {38665315},
issn = {2673-4842},
abstract = {INTRODUCTION: Infective Endocarditis (IE) is a rare, life-threatening infection of the endocardium with multisystem effects. Culprit microorganisms derived from different niches circulate through the bloodstream and attach to the endocardium, particularly the heart valves. This study aimed to investigate culprit microorganisms among a cross-sectional cohort of IE patients, their associated factors, and to explore the potential relationship to the oral microbiome.

METHODS: In this observational study, we undertook a cross-sectional analysis of 392 medical records from patients diagnosed with IE. The primary outcome of this study was to analyse the association between the IE culprit microorganisms and the underlying anatomical types of IE (native valve (NVE), prosthetic valve (PVE), or cardiac device-related (CDE)). Secondary outcomes encompassed a comparative analysis of additional factors, including: the treatment approaches for IE, and the categorisation of blood cultures, extending to both genus and species levels. Additionally, we cross-referenced and compared the species-level identification of IE bacteraemia outcome measures with data from the expanded Human Oral Microbiome Database (eHOMD).

RESULTS: A culprit microorganism was identified in 299 (76.28%) case participants. Staphylococcal infections were the most common (p < 0.001), responsible for 130 (33.16%) hospitalisations. There were 277 (70.66%) cases of NVE, 104 (26.53%) cases of PVE, and 11 (2.81%) cases of CDE. The majority of PVE occurred on prosthetic aortic valves (78/104, 75%), of which 72 (93.5%) were surgical aortic valve replacements (SAVR), 6 (7.8%) were transcatheter aortic valve implants, and one transcatheter pulmonary valve implant. Overall, underlying anatomy (p = 0.042) as well as the treatment approaches for IE (p < 0.001) were significantly associated with IE culprit microorganisms. Cross-reference between IE bacteraemia outcomes with the eHOMD was observed in 267/392 (68.11%) cases.

CONCLUSIONS: This study demonstrated that IE patients with a history of stroke, smoking, intravenous drug use, or dialysis were more likely to be infected with Staphylococcus aureus. CDE case participants and patients who had previous SAVR were most associated with Staphylococcus epidermidis. IE patients aged 78+ were more likely to develop enterococci IE than other age groups. Oral microorganisms indicated by the eHOMD are significantly observed in the IE population. Further research, through enhanced dental and medical collaboration, is required to correlate the presence of oral microbiota as causative factor for IE.},
}

@article {pmid38665301,
year = {2024},
author = {Esperança, VJR and Moreira, PIO and Chávez, DWH and Freitas-Silva, O},
title = {Evaluation of the safety and quality of Brazil nuts (Bertholletia excelsa) using the tools of dna sequencing technology and aflatoxin profile.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1357778},
pmid = {38665301},
issn = {2296-861X},
abstract = {INTRODUCTION: Brazil nuts (BNs) result from sustainable extraction and are widely exploited in the Amazon region. Due to the production characteristics in the forest and the nutritional characteristics of these nuts, the occurrence of fungal contamination and the presence of aflatoxins are extensively discussed in the literature as a great aspect of interest and concern. This study aims to evaluate the microbial profile through DNA sequencing and amplification of 16S and ITS genes for bacterial and fungal analysis, respectively, and the presence of mycotoxins using high-performance liquid chromatography with fluorescence detection (HPLC-FD) from different fractions of the nuts processed.

METHODS: The BN samples, harvest A (HA) and harvest B (HB), from two different harvests were collected in an extractive cooperative in the Amazon region for microbiological analysis (from DNA extraction and amplification of 16S genes, bacteria analysis, and ITS for fungi) and mycotoxins (aflatoxins AFB1, AFB2, AFG1, and AFG2) using HPLC-FD/KobraCell[®].

RESULTS AND DISCUSSION: The samples showed a very different microbiome and aflatoxin profile. Genera such as Rothia (HA) and Cronobacter (HB) were abundant during the analysis of bacteria; as for fungi, the genera Aspergillus, Fusarium, Penicillium, and Alternaria were also considered prevalent in these samples. Soil microorganisms, including those pathogenic and related to inadequate hygienic-sanitary production practices, as well as aflatoxins, were found in the samples. However, they were within the established limits permitted by Brazilian legislation. Nuts have a diverse microbiota and are not restricted to fungi of the genus Aspergillus. The microbiological and toxicological profile can vary significantly within the same nut in the same extraction region and can be exacerbated by global climate changes. Therefore, it is necessary to advance sanitary educational actions by applying good production practices and inspection programs to ensure the sustainability and quality of the BN production chain.},
}

@article {pmid38665235,
year = {2024},
author = {Cossart, P and Hacker, J and Holden, DH and Normark, S and Vogel, J},
title = {Meeting report 'Microbiology 2023: from single cell to microbiome and host', an international interacademy conference in Würzburg.},
journal = {microLife},
volume = {5},
number = {},
pages = {uqae008},
pmid = {38665235},
issn = {2633-6693},
abstract = {On September 20-22 September 2023, the international conference 'Microbiology 2023: from single cell to microbiome and host' convened microbiologists from across the globe for a very successful symposium, showcasing cutting-edge research in the field. Invited lecturers delivered exceptional presentations covering a wide range of topics, with a major emphasis on phages and microbiomes, on the relevant bacteria within these ecosystems, and their multifaceted roles in diverse environments. Discussions also spanned the intricate analysis of fundamental bacterial processes, such as cell division, stress resistance, and interactions with phages. Organized by four renowned Academies, the German Leopoldina, the French Académie des sciences, the Royal Society UK, and the Royal Swedish Academy of Sciences, the symposium provided a dynamic platform for experts to share insights and discoveries, leaving participants inspired and eager to integrate new knowledge into their respective projects. The success of Microbiology 2023 prompted the decision to host the next quadrennial academic meeting in Sweden. This choice underscores the commitment to fostering international collaboration and advancing the frontiers of microbiological knowledge. The transition to Sweden promises to be an exciting step in the ongoing global dialogue and specific collaborations on microbiology, a field where researchers will continue to push the boundaries of knowledge, understanding, and innovation not only in health and disease but also in ecology.},
}

@article {pmid38665155,
year = {2024},
author = {Babalola, OO and Adedayo, AA and Akinola, SA},
title = {High-throughput metagenomic assessment of Cango Cave microbiome-A South African limestone cave.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110381},
pmid = {38665155},
issn = {2352-3409},
abstract = {Microorganisms inhabiting caves exhibit medical or biotechnological promise, most of which have been attributed to factors such as antimicrobial activity or the induction of mineral precipitation. This dataset explored the shotgun metagenomic sequencing of the Cango cave microbial community in Oudtshoorn, South Africa. The aimed to elucidate both the structure and function of the microbial community linked to the cave. DNA sequencing was conducted using the Illumina NovaSeq platform, a next-generation sequencing. The data comprises 4,738,604 sequences, with a cumulative size of 1,180,744,252 base pairs and a GC content of 52%. Data derived from the metagenome sequences can be accessed through the bioproject number PRJNA982691 on NCBI. Using an online metagenome server, MG-RAST, the subsystem database revealed that bacteria displayed the highest taxonomical representation, constituting about 98.66%. Archaea accounted for 0.05%, Eukaryotes at 1.20%, viruses were 0.07%, while unclassified sequences had a representation of 0.02%. The most abundant phyla were Proteobacteria (81.74%), Bacteroidetes (10.57%), Actinobacteria (4.16%), Firmicutes (SK‒1.03%), Acidobacteria (0.20), and Planctomycetes (SK‒0.16%). Functional annotation using subsystem analysis revealed that clustering based on subsystems had 13.44%, while amino acids and derivatives comprised 11.41%. Carbohydrates sequences constituted 9.55%, along with other advantageous functional traits essential for growth promotion and plant management.},
}

@article {pmid38665074,
year = {2024},
author = {Gao, J and Lv, D and Wu, Z and Sun, Z and Sun, X and Liu, S and Tan, Z and Zhu, W and Cheng, Y},
title = {Dietary supplementing phytosterols improves the metabolic status of perinatal cows revealed by plasma metabolomics and faecal microbial metabolism.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.23.0422},
pmid = {38665074},
issn = {2765-0189},
abstract = {OBJECTIVE: Previous research reported that dietary addition with phytosterols improved the energy utilisation of the rumen microbiome, suggesting its potential to alleviate the negative energy balance of perinatal cows. This experiment aimed to explore the effects of feeding phytosterols on the metabolic status of perinatal cows through plasma metabolomics and faecal bacteria metabolism.

METHODS: Ten perinatal Holstein cows (multiparous, 2 parities) with a similar calving date were selected four weeks before calving. After 7 days for adaptation, cows were allocated to two groups (n=5), which respectively received the basal rations supplementing commercial phytosterols at 0 and 200 mg/d during a 42-day experiment. The milk yield of each cow was recorded daily after calving. On days 1 and 42, blood and faeces samples were all collected from perinatal cows before morning feeding for analysing plasma biochemicals and metabolome, and faecal bacteria metabolism.

RESULTS: Dietary addition with phytosterols at 200 mg/d had no effects on plasma cholesterol and numerically increased milk yield by 1.82 kg/d (p>0.10) but attenuated their negative energy balance in perinatal cows as observed from the significantly decreased plasma level of β-hydroxybutyric acid (p=0.002). Dietary addition with phytosterols significantly altered 12 and 15 metabolites (p<0.05) within the plasma and faeces of perinatal cows, respectively. Of these metabolites, 5 upregulated plasma fatty acids indicated an improved energy status (i.e., C18:1T, C14:0, C17:0, C18:0, and C16:0). Milk yield negatively correlated with plasma concentrations of ketone bodies (p=0.035) and 5-methoxytryptamine (p=0.039). Furthermore, dietary addition with phytosterols at 200 mg/d had no effects on fermentation characteristics and bacterial diversity of cow faeces (p>0.10) but improved potentially beneficial bacteria such as Christensenellaceae family (p<0.05) that positively correlated with feed efficiency.

CONCLUSION: Dietary addition with phytosterols at 200 mg/d could effectively improve the energy status in perinatal cows by attenuating their negative energy balance.},
}

@article {pmid38664929,
year = {2024},
author = {Fu, Q and Ma, X and Li, S and Shi, M and Song, T and Cui, J},
title = {New insights into the interactions between the gut microbiota and the inflammatory response to ulcerative colitis in a mouse model of dextran sodium sulfate and possible mechanisms of action for treatment with PE&AFWE.},
journal = {Animal models and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/ame2.12405},
pmid = {38664929},
issn = {2576-2095},
support = {81774449//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), is a heterogeneous state of chronic intestinal inflammation. Intestinal innate immunity, including innate immune cells, defends against pathogens and excessive entry of gut microbiota, while preserving immune tolerance to resident intestinal microbiota, and may be characterized by its capacity to produce a rapid and nonspecific reaction. The association between microbiota dysbiosis and the pathogenesis of IBD is complex and dynamic. When the intestinal ecosystem is in dysbiosis, the reduced abundance and diversity of intestinal gut microbiota make the host more vulnerable to the attack of exogenous and endogenous pathogenic gut microbiota. The aim of our study was to comprehensively assess the relationship between microbial populations within UC, the signaling pathways of pathogenic gut microbe therein and the inflammatory response, as well as to understand the effects of using PE&AFWE (poppy extract [Papaver nudicaule L.] and Artemisia frigida Willd. extract) on UC modulation.

METHODS: A UC mouse model was established by inducing SPF-grade C57BL/6 mice using dextrose sodium sulfate (DSS). Based on metagenomic sequencing to characterize the gut microbiome, the relationship between gut microbiota dysbiosis and gut microbiota was further studied using random forest and Bayesian network analysis methods, as well as histopathological analysis.

RESULTS: (1) We found that the 5 gut microbiota with the highest relative abundance of inflammatory bowel disease UC model gut microbiota were consistent with the top 5 ranked natural bacteria. There were three types of abundance changes in the model groups: increases (Chlamydiae/Proteobacteria and Deferribacteres), decreases (Firmicutes), and no significant changes (Bacteroidetes). The UC model group was significantly different from the control group, with 1308 differentially expressed species with abundance changes greater than or equal to 2-fold. (2) The proportion of the fecal flora in the UC group decreased by 37.5% in the Firmicutes and increased by 14.29% in the proportion of Proteobacteria compared to the control group before treatment. (3) The significantly enriched and increased signaling pathways screened were the 'arachidonic acid metabolic pathway' and the 'phagosomal pathway', which both showed a decreasing trend after drug administration. (4) Based on the causal relationship between different OTUs and the UC model/PE&AFWE administration, screening for directly relevant OTU networks, the UC group was found to directly affect OTU69, followed by a cascade of effects on OTU12, OTU121, OTU93, and OTU7, which may be the pathway of action that initiated the pathological changes in normal mice. (5) We identified a causal relationship between common differentially expressed OTUs and PE&AFWE and UC in the pre- and post-PE&AFWE-treated groups. Thereby, we learned that PE&AFWE can directly affect OTU90, after which it inhibits UC, inhibiting the activity of arachidonic acid metabolic pathway by affecting OTU118, which in turn inhibits the colonization of gut microbiota by OTU93 and OTU7. (6) Histopathological observation and scoring (HS) of the colon showed that there was a significant difference between the model group and the control group (p < 0.001), and that there was a significant recovery in both the sulfasalazine (SASP)and the PE&AFWE groups after the administration of the drug (p < 0.0001).

CONCLUSION: We demonstrated causal effects and inflammatory metabolic pathways in gut microbiota dysbiosis and IBD, with five opportunistic pathogens directly contributing to IBD. PE&AFWE reduced the abundance of proteobacteria in the gut microbiota, and histopathology showed significant improvement.},
}

@article {pmid38664737,
year = {2024},
author = {Dang, YR and Cha, QQ and Liu, SS and Wang, SY and Li, PY and Li, CY and Wang, P and Chen, XL and Tian, JW and Xin, Y and Chen, Y and Zhang, YZ and Qin, QL},
title = {Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {77},
pmid = {38664737},
issn = {2049-2618},
mesh = {*Polysaccharides/metabolism ; *Seawater/microbiology ; *Phytoplankton/metabolism/genetics ; *Nutrients/metabolism ; *Peptidoglycan/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenomics ; Microbiota ; },
abstract = {BACKGROUND: The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes.

RESULTS: In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench.

CONCLUSIONS: Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.},
}

*Polysaccharides/metabolism
*Seawater/microbiology
*Phytoplankton/metabolism/genetics
*Nutrients/metabolism
*Peptidoglycan/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Metagenomics
Microbiota

@article {pmid38664617,
year = {2024},
author = {Vergine, M and Vita, F and Casati, P and Passera, A and Ricciardi, L and Pavan, S and Aprile, A and Sabella, E and De Bellis, L and Luvisi, A},
title = {Characterization of the olive endophytic community in genotypes displaying a contrasting response to Xylella fastidiosa.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {337},
pmid = {38664617},
issn = {1471-2229},
mesh = {*Olea/microbiology ; *Xylella/physiology/genetics ; *Endophytes/physiology/genetics ; *Genotype ; *Plant Diseases/microbiology ; Microbiota ; Bacteria/genetics/classification ; Fungi/physiology/genetics ; },
abstract = {BACKGROUND: Endophytes mediate the interactions between plants and other microorganisms, and the functional aspects of interactions between endophytes and their host that support plant-growth promotion and tolerance to stresses signify the ecological relevance of the endosphere microbiome. In this work, we studied the bacterial and fungal endophytic communities of olive tree (Olea europaea L.) asymptomatic or low symptomatic genotypes sampled in groves heavily compromised by Xylella fastidiosa subsp. pauca, aiming to characterize microbiota in genotypes displaying differential response to the pathogen.

RESULTS: The relationships between bacterial and fungal genera were analyzed both separately and together, in order to investigate the intricate correlations between the identified Operational Taxonomic Units (OTUs). Results suggested a dominant role of the fungal endophytic community compared to the bacterial one, and highlighted specific microbial taxa only associated with asymptomatic or low symptomatic genotypes. In addition, they indicated the occurrence of well-adapted genetic resources surviving after years of pathogen pressure in association with microorganisms such as Burkholderia, Quambalaria, Phaffia and Rhodotorula.

CONCLUSIONS: This is the first study to overview endophytic communities associated with several putatively resistant olive genotypes in areas under high X. fastidiosa inoculum pressure. Identifying these negatively correlated genera can offer valuable insights into the potential antagonistic microbial resources and their possible development as biocontrol agents.},
}

*Olea/microbiology
*Xylella/physiology/genetics
*Endophytes/physiology/genetics
*Genotype
*Plant Diseases/microbiology
Microbiota
Bacteria/genetics/classification
Fungi/physiology/genetics

@article {pmid38664512,
year = {2024},
author = {Ahammad, I and Bhattacharjee, A and Chowdhury, ZM and Rahman, A and Hossain, MU and Dewan, G and Talukder, S and Das, KC and Keya, CA and Salimullah, M},
title = {Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {500},
pmid = {38664512},
issn = {2399-3642},
support = {MoST-2020//Ministry of Science and Technology, Government of the People's Republic of Bangladesh (Ministry of Science and Technology)/ ; },
mesh = {Bangladesh ; Humans ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Ethnicity ; Bacteria/genetics/classification ; Female ; Adult ; Male ; Indigenous Peoples ; *South Asian People ; },
abstract = {Ethnicity has a significant role in shaping the composition of the gut microbiome, which has implications in human physiology. This study intends to investigate the gut microbiome of Bengali people as well as several indigenous ethnicities (Chakma, Marma, Khyang, and Tripura) residing in the Chittagong Hill Tracts areas of Bangladesh. Following fecal sample collection from each population, part of the bacterial 16 s rRNA gene was amplified and sequenced using Illumina NovaSeq platform. Our findings indicated that Bangladeshi gut microbiota have a distinct diversity profile when compared to other countries. We also found out that Bangladeshi indigenous communities had a higher Firmicutes to Bacteroidetes ratio than the Bengali population. The investigation revealed an unclassified bacterium that was differentially abundant in Bengali samples while the genus Alistipes was found to be prevalent in Chakma samples. Further research on these bacteria might help understand diseases associated with these populations. Also, the current small sample-sized pilot study hindered the comprehensive understanding of the gut microbial diversity of the Bangladeshi population and its potential health implications. However, our study will help establish a basic understanding of the gut microbiome of the Bangladeshi population.},
}

Bangladesh
Humans
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
Feces/microbiology
Ethnicity
Bacteria/genetics/classification
Female
Adult
Male
Indigenous Peoples
*South Asian People

@article {pmid38664490,
year = {2024},
author = {Kolobaric, A and Andreescu, C and Jašarević, E and Hong, CH and Roh, HW and Cheong, JY and Kim, YK and Shin, TS and Kang, CS and Kwon, CO and Yoon, SY and Hong, SW and Aizenstein, HJ and Karim, HT and Son, SJ},
title = {Gut microbiome predicts cognitive function and depressive symptoms in late life.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {38664490},
issn = {1476-5578},
abstract = {Depression in older adults with cognitive impairment increases progression to dementia. Microbiota is associated with current mood and cognition, but the extent to which it predicts future symptoms is unknown. In this work, we identified microbial features that reflect current and predict future cognitive and depressive symptoms. Clinical assessments and stool samples were collected from 268 participants with varying cognitive and depressive symptoms. Seventy participants underwent 2-year follow-up. Microbial community diversity, structure, and composition were assessed using high-resolution 16 S rRNA marker gene sequencing. We implemented linear regression to characterize the relationship between microbiome composition, current cognitive impairment, and depressive symptoms. We leveraged elastic net regression to discover features that reflect current or future cognitive function and depressive symptoms. Greater microbial community diversity associated with lower current cognition in the whole sample, and greater depression in participants not on antidepressants. Poor current cognitive function associated with lower relative abundance of Bifidobacterium, while greater GABA degradation associated with greater current depression severity. Future cognitive decline associated with lower cognitive function, lower relative abundance of Intestinibacter, lower glutamate degradation, and higher baseline histamine synthesis. Future increase in depressive symptoms associated with higher baseline depression and anxiety, lower cognitive function, diabetes, lower relative abundance of Bacteroidota, and lower glutamate degradation. Our results suggest cognitive dysfunction and depression are unique states with an overall biological effect detectable through gut microbiota. The microbiome may present a noninvasive readout and prognostic tool for cognitive and psychiatric states.},
}

@article {pmid38664425,
year = {2024},
author = {Chui, ZSW and Chan, LML and Zhang, EWH and Liang, S and Choi, EPH and Lok, KYW and Tun, HM and Kwok, JYY},
title = {Effects of microbiome-based interventions on neurodegenerative diseases: a systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9558},
pmid = {38664425},
issn = {2045-2322},
mesh = {Humans ; *Neurodegenerative Diseases/microbiology/therapy ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation/methods ; Probiotics/therapeutic use ; Microbiota ; },
abstract = {Neurodegenerative diseases (NDDs) are characterized by neuronal damage and progressive loss of neuron function. Microbiome-based interventions, such as dietary interventions, biotics, and fecal microbiome transplant, have been proposed as a novel approach to managing symptoms and modulating disease progression. Emerging clinical trials have investigated the efficacy of interventions modulating the GM in alleviating or reversing disease progression, yet no comprehensive synthesis have been done. A systematic review of the literature was therefore conducted to investigate the efficacy of microbiome-modulating methods. The search yielded 4051 articles, with 15 clinical trials included. The overall risk of bias was moderate in most studies. Most microbiome-modulating interventions changed the GM composition. Despite inconsistent changes in GM composition, the meta-analysis showed that microbiome-modulating interventions improved disease burden (SMD, - 0.57; 95% CI - 0.93 to - 0.21; I[2] = 42%; P = 0.002) with a qualitative trend of improvement in constipation. However, current studies have high methodological heterogeneity and small sample sizes, requiring more well-designed and controlled studies to elucidate the complex linkage between microbiome, microbiome-modulating interventions, and NDDs.},
}

Humans
*Neurodegenerative Diseases/microbiology/therapy
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation/methods
Probiotics/therapeutic use
Microbiota

@article {pmid38664180,
year = {2024},
author = {Knorr, J and Lone, Z and Werneburg, G and Adler, A and Agudelo, J and Suryavanshi, M and Campbell, RA and Ericson, K and Qiu, H and Bajic, P and Haber, GP and Weight, CJ and Ahern, PP and Almassi, N and Miller, AW and Lee, BH},
title = {An exploratory study investigating the impact of the bladder tumor microbiome on Bacillus Calmette Guerin (BCG) response in non-muscle invasive bladder cancer.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2024.04.011},
pmid = {38664180},
issn = {1873-2496},
abstract = {PURPOSE: Intravesical Bacillus Calmette-Guerin (BCG) is standard of care for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). The effect of the bladder microbiome on response to BCG is unclear. We sought to characterize the microbiome of bladder tumors in BCG-responders and non-responders and identify potential mechanisms that drive treatment response.

MATERIALS AND METHODS: Patients with archival pre-treatment biopsy samples (2012-2018) were identified retrospectively. Prospectively, urine and fresh tumor samples were collected from individuals with high-risk NMIBC (2020-2023). BCG response was defined as tumor-free 2 years from induction therapy. Extracted DNA was sequenced for 16S rRNA and shotgun metagenomics. Primary outcomes were species richness (α-diversity) and microbial composition (β-diversity). Paired t-tests were performed for α-diversity (Observed species/Margalef). Statistical analysis for β-diversity (weighted and unweighted UniFrac distances, weighted Bray-Curtis dissimilarity) were conducted through Permanova, with 999 permutations.

RESULTS: Microbial species richness (P < 0.001) and composition (P = 0.001) differed between BCG responders and non-responders. Lactobacillus spp. were significantly enriched in BCG-responders. Shotgun metagenomics identified possible mechanistic pathways such as assimilatory sulfate reduction.

CONCLUSION: A compositional difference exists in the tumor microbiome of BCG responders and non-responders with Lactobacillus having increased abundance in BCG responders.},
}

@article {pmid38663906,
year = {2024},
author = {Zhu, J and Fan, X and Ding, L and Song, T},
title = {Idiopathic gingival fibromatosis and primary analysis of dominant bacteria in subgingival biofilm: a case report.},
journal = {The Journal of international medical research},
volume = {52},
number = {4},
pages = {3000605241245302},
pmid = {38663906},
issn = {1473-2300},
mesh = {Humans ; *Biofilms/growth & development ; *Fibromatosis, Gingival/diagnosis/pathology/microbiology ; *Gingiva/microbiology/pathology ; Female ; Adult ; Male ; Bacteria/isolation & purification ; Gingivectomy/methods ; },
abstract = {Idiopathic gingival fibromatosis (IGF), a rare fibroproliferative disease of unknown etiology, affects gingival tissue and has substantial adverse effects on patients. Therefore, the pathogenesis of IGF requires more extensive and in-depth research. In this case, a patient with confirmed IGF underwent initial nonsurgical periodontal therapy and gingivectomy, and the prognosis was good. The patient had no loss of periodontal attachment but had a history of swelling and bleeding of the gingiva prior to fibrous enlargement, which prompted further investigation. We explored the patient's subgingival microbiome and found a high abundance of periodontal pathogens. Gingival tissue biopsy revealed abundant fibrous tissue containing multiple inflammatory cell infiltrates. These results suggest that gingival inflammation secondary to periodontal pathogens can contribute to IGF onset.},
}

Humans
*Biofilms/growth & development
*Fibromatosis, Gingival/diagnosis/pathology/microbiology
*Gingiva/microbiology/pathology
Female
Adult
Male
Bacteria/isolation & purification
Gingivectomy/methods

@article {pmid38663780,
year = {2024},
author = {Dinat, S and Orchard, A and Van Vuuren, S},
title = {Antimicrobial activity of Southern African medicinal plants on Helicobacter pylori and Lactobacillus species.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {118238},
doi = {10.1016/j.jep.2024.118238},
pmid = {38663780},
issn = {1872-7573},
abstract = {Numerous medicinal plants have been used traditionally in South Africa for gastric ulcer treatment. Helicobacter pylori is known for causing inflammation and the onset of gastric ulcers. While several studies explored medicinal plants against H. pylori, investigation of medicinal plants used for gastric ulcers has been neglected, as well as the effects these plants would have on bacteria occurring naturally in the gut microbiome.

AIM OF THE STUDY: This study aimed to investigate Southern African medicinal plants used traditionally for treating gastric ulcers against H. pylori and against Lactobacillus species, as well as the effects of these plants combined with the Lactobacillus species against H. pylori.

METHODOLOGY: Based on evidence from the ethnobotanical literature, 21 plants were collected. Their antimicrobial activity was assessed against five clinical H. pylori strains, and in combination with each of three Lactobacillus species, using the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) broth microdilution assays. Toxicity was assessed using the brine shrimp lethality assay.

RESULTS: Noteworthy activity was observed against at least one H. pylori strain for 12 plant species. The lowest mean MICs were from organic extracts of Carissa edulis Vahl (0.18 mg/mL) and Chironia baccifera L. (0.20 mg/mL), and aqueous extracts of Sansevieria hyacinthoides (L.) Druce (0.26 mg/mL) and Dodonaea viscosa Jacq. (0.30 mg/mL). Aqueous extracts of the investigated plants were combined with Lactobacillus species, and the majority of combinations showed increased antimicrobial activity compared with the extracts alone. Combinations of Lactobacillus rhamnosus with 18 of the 21 aqueous plant extracts showed at least a two-fold decrease in the mean MBC against all H. pylori strains tested. Lactobacillus acidophilus combined with either Protea repens L., Carpobrotus edulis (L.) L.Bolus or Warburgia salutaris (Bertol.f.) Chiov. aqueous extracts had the best anti-H. pylori activity (mean MBCs of 0.10 mg/mL for each combination). Only four organic and one aqueous extract(s) were considered toxic.

CONCLUSION: These results highlight the potential of medicinal plants to inhibit H. pylori growth and their role in traditional treatments for the management of ulcers. The results also indicate that aqueous extracts of these plants do not hinder the growth of bacteria that occur naturally in the gut microbiome and play a role in maintaining gut health, as well as show the potential benefit of including Lactobacillus species in treatment as potentiators of H. pylori activity.},
}

@article {pmid38663650,
year = {2024},
author = {Fang, H and Hou, Q and Zhang, W and Su, Z and Zhang, J and Li, J and Lin, J and Wang, Z and Yu, X and Yang, Y and Wang, Q and Li, X and Li, Y and Hu, L and Li, S and Wang, X and Liao, L},
title = {Fecal Microbiota Transplantation Improves Clinical Symptoms of Fibromyalgia: An open-label, Randomized, Nonplacebo-Controlled Study.},
journal = {The journal of pain},
volume = {},
number = {},
pages = {104535},
doi = {10.1016/j.jpain.2024.104535},
pmid = {38663650},
issn = {1528-8447},
abstract = {Fibromyalgia (FM) is a complex and poorly understood disorder characterized by chronic and widespread musculoskeletal pain, of which the etiology remains unknown. Now, the disorder of the gut microbiome is considered as one of the main causes of FM. This study was aimed to investigate the potential benefits of fecal microbiota transplantation (FMT) in patients with FM. A total of 45 patients completed this open-label randomized, nonplacebo-controlled clinical study. The Numerical Rating Scale (NRS) scores in the FMT group were slightly lower than the control group at 1 month (P> 0.05), and they decreased significantly at 2, 3, 6, and 12 months after treatment (P < 0.001). Besides, compared with the control group, the Widespread Pain Index (WPI), Symptom Severity (SS), Hospital Anxiety and Depression Scale (HADS) and Pittsburgh Sleep Quality Index (PSQI) scores were significantly lower in the FMT group at different time points (P < 0.001). After 6 months of treatment, there was a significant increase in serotonin (5-HT) and gamma-aminobutyric acid (GABA) levels (P < 0.001), while glutamate levels significantly decreased in the FMT group (P < 0.001). The total effective rate was higher in the FMT group (90.9%) compared to the control group (56.5%) after 6 months of treatment (P < 0.05). FMT can effectively improve the clinical symptoms of FM. With the close relations between the changes of neurotransmitters and FM, certain neurotransmitters may serve as a diagnostic marker or potential target for FM patients. PERSPECTIVE: Fecal microbiota transplantation (FMT) is a novel therapy that aims to restore the gut microbial balance and modulate the gut-brain axis. It is valuable to further explore the therapeutic effect of FMT on FM. Furthermore, certain neurotransmitters may become a diagnostic marker or a new therapeutic target for FM patients.},
}

@article {pmid38663637,
year = {2024},
author = {Mao, X and Li, J and Meng, E and Jin, W and Han, W},
title = {Responses of physiological, microbiome and lipid metabolism to lignocellulose wastes in gut of yellow mealworm (Tenebrio molitor).},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130731},
doi = {10.1016/j.biortech.2024.130731},
pmid = {38663637},
issn = {1873-2976},
abstract = {There is limited research on physiological and degradation mechanisms of yellow mealworm, a novel organic waste converter, in processing lignocellulosic wastes. This study has selected two types of lignocellulosic wastes, distillers' grains (DG) and maize straw (MS), to feed yellow mealworms. This study investigated the effects of lignocellulosic wastes on the growth, antioxidant system, microbiome, and lipidome of yellow mealworms. The relative growth of lignocellulosic waste group was not significantly different from wheat bran. The antioxidant level was elevated in DG. MS was significantly enriched in cellulose-degrading bacteria in the gut and was accompanied by disturbances in lipid metabolism. The correlation coefficients were used to construct a network connecting diet, microbiota, and lipids. The correlation analysis indicated that two sphingolipids, hexylglyceramide and dihydroglyceramide, were strongly and positively linked with the dominating species. This study provides comprehensive information on physiological and mechanism of mealworms in process of treating lignocellulosic waste.},
}

@article {pmid38663293,
year = {2024},
author = {Li, N and Wang, X and Li, X and Yi, S and Guo, Y and Wu, N and Lin, H and Zhong, B and Wu, WM and He, Y},
title = {Anthropogenic and biological activities elevate microplastics pollution in headwater ecosystem of Yangtze tributaries in Hindu Kush-Himalayan region.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134395},
doi = {10.1016/j.jhazmat.2024.134395},
pmid = {38663293},
issn = {1873-3336},
abstract = {Microplastic (MP) pollution is widely spread in oceans, freshwater, and terrestrial environments but MPs in mountainous headwater ecosystem are rarely reported. This study focuses on the headwater of Yangtze tributaries of the Hindu Kush-Himalayan (HKH) region. Five streams at elevations of 900 to 3300 m were selected to investigate the distribution of MPs in water and sediments across altitudes. MPs were found in all water and sediment samples from top stream zone nearly in absence of anthropogenic activity, low anthropogenic zone, and high anthropogenic zone, increased from 12-54, 81-185 to 334-847 items/L, and 2-35, 26-84 to 124-428 items/kg, respectively. This elevation-dependent MP distribution indicated that as elevation decreased, anthropogenic activities intensified and increased MPs input and their abundance, size, and diversity. Notably, hydraulic projects, such as damming, were identified as potential barriers to the migration of MPs downstream. Microbiome analyses revealed the presence of bacterial genes associated with plastic biodegradation in all sediment samples. The study indicates that Shangri-la mountainous streams have been polluted with MPs for years with potential risk of generation of nano-sized particles via natural fragmentation and biodegradation, and thus raises concern on MPs pollution in headwaters streams in mountainous regions.},
}

@article {pmid38662827,
year = {2024},
author = {Giampazolias, E and Pereira da Costa, M and Lam, KC and Lim, KHJ and Cardoso, A and Piot, C and Chakravarty, P and Blasche, S and Patel, S and Biram, A and Castro-Dopico, T and Buck, MD and Rodrigues, RR and Poulsen, GJ and Palma-Duran, SA and Rogers, NC and Koufaki, MA and Minutti, CM and Wang, P and Vdovin, A and Frederico, B and Childs, E and Lee, S and Simpson, B and Iseppon, A and Omenetti, S and Kelly, G and Goldstone, R and Nye, E and Suárez-Bonnet, A and Priestnall, SL and MacRae, JI and Zelenay, S and Patil, KR and Litchfield, K and Lee, JC and Jess, T and Goldszmid, RS and Reis E Sousa, C},
title = {Vitamin D regulates microbiome-dependent cancer immunity.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6694},
pages = {428-437},
doi = {10.1126/science.adh7954},
pmid = {38662827},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Vitamin D/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Bacteroides fragilis ; Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Neoplasms/immunology/microbiology ; Mice, Inbred C57BL ; Immunotherapy ; Female ; Intestinal Mucosa/immunology/microbiology/metabolism ; Male ; },
abstract = {A role for vitamin D in immune modulation and in cancer has been suggested. In this work, we report that mice with increased availability of vitamin D display greater immune-dependent resistance to transplantable cancers and augmented responses to checkpoint blockade immunotherapies. Similarly, in humans, vitamin D-induced genes correlate with improved responses to immune checkpoint inhibitor treatment as well as with immunity to cancer and increased overall survival. In mice, resistance is attributable to the activity of vitamin D on intestinal epithelial cells, which alters microbiome composition in favor of Bacteroides fragilis, which positively regulates cancer immunity. Our findings indicate a previously unappreciated connection between vitamin D, microbial commensal communities, and immune responses to cancer. Collectively, they highlight vitamin D levels as a potential determinant of cancer immunity and immunotherapy success.},
}

Animals
Mice
*Vitamin D/pharmacology
*Gastrointestinal Microbiome/drug effects
Humans
*Bacteroides fragilis
Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Neoplasms/immunology/microbiology
Mice, Inbred C57BL
Immunotherapy
Female
Intestinal Mucosa/immunology/microbiology/metabolism
Male

@article {pmid38662573,
year = {2024},
author = {Bosch, TCG and Wigley, M and Colomina, B and Bohannan, B and Meggers, F and Amato, KR and Azad, MB and Blaser, MJ and Brown, K and Dominguez-Bello, MG and Ehrlich, SD and Elinav, E and Finlay, BB and Geddie, K and Geva-Zatorsky, N and Giles-Vernick, T and Gros, P and Guillemin, K and Haraoui, LP and Johnson, E and Keck, F and Lorimer, J and McFall-Ngai, MJ and Nichter, M and Pettersson, S and Poinar, H and Rees, T and Tropini, C and Undurraga, EA and Zhao, L and Melby, MK},
title = {The potential importance of the built-environment microbiome and its impact on human health.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {20},
pages = {e2313971121},
doi = {10.1073/pnas.2313971121},
pmid = {38662573},
issn = {1091-6490},
support = {HMB program//Canadian Institute for Advanced Research (ICRA)/ ; },
mesh = {Humans ; *Built Environment ; *Microbiota/physiology ; Animals ; },
abstract = {There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built structures host complex ecologies of microorganisms that are only starting to be mapped. These microbial ecologies of built environments are directly and interdependently affected by social, spatial, and technological norms. Advances in technology have made these organisms visible and forced the scientific community and architects to rethink gene-environment and microbe interactions respectively. Thus, built environment design must consider the microbiome, and research involving host-microbiome interaction must consider the built-environment. This paradigm shift becomes increasingly important as evidence grows that contemporary built environments are steadily reducing the microbial diversity essential for human health, well-being, and resilience while accelerating the symptoms of human chronic diseases including environmental allergies, and other more life-altering diseases. New models of design are required to balance maximizing exposure to microbial diversity while minimizing exposure to human-associated diseases. Sustained trans-disciplinary research across time (evolutionary, historical, and generational) and space (cultural and geographical) is needed to develop experimental design protocols that address multigenerational multispecies health and health equity in built environments.},
}

Humans
*Built Environment
*Microbiota/physiology
Animals

@article {pmid38662328,
year = {2024},
author = {Snelson, M and Vanuytsel, T and Marques, FZ},
title = {Breaking the Barrier: The Role of Gut Epithelial Permeability in the Pathogenesis of Hypertension.},
journal = {Current hypertension reports},
volume = {},
number = {},
pages = {},
pmid = {38662328},
issn = {1534-3111},
support = {106698/WT_/Wellcome Trust/United Kingdom ; 105663/WT_/Wellcome Trust/United Kingdom ; },
abstract = {PURPOSE OF THE REVIEW: To review what intestinal permeability is and how it is measured, and to summarise the current evidence linking altered intestinal permeability with the development of hypertension.

RECENT FINDINGS: Increased gastrointestinal permeability, directly measured in vivo, has been demonstrated in experimental and genetic animal models of hypertension. This is consistent with the passage of microbial substances to the systemic circulation and the activation of inflammatory pathways. Evidence for increased gut permeability in human hypertension has been reliant of a handful of blood biomarkers, with no studies directly measuring gut permeability in hypertensive cohorts. There is emerging literature that some of these putative biomarkers may not accurately reflect permeability of the gastrointestinal tract. Data from animal models of hypertension support they have increased gut permeability; however, there is a dearth of conclusive evidence in humans. Future studies are needed that directly measure intestinal permeability in people with hypertension.},
}

@article {pmid38662310,
year = {2024},
author = {Keum, GB and Pandey, S and Kim, ES and Doo, H and Kwak, J and Ryu, S and Choi, Y and Kang, J and Kim, S and Kim, HB},
title = {Understanding the Diversity and Roles of the Ruminal Microbiome.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38662310},
issn = {1976-3794},
support = {NRF-2019M3A9F3065227//Ministry of Education/ ; },
abstract = {The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.},
}

@article {pmid38662051,
year = {2024},
author = {Reuben, RC and Torres, C},
title = {Bacteriocins: potentials and prospects in health and agrifood systems.},
journal = {Archives of microbiology},
volume = {206},
number = {5},
pages = {233},
pmid = {38662051},
issn = {1432-072X},
support = {101034288//H2020 Marie Skłodowska-Curie Actions/ ; 101034288//H2020 Marie Skłodowska-Curie Actions/ ; },
mesh = {*Bacteriocins/metabolism/pharmacology ; Humans ; Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism/drug effects/genetics ; Food Microbiology ; Microbiota ; Food Packaging ; Food Safety ; },
abstract = {Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.},
}

*Bacteriocins/metabolism/pharmacology
Humans
Animals
*Anti-Bacterial Agents/pharmacology
Bacteria/metabolism/drug effects/genetics
Food Microbiology
Microbiota
Food Packaging
Food Safety

@article {pmid38661414,
year = {2024},
author = {Alexander, CC and Gaudier-Diaz, MM and Kleinschmit, AJ and Dihle, PJ and Salger, SA and Vega, N and Robertson, SD},
title = {A case study to engage students in the research design and ethics of high-throughput metagenomics.},
journal = {Journal of microbiology & biology education},
volume = {25},
number = {1},
pages = {e0007423},
pmid = {38661414},
issn = {1935-7877},
abstract = {Case studies present students with an opportunity to learn and apply course content through problem solving and critical thinking. Supported by the High-throughput Discovery Science & Inquiry-based Case Studies for Today's Students (HITS) Research Coordination Network, our interdisciplinary team designed, implemented, and assessed two case study modules entitled "You Are What You Eat." Collectively, the case study modules present students with an opportunity to engage in experimental research design and the ethical considerations regarding microbiome research and society. In this manuscript, we provide instructors with tools for adopting or adapting the research design and/or the ethics modules. To date, the case has been implemented using two modalities (remote and in-person) in three courses (Microbiology, Physiology, and Neuroscience), engaging over 200 undergraduate students. Our assessment data demonstrate gains in content knowledge and students' perception of learning following case study implementation. Furthermore, when reflecting on our experiences and student feedback, we identified ways in which the case study could be modified for different settings. In this way, we hope that the "You Are What You Eat" case study modules can be implemented widely by instructors to promote problem solving and critical thinking in the traditional classroom or laboratory setting when discussing next-generation sequencing and/or metagenomics research.},
}

@article {pmid38661383,
year = {2023},
author = {Bechberger, M and Eigenbrod, T and Boutin, S and Heeg, K and Bode, KA},
title = {IL-1β knockout increases the intestinal abundancy of Akkermansia muciniphila.},
journal = {Beneficial microbes},
volume = {14},
number = {4},
pages = {361-370},
doi = {10.1163/18762891-20220042},
pmid = {38661383},
issn = {1876-2891},
mesh = {Animals ; Mice ; *Akkermansia/genetics ; Colon/microbiology ; *Gastrointestinal Microbiome ; *Interleukin-1beta/genetics/metabolism ; Intestinal Mucosa/microbiology/metabolism ; Mice, Inbred C57BL ; Ribonuclease, Pancreatic/genetics/metabolism ; },
abstract = {The proinflammatory cytokine interleukin-1β (IL-1β) is known to be upregulated in patients suffering from metabolic syndrome. IL-1β contributes to insulin resistance in obesity and type 2 diabetes, yet its influence on the intestinal microbiome is incompletely understood. The data presented here demonstrate that mice genetically deficient in IL-1β show a specific alteration of intestinal colonisation of a small group of bacteria. Especially Akkermansia muciniphila, a bacterium reported to be inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation, showed increased colonisation in IL-1β knockout mice. In comparative microarray analysis from mucus scrapings of the colon mucosa of IL-1β knockout and wildtype mice, angiogenin 4 mRNA was strongly reduced in IL-1β knockout animals. Since the presence of angiogenin 4 in the culture medium showed a significant growth inhibition on A. muciniphila which was not detectable for other bacteria tested, IL-1β induced expression of angiogenin 4 is a strong candidate to be responsible for the IL-1β induced suppression of A. muciniphila colonisation. Thus, the data presented here indicate that IL-1β might be the lacking link between inflammation and suppression of A. muciniphila abundance as observed in a variety of chronic inflammatory disorders.},
}

Animals
Mice
*Akkermansia/genetics
Colon/microbiology
*Gastrointestinal Microbiome
*Interleukin-1beta/genetics/metabolism
Intestinal Mucosa/microbiology/metabolism
Mice, Inbred C57BL
Ribonuclease, Pancreatic/genetics/metabolism

@article {pmid38661361,
year = {2023},
author = {Hendrickx, DM and An, R and Boeren, S and Mutte, SK and , and Wopereis, H and Belzer, C},
title = {Trackability of proteins from probiotic Bifidobacterium spp. in the gut using metaproteomics.},
journal = {Beneficial microbes},
volume = {14},
number = {3},
pages = {269-280},
doi = {10.1163/18762891-20220137},
pmid = {38661361},
issn = {1876-2891},
mesh = {Humans ; *Feces/microbiology ; *Bifidobacterium/genetics/metabolism ; *Probiotics ; *Gastrointestinal Microbiome ; Infant ; *Proteomics ; *Synbiotics ; *RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Prebiotics/analysis ; Infant Formula ; Male ; DNA, Bacterial/genetics ; Female ; },
abstract = {Beneficial effects of Bifidobacterium spp. on gut microbiota development and infant health have been reported earlier. Therefore, supplementation of infant formulas with probiotic bifidobacteria, as well as prebiotics stimulating bifidobacterial growth, has been proposed. Here, we studied the faecal microbiome of infants supplemented with specialized nutrition, of which some received a standard amino acid-based formula (AAF) and others an AAF with a specific mixture of prebiotics and a probiotic (synbiotics) using metaproteomics and 16S rRNA gene sequencing. Faecal samples were taken at baseline, as well as after 6 and 12 months fed with the specialized formula. The aim was to compare microbial differences between infants treated with the standard AAF and those who received the additional synbiotics. Our findings show that infants who received AAF with synbiotics have significantly higher levels of Bifidobacteriaceae DNA as well as significantly increased levels of Coriobacteriaceae proteins, over time. Moreover, at visit 12 months higher levels of some bifidobacterial carbohydrate-active enzymes, known to metabolize oligosaccharides, were observed in the synbiotic group compared to the non-synbiotic group. The results indicate that the synbiotics provided in our study are trackable in faecal samples on the DNA and protein level during the intervention period.},
}

Humans
*Feces/microbiology
*Bifidobacterium/genetics/metabolism
*Probiotics
*Gastrointestinal Microbiome
Infant
*Proteomics
*Synbiotics
*RNA, Ribosomal, 16S/genetics
Bacterial Proteins/genetics/metabolism
Prebiotics/analysis
Infant Formula
Male
DNA, Bacterial/genetics
Female

@article {pmid38661353,
year = {2023},
author = {Zhu, Z and Hu, C and Liu, Y and Wang, F and Zhu, B},
title = {Inulin has a beneficial effect by modulating the intestinal microbiome in a BALB/c mouse model.},
journal = {Beneficial microbes},
volume = {14},
number = {4},
pages = {371-383},
doi = {10.1163/18762891-20220094},
pmid = {38661353},
issn = {1876-2891},
mesh = {Animals ; *Inulin/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Mice, Inbred BALB C ; Mice ; *Ovalbumin/immunology ; *Disease Models, Animal ; *Immunoglobulin E/blood/immunology ; *Food Hypersensitivity/microbiology/immunology/drug therapy ; Female ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/classification/drug effects/isolation & purification/genetics ; Immunoglobulin A, Secretory ; Immunoglobulin A/blood ; },
abstract = {Food allergy is an important health problem that affects human quality of life and socioeconomic development, and its treatment requires improvement. Intestinal flora dysbiosis is closely associated with food allergies. A sensitised mouse model was established by the intraperitoneal injection of ovalbumin (OVA). The mice were randomly divided into four groups: control, model, high-dose (H), and low-dose (L) inulin. The mice were administered water containing different concentrations of inulin four weeks before the OVA injection. Body weight changes were monitored. After the last OVA injection, the mice were scored for allergic reactions. The levels of total immunoglobulin E (IgE) and diamine oxidase (DAO) in the serum and secretory IgA (sIgA) in the small intestinal mucus were measured, and 16S rRNA sequencing of the faecal flora was performed to evaluate microbial parameters. The intestinal flora biomarkers, correlations between them, and biochemical indicators were analysed. Inulin treatment had no effect on the body weight of OVA-sensitised mice but attenuated allergic reactions and intestinal injury in mice. Compared with the control group, the model group had significantly higher levels of serum DAO and IgE and significantly lower levels of intestinal mucus IgA. IgA levels in the intestinal mucus of mice treated with inulin prior to OVA sensitisation were higher than those in non-inulin-treated OVA-sensitised mice. Furthermore, analysis of operational taxonomic units showed that inulin treatment decreased the abundance of Alloprevotella, Rikenellaceae RC9, Eubacterium siraeum, and Eubacterium xylanophilum, and increased the abundance of Blautia and Lachnospiraceae. Serum DAO levels were positively associated with Eubacterium siraeum, Alloprevotella, Eubacterium xylanophilum, and Odoribacter and negatively associated with Blautia, Tyzzerella, Alistipes, Desulfovibrionaceae, and Ruminococcaceae UCG005. In addition, IgE levels were positively associated with Eubacterium siraeum, Alloprevotella, Eubacterium xylanophilum, Odoribacter, and Citrobacter and negatively associated with Blautia, unclassified Ruminococcaceae, and Alistipes. IgA exhibited significant positive correlation with Blautia, norank_f_Eubacterium coprostanoligenes, Alistipes, norank Desulfovibrionaceae, Muribaculum, and Ruminococcaceae U C G 005 and significant negative correlation with Eubacterim siraeum, Eubacterium xylanophilum, Odoribacter, and Citrobacter. Inulin exerts a protective effect against food allergies in mice, which is partially mediated by alterations in the gut microbiota.},
}

Animals
*Inulin/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Mice, Inbred BALB C
Mice
*Ovalbumin/immunology
*Disease Models, Animal
*Immunoglobulin E/blood/immunology
*Food Hypersensitivity/microbiology/immunology/drug therapy
Female
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Bacteria/classification/drug effects/isolation & purification/genetics
Immunoglobulin A, Secretory
Immunoglobulin A/blood

@article {pmid38661345,
year = {2023},
author = {Jackson, PPJ and Wijeyesekera, A and Theis, S and Van Harsselaar, J and Rastall, RA},
title = {Effects of food matrix on the prebiotic efficacy of inulin-type fructans: a randomised trial.},
journal = {Beneficial microbes},
volume = {14},
number = {4},
pages = {317-334},
doi = {10.1163/18762891-20220120},
pmid = {38661345},
issn = {1876-2891},
mesh = {*Prebiotics ; *Inulin/pharmacology ; Humans ; *Bifidobacterium/genetics/drug effects ; *Feces/microbiology ; *Fructans/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Oryza ; Female ; Male ; Gastrointestinal Microbiome/drug effects ; Adult ; Chocolate ; Young Adult ; In Situ Hybridization, Fluorescence ; },
abstract = {Recently there is much debate in the scientific community over the impact of the food matrix on prebiotic efficacy of inulin-type fructans. Previous studies suggest that prebiotic selectivity of inulin-type fructans towards bifidobacteria is unaffected by the food matrix. Due to differences in study design, definitive conclusions cannot be drawn from these findings with any degree of certainty. In this randomised trial, we aimed to determine the effects that different food matrices had on the prebiotic efficacy of inulin-type fructans following a standardised 10-day, 4-arm, parallel, randomised protocol with inulin either in pure form or incorporated into shortbread biscuits, milk chocolate or a rice drink. Similar increases in Bifidobacterium counts were documented across all four interventions using both fluorescence in situ hybridisation (pure inulin: +0.63; shortbread: +0.59; milk chocolate: +0.65 and rice drink: +0.71 (log10 cells/g wet faeces) and 16S rRNA sequencing quantitative microbiome profiling data (pure inulin: +1.21 × 109; shortbread: +1.47 × 109; milk chocolate: +8.59 × 108 and rice drink: +1.04 × 109 (cells/g wet faeces) (all P ≤ 0.05). From these results, we can confirm that irrespective of the food matrix, the selectivity of inulin-type fructans towards Bifidobacterium is unaffected, yet the compositional make-up of the food matrix may have implications regarding wider changes in the microbiota.},
}

*Prebiotics
*Inulin/pharmacology
Humans
*Bifidobacterium/genetics/drug effects
*Feces/microbiology
*Fructans/pharmacology
*RNA, Ribosomal, 16S/genetics
Oryza
Female
Male
Gastrointestinal Microbiome/drug effects
Adult
Chocolate
Young Adult
In Situ Hybridization, Fluorescence

@article {pmid38661344,
year = {2024},
author = {Phan, J and Calvo, DC and Nair, D and Jain, S and Montagne, T and Dietsche, S and Blanchard, K and Treadwell, S and Adams, J and Krajmalnik-Brown, R},
title = {Precision synbiotics increase gut microbiome diversity and improve gastrointestinal symptoms in a pilot open-label study for autism spectrum disorder.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0050324},
doi = {10.1128/msystems.00503-24},
pmid = {38661344},
issn = {2379-5077},
abstract = {UNLABELLED: The efficacy of prebiotics and probiotics (synbiotics when combined) to improve symptoms associated with autism spectrum disorder (ASD) has shown considerable inter-study variation, likely due to the complex, heterogeneous nature of the disorder and its associated behavioral, developmental, and gastrointestinal symptoms. Here, we present a precision synbiotic supplementation study in 296 children and adults diagnosed with ASD versus 123 age-matched neurotypical controls. One hundred seventy ASD participants completed the study. Baseline and post-synbiotic assessment of ASD and gastrointestinal (GI) symptoms and deep metagenomic sequencing were performed. Within the ASD cohort, there were significant differences in microbes between subpopulations based on the social responsiveness scale (SRS2) survey (Prevotella spp., Bacteroides, Fusicatenibacter, and others) and gluten and dairy-free diets (Bifidobacterium spp., Lactococcus, Streptococcus spp., and others). At the baseline, the ASD cohort maintained a lower taxonomic alpha diversity and significant differences in taxonomic composition, metabolic pathways, and gene families, with a greater proportion of potential pathogens, including Shigella, Klebsiella, and Clostridium, and lower proportions of beneficial microbes, including Faecalibacterium compared to controls. Following the 3-month synbiotic supplementation, the ASD cohort showed increased taxonomic alpha diversity, shifts in taxonomy and metabolic pathway potential, and improvements in some ASD-related symptoms, including a significant reduction in GI discomfort and overall improved language, comprehension, cognition, thinking, and speech. However, the open-label study design may include some placebo effects. In summary, we found that precision synbiotics modulated the gut microbiome and could be used as supplementation to improve gastrointestinal and ASD-related symptoms.

IMPORTANCE: Autism spectrum disorder (ASD) is prevalent in 1 out of 36 children in the United States and contributes to health, financial, and psychological burdens. Attempts to identify a gut microbiome signature of ASD have produced varied results. The limited pre-clinical and clinical population sizes have hampered the success of these trials. To understand the microbiome associated with ASD, we employed whole metagenomic shotgun sequencing to classify microbial composition and genetic functional potential. Despite being one of the most extensive ASD post-synbiotic assessment studies, the results highlight the complexity of performing such a case-control supplementation study in this population and the potential for a future therapeutic approach in ASD.},
}

@article {pmid38661014,
year = {2024},
author = {Dalgard, F and Bewley, A},
title = {New insights to the mind-body connection: The importance of the brain-gut microbiome for inflammatory skin diseases.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {38},
number = {5},
pages = {784-785},
doi = {10.1111/jdv.19946},
pmid = {38661014},
issn = {1468-3083},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Brain-Gut Axis/physiology ; Skin Diseases/microbiology ; Brain ; },
}

Humans
*Gastrointestinal Microbiome/physiology
Brain-Gut Axis/physiology
Skin Diseases/microbiology
Brain

@article {pmid38660637,
year = {2024},
author = {Qi, JH and Huang, SL and Jin, SZ},
title = {Novel milestones for early esophageal carcinoma: From bench to bed.},
journal = {World journal of gastrointestinal oncology},
volume = {16},
number = {4},
pages = {1104-1118},
pmid = {38660637},
issn = {1948-5204},
abstract = {Esophageal cancer (EC) is the seventh most common cancer worldwide, and esophageal squamous cell carcinoma (ESCC) accounts for the majority of cases of EC. To effectively diagnose and treat ESCC and improve patient prognosis, timely diagnosis in the initial phase of the illness is necessary. This article offers a detailed summary of the latest advancements and emerging technologies in the timely identification of ECs. Molecular biology and epigenetics approaches involve the use of molecular mechanisms combined with fluorescence quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology (next-generation sequencing), and digital PCR technology to study endogenous or exogenous biomolecular changes in the human body and provide a decision-making basis for the diagnosis, treatment, and prognosis of diseases. The investigation of the microbiome is a swiftly progressing area in human cancer research, and microorganisms with complex functions are potential components of the tumor microenvironment. The intratumoral microbiota was also found to be connected to tumor progression. The application of endoscopy as a crucial technique for the early identification of ESCC has been essential, and with ongoing advancements in technology, endoscopy has continuously improved. With the advancement of artificial intelligence (AI) technology, the utilization of AI in the detection of gastrointestinal tumors has become increasingly prevalent. The implementation of AI can effectively resolve the discrepancies among observers, improve the detection rate, assist in predicting the depth of invasion and differentiation status, guide the pericancerous margins, and aid in a more accurate diagnosis of ESCC.},
}

@article {pmid38660491,
year = {2024},
author = {Serrage, HJ and O' Neill, CA and Uzunbajakava, NE},
title = {Illuminating microflora: shedding light on the potential of blue light to modulate the cutaneous microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1307374},
pmid = {38660491},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *Skin/microbiology/radiation effects ; *Light ; Skin Diseases/microbiology ; Dysbiosis/microbiology ; Animals ; Blue Light ; },
abstract = {Cutaneous diseases (such as atopic dermatitis, acne, psoriasis, alopecia and chronic wounds) rank as the fourth most prevalent human disease, affecting nearly one-third of the world's population. Skin diseases contribute to significant non-fatal disability globally, impacting individuals, partners, and society at large. Recent evidence suggests that specific microbes colonising our skin and its appendages are often overrepresented in disease. Therefore, manipulating interactions of the microbiome in a non-invasive and safe way presents an attractive approach for management of skin and hair follicle conditions. Due to its proven anti-microbial and anti-inflammatory effects, blue light (380 - 495nm) has received considerable attention as a possible 'magic bullet' for management of skin dysbiosis. As humans, we have evolved under the influence of sun exposure, which comprise a significant portion of blue light. A growing body of evidence indicates that our resident skin microbiome possesses the ability to detect and respond to blue light through expression of chromophores. This can modulate physiological responses, ranging from cytotoxicity to proliferation. In this review we first present evidence of the diverse blue light-sensitive chromophores expressed by members of the skin microbiome. Subsequently, we discuss how blue light may impact the dialog between the host and its skin microbiome in prevalent skin and hair follicle conditions. Finally, we examine the constraints of this non-invasive treatment strategy and outline prospective avenues for further research. Collectively, these findings present a comprehensive body of evidence regarding the potential utility of blue light as a restorative tool for managing prevalent skin conditions. Furthermore, they underscore the critical unmet need for a whole systems approach to comprehend the ramifications of blue light on both host and microbial behaviour.},
}

Humans
*Microbiota
*Skin/microbiology/radiation effects
*Light
Skin Diseases/microbiology
Dysbiosis/microbiology
Animals
Blue Light

@article {pmid38660490,
year = {2024},
author = {Ramos Peña, DE and Pillet, S and Grupioni Lourenço, A and Pozzetto, B and Bourlet, T and Motta, ACF},
title = {Human immunodeficiency virus and oral microbiota: mutual influence on the establishment of a viral gingival reservoir in individuals under antiretroviral therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1364002},
pmid = {38660490},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/drug therapy/microbiology/complications/virology ; *Microbiota ; *Gingiva/microbiology/virology ; Mouth/microbiology/virology ; Disease Reservoirs/microbiology/virology ; Periodontitis/microbiology/virology ; Virome ; Dysbiosis/microbiology ; Anti-Retroviral Agents/therapeutic use ; HIV ; },
abstract = {The role of the oral microbiota in the overall health and in systemic diseases has gained more importance in the recent years, mainly due to the systemic effects that are mediated by the chronic inflammation caused by oral diseases, such as periodontitis, through the microbial communities of the mouth. The chronic infection by the human immunodeficiency virus (HIV) interacts at the tissue level (e.g. gut, genital tract, brain) to create reservoirs; the modulation of the gut microbiota by HIV infection is a good example of these interactions. The purpose of the present review is to assess the state of knowledge on the oral microbiota (microbiome, mycobiome and virome) of HIV-infected patients in comparison to that of HIV-negative individuals and to discuss the reciprocal influence of HIV infection and oral microbiota in patients with periodontitis on the potential establishment of a viral gingival reservoir. The influence of different clinical and biological parameters are reviewed including age, immune and viral status, potent antiretroviral therapies, smoking, infection of the airway and viral coinfections, all factors that can modulate the oral microbiota during HIV infection. The analysis of the literature proposed in this review indicates that the comparisons of the available studies are difficult due to their great heterogeneity. However, some important findings emerge: (i) the oral microbiota is less influenced than that of the gut during HIV infection, although some recurrent changes in the microbiome are identified in many studies; (ii) severe immunosuppression is correlated with altered microbiota and potent antiretroviral therapies correct partially these modifications; (iii) periodontitis constitutes a major factor of dysbiosis, which is exacerbated in HIV-infected patients; its pathogenesis can be described as a reciprocal reinforcement of the two conditions, where the local dysbiosis present in the periodontal pocket leads to inflammation, bacterial translocation and destruction of the supporting tissues, which in turn enhances an inflammatory environment that perpetuates the periodontitis cycle. With the objective of curing viral reservoirs of HIV-infected patients in the future years, it appears important to develop further researches aimed at defining whether the inflamed gingiva can serve of viral reservoir in HIV-infected patients with periodontitis.},
}

Humans
*HIV Infections/drug therapy/microbiology/complications/virology
*Microbiota
*Gingiva/microbiology/virology
Mouth/microbiology/virology
Disease Reservoirs/microbiology/virology
Periodontitis/microbiology/virology
Virome
Dysbiosis/microbiology
Anti-Retroviral Agents/therapeutic use
HIV

@article {pmid38660489,
year = {2024},
author = {Zhang, J and Wang, H and Liu, Y and Shi, M and Zhang, M and Zhang, H and Chen, J},
title = {Advances in fecal microbiota transplantation for the treatment of diabetes mellitus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1370999},
pmid = {38660489},
issn = {2235-2988},
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus/therapy/microbiology ; Dysbiosis/therapy ; Animals ; Feces/microbiology ; },
abstract = {Diabetes mellitus (DM) refers to a group of chronic diseases with global prevalence, characterized by persistent hyperglycemia resulting from various etiologies. DM can harm various organ systems and lead to acute or chronic complications, which severely endanger human well-being. Traditional treatment mainly involves controlling blood sugar levels through replacement therapy with drugs and insulin; however, some patients still find a satisfactory curative effect difficult to achieve. Extensive research has demonstrated a close correlation between enteric dysbacteriosis and the pathogenesis of various types of DM, paving the way for novel therapeutic approaches targeting the gut microbiota to manage DM. Fecal microbiota transplantation (FMT), a method for re-establishing the intestinal microbiome balance, offers new possibilities for treating diabetes. This article provides a comprehensive review of the correlation between DM and the gut microbiota, as well as the current advancements in FMT treatment for DM, using FMT as an illustrative example. This study aims to offer novel perspectives and establish a theoretical foundation for the clinical diagnosis and management of DM.},
}

*Fecal Microbiota Transplantation/methods
Humans
*Gastrointestinal Microbiome
*Diabetes Mellitus/therapy/microbiology
Dysbiosis/therapy
Animals
Feces/microbiology

@article {pmid38660030,
year = {2024},
author = {Lourenço, KS and Suleiman, AKA and Pijl, A and Dimitrov, MR and Cantarella, H and Kuramae, EE},
title = {Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments.},
journal = {MethodsX},
volume = {12},
number = {},
pages = {102699},
pmid = {38660030},
issn = {2215-0161},
abstract = {In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).},
}

@article {pmid38659993,
year = {2024},
author = {He, J and Mao, N and Lyu, W and Zhou, S and Zhang, Y and Liu, Z and Xu, Z},
title = {Association between oral microbiome and five types of respiratory infections: a two-sample Mendelian randomization study in east Asian population.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1392473},
pmid = {38659993},
issn = {1664-302X},
abstract = {OBJECTIVE: To explore the causal relationship between the oral microbiome and specific respiratory infections including tonsillitis, chronic sinusitis, bronchiectasis, bronchitis, and pneumonia, assessing the impact of genetic variations associated with the oral microbiome.

METHODS: Mendelian randomization was used to analyze genetic variations, leveraging data from genome-wide association studies in an East Asian cohort to identify connections between specific oral microbiota and respiratory infections.

RESULTS: Our analysis revealed that Prevotella, Streptococcus, Fusobacterium, Pauljensenia, and Capnocytophaga play crucial roles in influencing respiratory infections. Prevotella is associated with both promoting bronchitis and inhibiting pneumonia and tonsillitis, with a mixed effect on chronic sinusitis. Streptococcus and Fusobacterium show varied impacts on respiratory diseases, with Fusobacterium promoting chronic sinusitis, bronchiectasis, and bronchitis. Conversely, Pauljensenia and Capnocytophaga are linked to reduced bronchitis and tonsillitis, and inhibited pneumonia and bronchitis, respectively.

DISCUSSION: These findings underscore the significant impact of the oral microbiome on respiratory health, suggesting potential strategies for disease prevention and management through microbiome targeting. The study highlights the complexity of microbial influences on respiratory infections and the importance of further research to elucidate these relationships.},
}

@article {pmid38659992,
year = {2024},
author = {Qiu, Y and Hou, Y and Wei, X and Wang, M and Yin, Z and Xie, M and Duan, A and Ma, C and Si, K and Wang, Z},
title = {Causal association between gut microbiomes and different types of aneurysms: a Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1267888},
pmid = {38659992},
issn = {1664-302X},
abstract = {BACKGROUND: Previous studies suggests that gut microbiomes are associated with the formation and progression of aneurysms. However, the causal association between them remains unclear.

METHODS: A two-sample Mendelian randomization was conducted to investigate whether gut microbiomes have a causal effect on the risk of intracerebral aneurysm (IA), thoracic aortic aneurysm (TAA) and abdominal aortic aneurysm (AAA), and aortic aneurysm (AA). Single nucleotide polymorphisms (SNPs) smaller than the locus-wide significance level (1 × 10[-5]) were selected as instrumental variables. We used inverse-variance weighted (IVW) test as the primary method for the evaluation of causal association. MR-Egger, weighted median, weighted mode, and MR Pleiotropy Residual Sum and Outlier (MR-PRESSO) methods were conducted for sensitive analysis. The p-value was adjusted by the false discovery rate (FDR) which adjust the results of multiple comparisons, a p < 0.05 and q < 0.1 was considered a significant causal association. Additionally, a p < 0.05 and q > 0.1 was considered a suggestive causal effect. Additionally, reverse MR was also performed to exclude the possibility of reverse causality.

RESULTS: The phylum Firmicutes (OR = 0.62; 95% CI, 0.48-0.81), class Lentisphaeria (OR = 0.75; 95% CI, 0.62-0.89), and order Victivallales (OR = 0.75; 95% CI, 0.62-0.89) have a causal protective effect on the risk of AAA. Additionally, class Verrucomicrobia, class Deltaproteobacteria, order Verrucomicrobiale, family Verrucomicrobiacea, genus Eubacterium rectale group, genus Akkermansia, and genus Clostridium innocuum group were negatively associated with the risk of different types of aneurysms, whereas class Negativicutes, order Selenomonadales, and genus Roseburia had positive causal association with different types of aneurysms (p < 0.05; q > 0.1). Further sensitivity analysis validated the robustness of our MR results, and no reverse causality was found with these gut microbiomes (p > 0.05).

CONCLUSION: Our MR analysis confirmed the causal association of specific gut microbiomes with AAA, and these microbiomes were considered as protective factors. Our result may provide novel insights and theoretical basis for the prevention of aneurysms through regulation of gut microbiomes.},
}

@article {pmid38659984,
year = {2024},
author = {Ovsepian, A and Kardaras, FS and Skoulakis, A and Hatzigeorgiou, AG},
title = {Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1383404},
pmid = {38659984},
issn = {1664-302X},
}

@article {pmid38659980,
year = {2024},
author = {Sarpong, N and Seifert, J and Bennewitz, J and Rodehutscord, M and Camarinha-Silva, A},
title = {Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1354537},
pmid = {38659980},
issn = {1664-302X},
abstract = {As global demand for pork continues to rise, strategies to enhance nitrogen utilization efficiency (NUE) in pig farming have become vital for environmental sustainability. This study explored the relationship between the fecal microbiota, their metabolites, and NUE in crossbreed fattening pigs with a defined family structure. Pigs were kept under standardized conditions and fed in a two-phase feeding regime. In each phase, one fecal sample was collected from each pig. DNA was extracted from a total of 892 fecal samples and subjected to target amplicon sequencing. The results indicated an influence of sire, sampling period (SP), and sex on the fecal microbiota. Streptococcus emerged as a potential biomarker in comparing high and low NUE pigs in SP 1, suggesting a genetic predisposition to NUE regarding the fecal microbiota. All fecal samples were grouped into two enterotype-like clusters named cluster LACTO and cluster CSST. Pigs' affiliation with enterotype-like clusters altered over time and might be sex-dependent. The stable cluster CSST demonstrated the highest NUE despite containing pigs with lower performance characteristics such as average daily gain, dry matter intake, and daily nitrogen retention. This research contributes with valuable insights into the microbiome's role in NUE, paving the way for future strategies to enhance sustainable pig production.},
}

@article {pmid38659839,
year = {2024},
author = {Chen, T and Way, R and Templeton, H and Ball, D and Cheng, MH and Tobet, S},
title = {A Microphysiological System for Studying Barrier Health of Live Tissues in Real Time.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4078220/v1},
pmid = {38659839},
abstract = {Epithelial cells create barriers that protect many different components in the body from their external environment. The gut in particular carries bacteria and other infectious agents. A healthy gut epithelial barrier prevents unwanted substances from accessing the underlying lamina propria while maintaining the ability to digest and absorb nutrients. Increased gut barrier permeability, better known as leaky gut , has been linked to several chronic inflammatory diseases. Yet understanding the cause of leaky gut and developing effective interventions are still elusive due to the lack of tools to maintain tissue's physiological environment while elucidating cellular functions under various stimuli ex vivo. This paper presents a microphysiological system capable of recording real-time barrier permeability of mouse gut tissues in a realistic physiological environment over extended durations. Key components of the microphysiological system include a microfluidic chamber designed to hold the live tissue explant and create a sufficient microphysiological environment to maintain tissue viability; proper media composition that preserves a microbiome and creates necessary oxygen gradients across the barrier; integrated sensor electrodes and supporting electronics for acquiring and calculating transepithelial electrical resistance (TEER); and a scalable system architecture to allow multiple chambers running in parallel for increased throughput. The experimental results demonstrate that the system can maintain tissue viability for up to 72 hours. The results also show that the custom-built and integrated TEER sensors are sufficiently sensitive to distinguish differing levels of barrier permeability when treated with collagenase and low pH media compared to control. Permeability variations in tissue explants from different positions in the intestinal tract were also investigated using TEER revealing their disparities in permeability. Finally, the results also quantitatively determine the effect of the muscle layer on total epithelial resistance.},
}

@article {pmid38659779,
year = {2024},
author = {Moraes, JGN and Gull, TB and Ericsson, AC and Caldeira, MO and Evans, TJ and Poock, SE and Lucy, MC},
title = {Systemic antibiotic treatment of cows with metritis early postpartum does not change the progression of uterine disease or the uterine microbiome at 1 month postpartum.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4233045/v1},
pmid = {38659779},
abstract = {Background: Postpartum uterine disease (metritis) is common in dairy cows. The disease develops within 1 week after calving and is associated with microbial dysbiosis, fever, and fetid uterine discharge. Cows with metritis have a greater likelihood of developing endometritis and infertility later postpartum. Antibiotic treatment is used to relieve symptoms of metritis but the capacity of antibiotic treatment to improve fertility later postpartum is inconsistent across published studies. We hypothesized that an antibiotic has only a short-term effect on the uterine microbiome and does not change the progression of disease from metritis to endometritis. To test this hypothesis, we studied the effects of systemic antibiotic given to cows diagnosed with metritis and healthy cows early postpartum on the development of endometritis and the uterine microbiome at 1 month postpartum. Results: Cows diagnosed with metritis were compared to healthy ones in a 2 x 2 factorial design, where they were either treated with an antibiotic (ceftiofur hydrochloride) at 7 to 10 days postpartum or left untreated. Cows were slaughtered at one month postpartum and the uterus was assessed for endometritis (presence of purulent material in the uterine lumen and inflammation in the endometrium) and uterine samples were collected for bacteriology and metagenomics (16S rRNA gene sequencing). As expected, the uterine microbiome at disease diagnosis had dysbiosis of typical metritis pathogens (e.g., Fusobacterium , Bacteroides , and Porphyromonas) in diseased compared with healthy cows. At one month postpartum, there was a tendency for more endometritis in metritis cows compared with healthy but antibiotic treatment had no effect on endometritis prevalence regardless of the original disease diagnosis. Likewise, when bacteria were cultured or sequenced, there were a greater number of species (culture) or amplicon sequence variants (ASV; sequencing) in the uterine lumen of cows with metritis. However, antibiotic treatment had no effect on the prevalence of cultured species or the composition of the detected ASV. The uterine microbiome at 1 month postpartum was associated with the clinical observation of the uterus (endometritis or healthy). Conclusions: Early postpartum antibiotic treatment only provides temporary resolution of uterine dysbiosis that is not sustained long-term. Failure to resolve the dysbiosis is associated with a greater prevalence of endometritis in cows with metritis, and the occurrence of endometritis significantly impacts fertility later postpartum.},
}

@article {pmid38659758,
year = {2024},
author = {Occhino, JA and D O, JNB and Wu, PY and Walther-Antonio, MR and Chen, J},
title = {Preoperative Vaginal Microbiome as a Predictor of Postoperative Urinary Tract Infection.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4069233/v1},
pmid = {38659758},
abstract = {This is a single Institute, prospective cohort study. We collected twenty- two postmenopausal women with pelvic organ prolapse planning to undergo vaginal hysterectomy with transvaginal pelvic reconstructive surgery, with or without a concomitant anti-incontinence procedure. Vaginal swabs and urine samples were longitudinally collected at five time points: preoperative consult visit (T1), day of surgery prior to surgical scrub (T2), immediately postoperative (T3), day of hospital discharge (T4), and at the postoperative exam visit (T5). Women experiencing urinary tract infection symptoms provided a sample set prior to antibiotic administration (T6). Microbiome analysis on vaginal and urinary specimens at each time point. Region V3-V5 of the 16S ribosomal RNA gene was amplified and sequenced. Sample DNA was analyzed with visit T1, T2, T5 and T6. Six (27.3%) participants developed postoperative urinary tract infection whose vaginal sample at first clinical visit (T1) revealed beta-diversity analysis with significant differences in microbiome structure and composition. Women diagnosed with a postoperative urinary tract infection had a vaginal microbiome characterized by low abundance of Lactobacillus and high prevalence of Prevotella and Gardnerella species. In our cohort, preoperative vaginal swabs can predict who will develop a urinary tract infection following transvaginal surgery for pelvic organ prolapse.},
}

@article {pmid38659744,
year = {2024},
author = {Usyk, M and Hayes, RB and Knight, R and Gonzalez, A and Li, H and Osman, I and Weber, JS and Ahn, J},
title = {Gut microbiome is associated with recurrence-free survival in patients with resected Stage IIIB-D or Stage IV melanoma treated with immune checkpoint inhibitors.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.16.589761},
pmid = {38659744},
abstract = {UNLABELLED: The gut microbiome (GMB) has been associated with outcomes of immune checkpoint blockade therapy in melanoma, but there is limited consensus on the specific taxa involved, particularly across different geographic regions. We analyzed pre-treatment stool samples from 674 melanoma patients participating in a phase-III trial of adjuvant nivolumab plus ipilimumab versus nivolumab, across three continents and five regions. Longitudinal analysis revealed that GMB was largely unchanged following treatment, offering promise for lasting GMB-based interventions. In region-specific and cross-region meta-analyses, we identified pre-treatment taxonomic markers associated with recurrence, including Eubacterium, Ruminococcus, Firmicutes , and Clostridium . Recurrence prediction by these markers was best achieved across regions by matching participants on GMB compositional similarity between the intra-regional discovery and external validation sets. AUCs for prediction ranged from 0.83-0.94 (depending on the initial discovery region) for patients closely matched on GMB composition (e.g., JSD ≤0.11). This evidence indicates that taxonomic markers for prediction of recurrence are generalizable across regions, for individuals of similar GMB composition.

HIGHLIGHTS: Overall gut microbiome (GMB) composition is largely unchanged during ICB treatment.GMB composition varies by geographic regionWe identified gut bacterial markers associated with recurrence in region-specific analyses.Region-identified markers are generalizable if GMB composition is taken into account by matching.},
}

@article {pmid38659636,
year = {2024},
author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG},
title = {Assessing Engraftment Following Fecal Microbiota Transplant.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {38659636},
issn = {2331-8422},
abstract = {Fecal Microbiota Transplant (FMT) is an FDA approved treatment for recurrent Clostridium difficile infections, and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to priming the microbiome for cancer treatment, and restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in determining if a recipient didn't respond because the engrafted microbiome didn't produce the desired outcomes (a successful FMT, but negative treatment outcome), or the microbiome didn't engraft (an unsuccessful FMT and negative treatment outcome). The lack of a consistent methodology for quantifying FMT engraftment extent hinders the assessment of FMT success and its relation to clinical outcomes, and presents challenges for comparing FMT results and protocols across studies. Here we review 46 studies of FMT in humans and model organisms and group their approaches for assessing the extent to which an FMT engrafts into three criteria: 1) Chimeric Asymmetric Community Coalescence investigates microbiome shifts following FMT engraftment. 2) Donated Microbiome Indicator Features tracks donated microbiome features as a signal of engraftment with methods such as differential abundance testing based on the current sample collection, or tracking changes in feature abundances that have been previously identified. 3) Temporal Stability examines how resistant post-FMT recipient's microbiomes are to reverting back to their baseline microbiome. Investigated together, these criteria provide a clear assessment of microbiome engraftment. We discuss the pros and cons of each of these criteria, providing illustrative examples of their application. We also introduce key terminology and recommendations on how FMT studies can be analyzed for rigorous engraftment extent assessment.},
}

@article {pmid38659586,
year = {2024},
author = {Li, Y and Chen, J and Xing, Y and Wang, J and Liang, Q and Zeng, J and Wang, S and Yang, Q and Lu, J and Hu, J and Lu, W},
title = {Bufei Huoxue capsule attenuates COPD-related inflammation and regulates intestinal microflora, metabolites.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1270661},
pmid = {38659586},
issn = {1663-9812},
abstract = {Background: Bufei Huoxue capsule (BFHX) is widely used for the clinical treatment of chronic obstructive pulmonary disease (COPD) in China. Objectives: The aim of this study is to explore the effects on COPD and the underlying mechanism of BFHX. The process and methods: In this study, we established a COPD mouse model through cigarette smoke (CS) exposure in combination with lipopolysaccharide (LPS) intratracheal instillation. Subsequently, BFHX was orally administrated to COPD mice, and their pulmonary function, lung pathology, and lung inflammation, including bronchoalveolar lavage fluid (BALF) cell count and classification and cytokines, were analyzed. In addition, the anti-oxidative stress ability of BFHX was detected by Western blotting, and the bacterial diversity, abundance, and fecal microbiome were examined using 16S rRNA sequencing technology. Outcome: BFHX was shown to improve pulmonary function, suppress lung inflammation, decrease emphysema, and increase anti-oxidative stress, whereas 16S rRNA sequencing indicated that BFHX can dynamically regulate the diversity, composition, and distribution of the intestinal flora microbiome and regulate the lysine degradation and phenylalanine metabolism of COPD mice. These results highlight another treatment option for COPD and provide insights into the mechanism of BFHX.},
}

@article {pmid38659457,
year = {2024},
author = {Abdel-Wareth, AAA and Williams, AN and Salahuddin, M and Gadekar, S and Lohakare, J},
title = {Algae as an alternative source of protein in poultry diets for sustainable production and disease resistance: present status and future considerations.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1382163},
pmid = {38659457},
issn = {2297-1769},
abstract = {Integrating algae into poultry diets offers a promising avenue for enhancing nutrition, boosting sustainability efforts, and potentially stimulating disease resistance. This comprehensive review delves into the essence, diversity, chemical composition, and nutritional merits of algae, spotlighting their emergence as innovative nutrient sources and health supplements for poultry. The growing interest in algae within poultry nutrition stems from their diverse nutritional profile, boasting a rich array of proteins, lipids, amino acids, vitamins, minerals, and antioxidants, thus positioning them as valuable feed constituents. A key highlight of incorporating both macroalgae and microalgae lies in their elevated protein content, with microalgae varieties like Spirulina and Chlorella exhibiting protein levels of up to 50-70%, outperforming traditional sources like soybean meal. This premium protein source not only furnishes vital amino acids crucial for muscular development and overall health in poultry but also serves as an exceptional reservoir of omega-3 fatty acids, notably eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), presenting multiple health benefits for both poultry and consumers alike. Moreover, algae boast antioxidant properties attributed to bioactive compounds like phycocyanin and astaxanthin, mitigating oxidative stress and boosting the bird's immune response, thereby fostering robust health and disease resilience. Incorporating macroalgae and microalgae into poultry diets yields positive impacts on performance metrics. Research evidence underscores the enhancement of growth rates, feed conversion ratios, carcass quality, and meat attributes in broilers, while in layers, supplementation promotes increased egg production, superior egg quality, and increased concentrations of beneficial nutrients such as omega-3 fatty acids. Furthermore, algae hold promise for mitigating the environmental footprint of poultry production, though significant outcomes from trials remain sporadic, necessitating further research to elucidate optimal dosages and blends for different algae species in poultry diets. Standardizing the composition of algae utilized in research is imperative, paving the way for potential applications in poultry nutrition as growth stimulants and substitutes for antibiotics. Nonetheless, a deeper understanding of dosage, combination, and mechanism of action through rigorous scientific investigation is key to unlocking algae's full potential within poultry nutrition.},
}

@article {pmid38659448,
year = {2024},
author = {Shterzer, N and Sbehat, Y and Poudel, B and Rothschild, N and Oloko, OE and Druyan, S and Mills, E},
title = {Comparative analysis of reproductive tract microbiomes in modern and slower-growing broiler breeder lines.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1386410},
pmid = {38659448},
issn = {2297-1769},
abstract = {INTRODUCTION: The reproductive tract microbiome in hens is of interest because bacteria in the reproductive tract could potentially affect fertilization and egg production, as well as integrate into the forming egg and vertically transmit to progeny.

METHODS: The reproductive tract microbiome of 37-week-old modern commercial Cobb breeding dams was compared with that of dams from a broiler Legacy line which has not undergone selection since 1986. All animals were kept together under the same management protocol from day of hatch to avoid confounders.

RESULTS: In regards to reproductive abilities, Cobb dams' eggs weighed more and the magnum section of their reproductive tract was longer. In regards to microbiome composition, it was found that the reproductive tract microbiomes of the two lines had a lot in common but also that the two breeds have unique reproductive tract microbiomes. Specifically, the order Pseudomonadales was higher in the magnum of Legacy dams, while Verrucomicrobiales was lower. In the infundibulum, Lactobacillales were higher in the Legacy dams while Verrucomicrobiales, Bacteroidales, RF32 and YS2 were lower.

DISCUSSION: our results show that breeding programs have modified not only the physiology of the reproductive tract but also the reproductive tract microbiome. Additional research is required to understand the implications of these changes in the reproductive tract microbiome on the chicken host.},
}

@article {pmid38659246,
year = {2024},
author = {Li, D and Zhong, C and Yang, M and He, L and Chang, H and Zhu, N and Celniker, SE and Threadgill, DW and Snijders, AM and Mao, JH and Yuan, Y},
title = {Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2341647},
doi = {10.1080/19490976.2024.2341647},
pmid = {38659246},
issn = {1949-0984},
support = {R01 ES031322/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; *Colorectal Neoplasms/microbiology/genetics/chemically induced ; *Azoxymethane ; Humans ; Mice ; *Polymorphism, Single Nucleotide ; *Gastrointestinal Microbiome ; *Collaborative Cross Mice/genetics ; Dual Oxidases/genetics/metabolism ; Genetic Predisposition to Disease ; Male ; Bacteria/genetics/classification/metabolism/isolation & purification ; Disease Models, Animal ; Female ; },
abstract = {The insights into interactions between host genetics and gut microbiome (GM) in colorectal tumor susceptibility (CTS) remains lacking. We used Collaborative Cross mouse population model to identify genetic and microbial determinants of Azoxymethane-induced CTS. We identified 4417 CTS-associated single nucleotide polymorphisms (SNPs) containing 334 genes that were transcriptionally altered in human colorectal cancers (CRCs) and consistently clustered independent human CRC cohorts into two subgroups with different prognosis. We discovered a set of genera in early-life associated with CTS and defined a 16-genus signature that accurately predicted CTS, the majority of which were correlated with human CRCs. We identified 547 SNPs associated with abundances of these genera. Mediation analysis revealed GM as mediators partially exerting the effect of SNP UNC3869242 within Duox2 on CTS. Intestine cell-specific depletion of Duox2 altered GM composition and contribution of Duox2 depletion to CTS was significantly influenced by GM. Our findings provide potential novel targets for personalized CRC prevention and treatment.},
}

Animals
*Colorectal Neoplasms/microbiology/genetics/chemically induced
*Azoxymethane
Humans
Mice
*Polymorphism, Single Nucleotide
*Gastrointestinal Microbiome
*Collaborative Cross Mice/genetics
Dual Oxidases/genetics/metabolism
Genetic Predisposition to Disease
Male
Bacteria/genetics/classification/metabolism/isolation & purification
Disease Models, Animal
Female

@article {pmid38659162,
year = {2024},
author = {Jhanji, V and Prescott, C},
title = {Inflammatory Dry Eye: Nerves, Microbiome, Onset, and New Treatments.},
journal = {Eye & contact lens},
volume = {50},
number = {5},
pages = {199},
pmid = {38659162},
issn = {1542-233X},
mesh = {Humans ; *Dry Eye Syndromes/drug therapy ; *Microbiota ; },
}

Humans
*Dry Eye Syndromes/drug therapy
*Microbiota

@article {pmid38659131,
year = {2024},
author = {Kandlikar, GS},
title = {Quantifying soil microbial effects on plant species coexistence: A conceptual synthesis.},
journal = {American journal of botany},
volume = {111},
number = {4},
pages = {e16316},
doi = {10.1002/ajb2.16316},
pmid = {38659131},
issn = {1537-2197},
mesh = {*Soil Microbiology ; *Plants/microbiology ; Models, Biological ; Biodiversity ; },
abstract = {Soil microorganisms play a critical role in shaping the biodiversity dynamics of plant communities. These microbial effects can arise through direct mediation of plant fitness by pathogens and mutualists, and over the past two decades, numerous studies have shined a spotlight on the role of dynamic feedbacks between plants and soil microorganisms as key determinants of plant species coexistence. Such feedbacks occur when plants modify the composition of the soil community, which in turn affects plant performance. Stimulated by a theoretical model developed in the 1990s, a bulk of the empirical evidence for microbial controls over plant coexistence comes from experiments that quantify plant growth in soil communities that were previously conditioned by conspecific or heterospecific plants. These studies have revealed that soil microbes can generate strong negative to positive frequency-dependent dynamics among plants. Even as soil microbes have become recognized as a key player in determining plant coexistence outcomes, the past few years have seen a renewed interest in expanding the conceptual foundations of this field. New results include re-interpretations of key metrics from classic two-species models, extensions of plant-soil feedback theory to multispecies communities, and frameworks to integrate plant-soil feedbacks with processes like intra- and interspecific competition. Here, I review the implications of theoretical developments for interpreting existing empirical results and highlight proposed analyses and designs for future experiments that can enable a more complete understanding of microbial regulation of plant community dynamics.},
}

*Soil Microbiology
*Plants/microbiology
Models, Biological
Biodiversity

@article {pmid38659112,
year = {2024},
author = {Martin, FM and Öpik, M and Dickie, IA},
title = {Mycorrhizal research now: from the micro- to the macro-scale.},
journal = {The New phytologist},
volume = {242},
number = {4},
pages = {1399-1403},
doi = {10.1111/nph.19758},
pmid = {38659112},
issn = {1469-8137},
support = {//Huazhong Agricultural University/ ; //BioProtection Aotearoa/ ; ANR-11-LABX-0002-01//Laboratory of Excellence ARBRE/ ; 1789//Eesti Teadusagentuur/ ; },
mesh = {*Mycorrhizae/physiology ; *Research ; },
}

*Mycorrhizae/physiology
*Research

@article {pmid38658841,
year = {2024},
author = {Jeong, S and Liao, YT and Tsai, MH and Wang, YK and Wu, IC and Liu, CJ and Wu, MS and Chan, TS and Chen, MY and Hu, PJ and Kao, WY and Liu, HC and Tsai, MJ and Liu, CY and Chang, CC and Wu, DC and Hsu, YH},
title = {Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {139},
pmid = {38658841},
issn = {1471-2180},
mesh = {Humans ; *Stomach Neoplasms/microbiology ; Male ; Female ; Middle Aged ; *Gastritis/microbiology ; *Feces/microbiology ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification ; Aged ; Gastrointestinal Microbiome/genetics ; Adult ; },
abstract = {BACKGROUND: Gastric cancer is one of the global health concerns. A series of studies on the stomach have confirmed the role of the microbiome in shaping gastrointestinal diseases. Delineation of microbiome signatures to distinguish chronic gastritis from gastric cancer will provide a non-invasive preventative and treatment strategy. In this study, we performed whole metagenome shotgun sequencing of fecal samples to enhance the detection of rare bacterial species and increase genome sequence coverage. Additionally, we employed multiple bioinformatics approaches to investigate the potential targets of the microbiome as an indicator of differentiating gastric cancer from chronic gastritis.

RESULTS: A total of 65 patients were enrolled, comprising 33 individuals with chronic gastritis and 32 with gastric cancer. Within each group, the chronic gastritis group was sub-grouped into intestinal metaplasia (n = 15) and non-intestinal metaplasia (n = 18); the gastric cancer group, early stage (stages 1 and 2, n = 13) and late stage (stages 3 and 4, n = 19) cancer. No significant differences in alpha and beta diversities were detected among the patient groups. However, in a two-group univariate comparison, higher Fusobacteria abundance was identified in phylum; Fusobacteria presented higher abundance in gastric cancer (LDA scored 4.27, q = 0.041 in LEfSe). Age and sex-adjusted MaAsLin and Random Forest variable of importance (VIMP) analysis in species provided meaningful features; Bacteria_caccae was the most contributing species toward gastric cancer and late-stage cancer (beta:2.43, se:0.891, p:0.008, VIMP score:2.543). In contrast, Bifidobacterium_longum significantly contributed to chronic gastritis (beta:-1.8, se:0.699, p:0.009, VIMP score:1.988). Age, sex, and BMI-adjusted MasAsLin on metabolic pathway analysis showed that GLCMANNANAUT-PWY degradation was higher in gastric cancer and one of the contributing species was Fusobacterium_varium.

CONCLUSION: Microbiomes belonging to the pathogenic phylum Fusobacteria and species Bacteroides_caccae and Streptococcus_anginosus can be significant targets for monitoring the progression of gastric cancer. Whereas Bifidobacterium_longum and Lachnospiraceae_bacterium_5_1_63FAA might be protection biomarkers against gastric cancer.},
}

Humans
*Stomach Neoplasms/microbiology
Male
Female
Middle Aged
*Gastritis/microbiology
*Feces/microbiology
*Metagenome
*Bacteria/genetics/classification/isolation & purification
Aged
Gastrointestinal Microbiome/genetics
Adult

@article {pmid38658829,
year = {2024},
author = {Han, M and Wang, X and Zhang, J and Su, L and Ishaq, HM and Li, D and Cui, J and Zhao, H and Yang, F},
title = {Gut bacterial and fungal dysbiosis in tuberculosis patients.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {141},
pmid = {38658829},
issn = {1471-2180},
support = {82061128001//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Fungi/classification/isolation & purification/genetics ; Male ; Female ; *Bacteria/classification/isolation & purification/genetics ; Adult ; Middle Aged ; Tuberculosis/microbiology/complications ; Feces/microbiology ; Cytokines/blood ; Interleukin-17/blood ; },
abstract = {BACKGROUND: Recent studies have more focused on gut microbial alteration in tuberculosis (TB) patients. However, no detailed study on gut fungi modification has been reported till now. So, current research explores the characteristics of gut microbiota (bacteria)- and mycobiota (fungi)-dysbiosis in TB patients and also assesses the correlation between the gut microbiome and serum cytokines. It may help to screen the potential diagnostic biomarker for TB.

RESULTS: The results show that the alpha diversity of the gut microbiome (including bacteria and fungi) decreased and altered the gut microbiome composition of TB patients. The bacterial genera Bacteroides and Prevotella were significantly increased, and Blautia and Bifidobacterium decreased in the TB patients group. The fungi genus Saccharomyces was increased while decreased levels of Aspergillus in TB patients. It indicates that gut microbial equilibrium between bacteria and fungi has been altered in TB patients. The fungal-to-bacterial species ratio was significantly decreased, and the bacterial-fungal trans-kingdom interactions have been reduced in TB patients. A set model including Bacteroides, Blautia, Eubacterium_hallii_group, Apiotrichum, Penicillium, and Saccharomyces may provide a better TB diagnostics option than using single bacterial or fungi sets. Also, gut microbial dysbiosis has a strong correlation with the alteration of IL-17 and IFN-γ.

CONCLUSIONS: Our results demonstrate that TB patients exhibit the gut bacterial and fungal dysbiosis. In the clinics, some gut microbes may be considered as potential biomarkers for auxiliary TB diagnosis.},
}

Humans
*Dysbiosis/microbiology
*Gastrointestinal Microbiome
*Fungi/classification/isolation & purification/genetics
Male
Female
*Bacteria/classification/isolation & purification/genetics
Adult
Middle Aged
Tuberculosis/microbiology/complications
Feces/microbiology
Cytokines/blood
Interleukin-17/blood

@article {pmid38658823,
year = {2024},
author = {Zhang, X and Nurxat, N and Aili, J and Yasen, Y and Wang, Q and Liu, Q},
title = {The characteristics of microbiome in the upper respiratory tract of COVID-19 patients.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {138},
pmid = {38658823},
issn = {1471-2180},
support = {82072235//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology ; *Microbiota/genetics ; Male ; *Candida albicans/isolation & purification/genetics ; Female ; *Sputum/microbiology/virology ; Middle Aged ; *SARS-CoV-2/genetics/isolation & purification ; *Bacteria/classification/isolation & purification/genetics ; *Respiratory System/microbiology/virology ; Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Coinfection/microbiology/virology ; },
abstract = {BACKGROUND: Co-infection with other pathogens in coronavirus disease 2019 (COVID-19) patients exacerbates disease severity and impacts patient prognosis. Clarifying the exact pathogens co-infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is premise of the precise treatment for COVID-19 patients.

METHODS: Sputum samples were collected from 17 patients in the COVID-19 positive group and 18 patients in the COVID-19 negative group. DNA extraction was performed to obtain the total DNA. Sequencing analysis using 16S and ITS rRNA gene was carried out to analyze the composition of bacterial and fungal communities. Meanwhile, all the samples were inoculated for culture.

RESULTS: We did not observe significant differences in bacterial composition between the COVID-19 positive and negative groups. However, a significantly higher abundance of Candida albicans was observed in the upper respiratory tract samples from the COVID-19 positive group compared to the COVID-19 negative group. Moreover, the Candida albicans strains isolated from COVID-19 positive group exhibited impaired secretion of aspartyl proteinases.

CONCLUSION: COVID-19 positive patients demonstrate a notable increase in the abundance of Candida albicans, along with a decrease in the levels of aspartyl proteinases, indicating the alteration of microbiota composition of upper respiratory tract.},
}

Humans
*COVID-19/microbiology/virology
*Microbiota/genetics
Male
*Candida albicans/isolation & purification/genetics
Female
*Sputum/microbiology/virology
Middle Aged
*SARS-CoV-2/genetics/isolation & purification
*Bacteria/classification/isolation & purification/genetics
*Respiratory System/microbiology/virology
Aged
RNA, Ribosomal, 16S/genetics
Adult
Coinfection/microbiology/virology

@article {pmid38658578,
year = {2024},
author = {Pedrazzoli, E and Demozzi, M and Visentin, E and Ciciani, M and Bonuzzi, I and Pezzè, L and Lucchetta, L and Maule, G and Amistadi, S and Esposito, F and Lupo, M and Miccio, A and Auricchio, A and Casini, A and Segata, N and Cereseto, A},
title = {CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3478},
pmid = {38658578},
issn = {2041-1723},
support = {825825//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101071041//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 1U01CA230551//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; MetaPG-716575//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Gene Editing/methods ; Humans ; *CRISPR-Cas Systems ; Animals ; Mice ; *Microbiota/genetics ; Dependovirus/genetics ; CRISPR-Associated Protein 9/metabolism/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; Retina/metabolism ; Clostridiales/genetics/enzymology ; HEK293 Cells ; Genetic Vectors/metabolism/genetics ; },
abstract = {The expansion of the CRISPR-Cas toolbox is highly needed to accelerate the development of therapies for genetic diseases. Here, through the interrogation of a massively expanded repository of metagenome-assembled genomes, mostly from human microbiomes, we uncover a large variety (n = 17,173) of type II CRISPR-Cas loci. Among these we identify CoCas9, a strongly active and high-fidelity nuclease with reduced molecular size (1004 amino acids) isolated from an uncultivated Collinsella species. CoCas9 is efficiently co-delivered with its sgRNA through adeno associated viral (AAV) vectors, obtaining efficient in vivo editing in the mouse retina. With this study we uncover a collection of previously uncharacterized Cas9 nucleases, including CoCas9, which enriches the genome editing toolbox.},
}

*Gene Editing/methods
Humans
*CRISPR-Cas Systems
Animals
Mice
*Microbiota/genetics
Dependovirus/genetics
CRISPR-Associated Protein 9/metabolism/genetics
RNA, Guide, CRISPR-Cas Systems/genetics/metabolism
Retina/metabolism
Clostridiales/genetics/enzymology
HEK293 Cells
Genetic Vectors/metabolism/genetics

@article {pmid38658192,
year = {2024},
author = {Mikkelsen, D and McGowan, AM and Gibson, JS and Lanyon, JM and Horsman, S and Seddon, JM},
title = {Faecal bacterial communities differ amongst discrete foraging populations of dugongs along the east Australian coast.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae051},
pmid = {38658192},
issn = {1574-6941},
abstract = {Gut bacterial communities play a vital role in a host's digestion, fermentation of complex carbohydrates, absorption of nutrients and energy harvest/storage. Dugongs are obligate seagrass grazers with an expanded hindgut and associated microbiome. Here, we characterised and compared the faecal bacterial communities of dugongs from genetically distinct populations along the east coast of Australia, between subtropical Moreton Bay and tropical Cleveland Bay. Amplicon sequencing of fresh dugong faecal samples (n=47) revealed Firmicutes (62%) dominating the faecal bacterial communities across all populations. Several bacterial genera (Bacteroides, Clostridium sensu stricto 1, Blautia and Polaribacter) were detected in samples from all locations, suggesting their importance in seagrass digestion. Principal coordinate analysis showed the three southern-most dugong populations having different faecal bacterial community compositions from northern populations. The relative abundances of the genera Clostridium sensu stricto 13 and dgA-11 gut group were higher, but Bacteroides was lower, in the southern dugong populations, compared to the northern populations, suggesting potential adaptive changes associated with location. This study contributes to our knowledge of the faecal bacterial communities of dugongs inhabiting Australian coastal waters. Future studies of diet selection in relation to seagrass availability throughout the dugong's range will help to advance our understanding of the roles that seagrass species may play in affecting the dugong's faecal bacterial community composition.},
}

@article {pmid38657948,
year = {2024},
author = {Gu, LJ and Li, L and Li, QN and Xu, K and Yue, W and Qiao, JY and Meng, TG and Dong, MZ and Lei, WL and Guo, JN and Wang, ZB and Sun, QY},
title = {The transgenerational effects of maternal low-protein diet during lactation on offspring.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.04.008},
pmid = {38657948},
issn = {1673-8527},
abstract = {Environment factors such as diet and lifestyle can influence the health of both mothers and offspring. However, its transgenerational transmission and underlying mechanisms remain largely unknown. Here, using a maternal lactation-period low-protein diet (LPD) mouse model, we show that maternal LPD during lactation causes decreased survival and stunted growth, significantly reduces ovulation and litter size, and alters the gut microbiome in the female LPD-F1 offspring. The transcriptome of LPD-F1 metaphase II (MII) oocytes shows that differentially expressed genes are enriched in female pregnancy and multiple metabolic processes. Moreover, maternal LPD causes early stunted growth and impairs metabolic health, which is transmitted for two generations. The methylome alteration of LPD-F1 oocytes can be partly transmitted to the F2 oocytes. Together, our results reveal that LPD during lactation transgenerationally affects offspring health, probably via oocyte epigenetic changes.},
}

@article {pmid38657605,
year = {2024},
author = {Su, Q and Lau, RI and Liu, Q and Li, MKT and Yan Mak, JW and Lu, W and Lau, ISF and Lau, LHS and Yeung, GTY and Cheung, CP and Tang, W and Liu, C and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC},
title = {The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.04.005},
pmid = {38657605},
issn = {1934-6069},
abstract = {The mechanisms underlying the many phenotypic manifestations of post-acute COVID-19 syndrome (PACS) are poorly understood. Herein, we characterized the gut microbiome in heterogeneous cohorts of subjects with PACS and developed a multi-label machine learning model for using the microbiome to predict specific symptoms. Our processed data covered 585 bacterial species and 500 microbial pathways, explaining 12.7% of the inter-individual variability in PACS. Three gut-microbiome-based enterotypes were identified in subjects with PACS and associated with different phenotypic manifestations. The trained model showed an accuracy of 0.89 in predicting individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting upcoming symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrates that the gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS.},
}

@article {pmid38657546,
year = {2024},
author = {Zhao, B and Yan, Y and Cao, D and Xia, Y},
title = {Germinating rice seeds shape rhizospheric bacteria via releasing benzaldehyde.},
journal = {Plant physiology and biochemistry : PPB},
volume = {210},
number = {},
pages = {108632},
doi = {10.1016/j.plaphy.2024.108632},
pmid = {38657546},
issn = {1873-2690},
abstract = {Plants are not passively exposed to microbes during their life cycles, but rather shape the microbiome in their own way. However, little information is available about when and how plants recruit their microbes in the life cycles. We scrutinized the recruitment of soil microbes by rice (Oryza sativa) at the seed germination stage. Bacteria of Enterobacteria and Weeksellaceae were the most preferentially recruited by the germinating seeds, despite of many other bacteria in the soil. The seedlings that recruited Enterobacteria and Weeksellaceae bacteria notably outperformed those without these microbes in leaf length (by 54.21%), root length (by 188.11%) and biomass (by 88.65%). Further, we detected benzaldehyde, a plant-specific volatile metabolite, in the exudates of germinating seeds. Addition of benzaldehyde to the soil resulted in enrichment of Enterobacteria bacteria, suggesting that seed-released benzaldehyde could be a cue to recruit beneficial bacteria. Taken together, our results demonstrated that plants could recruit beneficial bacteria from the soil at the very early life stage of seed germination via releasing specific metabolites.},
}

@article {pmid38657507,
year = {2024},
author = {Fu, Y and Jia, F and Su, J and Xu, X and Zhang, Y and Li, X and Jiang, X and Schäffer, A and Virta, M and Tiedje, JM and Wang, F},
title = {Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134252},
doi = {10.1016/j.jhazmat.2024.134252},
pmid = {38657507},
issn = {1873-3336},
abstract = {The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.},
}

@article {pmid38657418,
year = {2024},
author = {Knez, E and Kadac-Czapska, K and Grembecka, M},
title = {The importance of food quality, gut motility, and microbiome in SIBO development and treatment.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {124},
number = {},
pages = {112464},
doi = {10.1016/j.nut.2024.112464},
pmid = {38657418},
issn = {1873-1244},
abstract = {The prevalence of small intestinal bacterial overgrowth (SIBO) is rising worldwide, particularly in nations with high rates of urbanization. Irritable bowel syndrome, inflammatory bowel illnesses, and nonspecific dysmotility are strongly linked to SIBO. Moreover, repeated antibiotic therapy promotes microorganisms' overgrowth through the development of antibiotic resistance. The primary cause of excessive fermentation in the small intestine is a malfunctioning gastrointestinal motor complex, which results in the gut's longer retention of food residues. There are anatomical and physiological factors affecting the functioning of the myoelectric motor complex. Except for them, diet conditions the activity of gastrointestinal transit. Indisputably, the Western type of nutrition is unfavorable. Some food components have greater importance in the functioning of the gastrointestinal motor complex than others. Tryptophan, an essential amino acid and precursor of the serotonin hormone, accelerates intestinal transit, and gastric emptying, similarly to fiber and polyphenols. Additionally, the effect of food on the microbiome is important, and diet should prevent bacterial overgrowth and exhibit antimicrobial effects against pathogens. Therefore, knowledge about proper nutrition is essential to prevent the development and recurrence of SIBO. Since the scientific world was unsure whether there was a long-term or potential solution for SIBO until quite recently, research on a number of the topics included in the article should be performed. The article aimed to summarize current knowledge about proper nutrition after SIBO eradication and the prevention of recurrent bacterial overgrowth. Moreover, a connection was found between diet, gut dysmotility, and SIBO.},
}

@article {pmid38657391,
year = {2024},
author = {Bains, RK and Nasseri, SA and Wardman, JF and Withers, SG},
title = {Advances in the understanding and exploitation of carbohydrate-active enzymes.},
journal = {Current opinion in chemical biology},
volume = {80},
number = {},
pages = {102457},
doi = {10.1016/j.cbpa.2024.102457},
pmid = {38657391},
issn = {1879-0402},
abstract = {Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.},
}

@article {pmid38657162,
year = {2024},
author = {Quarta, G and Schlick, T},
title = {Riboswitch Distribution in the Human Gut Microbiome Reveals Common Metabolite Pathways.},
journal = {The journal of physical chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jpcb.4c00267},
pmid = {38657162},
issn = {1520-5207},
support = {R35 GM122562/GM/NIGMS NIH HHS/United States ; },
abstract = {Riboswitches are widely distributed, conserved RNAs which regulate metabolite levels in bacterial cells through direct, noncovalent binding of their cognate metabolite. Various riboswitch families are highly enriched in gut bacteria, suggestive of a symbiotic relationship between the host and bacteria. Previous studies of the distribution of riboswitches have examined bacterial taxa broadly. Thus, the distribution of riboswitches associated with bacteria inhabiting the intestines of healthy individuals is not well understood. To address these questions, we survey the gut microbiome for riboswitches by including an international database of prokaryotic genomes from the gut samples. Using Infernal, a program that uses RNA-specific sequence and structural features, we survey this data set using existing riboswitch models. We identify 22 classes of riboswitches with vitamin cofactors making up the majority of riboswitch-associated pathways. Our finding is reproducible in other representative databases from the oral as well as the marine microbiomes, underscoring the importance of thiamine pyrophosphate, cobalamin, and flavin mononucleotide in gene regulation. Interestingly, riboswitches do not vary significantly across microbiome representatives from around the world despite major taxonomic differences; this suggests an underlying conservation. Further studies elucidating the role of bacterial riboswitches in the host metabolome are needed to illuminate the consequences of our finding.},
}

@article {pmid38656971,
year = {2024},
author = {Alahdal, H and Almuneef, G and Alkhulaifi, MM and Aldibasi, O and Aljouie, A and Alharbi, O and Almohawes, ZN and Basingab, F and Rejili, M},
title = {Gut microbiota composition in patients with Crohn's disease in Saudi Arabia.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0299749},
doi = {10.1371/journal.pone.0299749},
pmid = {38656971},
issn = {1932-6203},
mesh = {Humans ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome ; Saudi Arabia/epidemiology ; Male ; Female ; Adult ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Dysbiosis/microbiology ; Young Adult ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Quality of Life ; },
abstract = {Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls. The results were correlated with the demographic and lifestyle information, which the participants provided via a questionnaire. α-diversity measures indicated lower bacterial diversity and richness in the active and inactive CD groups compared to the control group. Greater dysbiosis was observed in the active CD patients compared to the inactive form of the disease, showed by a reduction in microbial diversity. Specific pathogenic bacteria such as Filifactor, Peptoniphilus, and Sellimonas were identified as characteristic of CD groups. In contrast, anti-inflammatory bacteria like Defluviitalea, Papillibacter, and Petroclostridium were associated with the control group. Among the various factors influencing disease activity and microbiota dysbiosis, smoking emerged as the most significant, with reduced α-diversity and richness for the smokers in all groups, and proinflammatory Fusobacteria was more present (p<0.05). Opposite to the control group, microbial diversity and richness were lower in CD participants of older age compared to younger ones, and male CD participants showed less diversity compared to women participants from the same groups. Our results describe the first report on the relationship between microbiota and Crohn's disease progress in Saudi Arabia, which may provide a theoretical basis for the application of therapeutic methods to regulate gut microbes in CD.},
}

Humans
*Crohn Disease/microbiology
*Gastrointestinal Microbiome
Saudi Arabia/epidemiology
Male
Female
Adult
*RNA, Ribosomal, 16S/genetics
Middle Aged
Dysbiosis/microbiology
Young Adult
Bacteria/genetics/classification/isolation & purification
Case-Control Studies
Quality of Life

@article {pmid38656809,
year = {2024},
author = {Pérez-Prieto, I and Rodríguez-Santisteban, A and Altmäe, S},
title = {Beyond the reproductive tract: gut microbiome and its influence on gynecological health.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {36},
number = {3},
pages = {134-147},
pmid = {38656809},
issn = {1473-6519},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; *Endometriosis/microbiology ; *Polycystic Ovary Syndrome/microbiology ; *Reproductive Health ; Genitalia, Female/microbiology ; Genital Neoplasms, Female/microbiology ; Infertility, Female/microbiology ; Genital Diseases, Female/microbiology ; },
abstract = {PURPOSE OF REVIEW: The analysis of microbiome in association with female health is today a "hot topic" with the main focus on microbes in the female reproductive tract. Nevertheless, recent studies are providing novel information of the possible influence of the gut microbiome on gynecological health outcomes, especially as we start to understand that the gut microbiome is an extended endocrine organ influencing female hormonal levels. This review summarizes the current knowledge of the gut microbes in association with gynecological health.

RECENT FINDINGS: The gut microbiome has been associated with endometriosis, polycystic ovary syndrome, gynecological cancers, and infertility, although there is a lack of consistency and consensus among studies due to different study designs and protocols used, and the studies in general are underpowered.

SUMMARY: The interconnection between the gut microbiome and reproductive health is complex and further research is warranted. The current knowledge in the field emphasizes the link between the microbiome and gynecological health outcomes, with high potential for novel diagnostic and treatment tools via modulation of the microenvironment.},
}

Humans
Female
*Gastrointestinal Microbiome/physiology
*Endometriosis/microbiology
*Polycystic Ovary Syndrome/microbiology
*Reproductive Health
Genitalia, Female/microbiology
Genital Neoplasms, Female/microbiology
Infertility, Female/microbiology
Genital Diseases, Female/microbiology

@article {pmid38656326,
year = {2024},
author = {Ma, O and Dutta, A and Bliss, DW and Nakatsu, CH and Weaver, CM and Whisner, CM},
title = {Identifying Gut Microbiome Features that Predict Responsiveness Toward a Prebiotic Capable of Increasing Calcium Absorption: A Pilot Study.},
journal = {Calcified tissue international},
volume = {},
number = {},
pages = {},
pmid = {38656326},
issn = {1432-0827},
abstract = {Previously, we demonstrated that prebiotics may provide a complementary strategy for increasing calcium (Ca) absorption in adolescents which may improve long-term bone health. However, not all children responded to prebiotic intervention. We determine if certain baseline characteristics of gut microbiome composition predict prebiotic responsiveness. In this secondary analysis, we compared differences in relative microbiota taxa abundance between responders (greater than or equal to 3% increase in Ca absorption) and non-responders (less than 3% increase). Dual stable isotope methodologies were used to assess fractional Ca absorption at the end of crossover treatments with placebo, 10, and 20 g/day of soluble corn fiber (SCF). Microbial DNA was obtained from stool samples collected before and after each intervention. Sequencing of the 16S rRNA gene was used to taxonomically characterize the gut microbiome. Machine learning techniques were used to build a predictive model for identifying responders based on baseline relative taxa abundances. Model output was used to infer which features contributed most to prediction accuracy. We identified 19 microbial features out of the 221 observed that predicted responsiveness with 96.0% average accuracy. The results suggest a simplified prescreening can be performed to determine if a subject's bone health may benefit from a prebiotic. Additionally, the findings provide insight and prompt further investigation into the metabolic and genetic underpinnings affecting calcium absorption during pubertal bone development.},
}

@article {pmid38655910,
year = {2024},
author = {Salvado, R and Santos-Minguez, S and Lugones-Sánchez, C and Gonzalez-Sánchez, S and Tamayo-Morales, O and Quesada-Rico, JA and Benito, R and Rodríguez-Sánchez, E and Gómez-Marcos, MA and Casado-Vicente, V and Guimarães-Cunha, P and Hernandez-Rivas, JM and Mira, A and García-Ortiz, L and , },
title = {Gut microbiota and its relationship with early vascular ageing in a Spanish population (MIVAS study).},
journal = {European journal of clinical investigation},
volume = {},
number = {},
pages = {e14228},
doi = {10.1111/eci.14228},
pmid = {38655910},
issn = {1365-2362},
support = {PI20/00321//Instituto de Salud Carlos III/ ; RD21/0016/0010//Instituto de Salud Carlos III/ ; GRS 2148/B/2020//Junta de Castilla y León/ ; GRS: 2305/B/21//Junta de Castilla y León/ ; GRS: 2505/B/22//Junta de Castilla y León/ ; },
abstract = {BACKGROUND: Gut microbiota and its by-products are increasingly recognized as having a decisive role in cardiovascular diseases. The aim is to study the relationship between gut microbiota and early vascular ageing (EVA).

METHODS: A cross-sectional study was developed in Salamanca (Spain) in which 180 subjects aged 45-74 years were recruited. EVA was defined by the presence of at least one of the following: carotid-femoral pulse wave velocity (cf-PWV), cardio-ankle vascular index (CAVI) or brachial-ankle pulse wave velocity (ba-PWV) above the 90th percentile of the reference population. All other cases were considered normal vascular ageing (NVA).

MEASUREMENTS: cf-PWV was measured by SphygmoCor® System; CAVI and ba-PWV were determined by Vasera 2000® device. Gut microbiome composition in faecal samples was determined by 16S rRNA Illumina sequencing.

RESULTS: Mean age was 64.4 ± 6.9 in EVA group and 60.4 ± 7.6 years in NVA (p < .01). Women in EVA group were 41% and 53% in NVA. There were no differences in the overall composition of gut microbiota between the two groups when evaluating Firmicutes/Bacteriodetes ratio, alfa diversity (Shannon Index) and beta diversity (Bray-Curtis). Bilophila, Faecalibacterium sp.UBA1819 and Phocea, are increased in EVA group. While Cedecea, Lactococcus, Pseudomonas, Succiniclasticum and Dielma exist in lower abundance. In logistic regression analysis, Bilophila (OR: 1.71, 95% CI: 1.12-2.6, p = .013) remained significant.

CONCLUSIONS: In the studied Spanish population, early vascular ageing is positively associated with gut microbiota abundance of the genus Bilophila. No relationship was found between phyla abundance and measures of diversity.},
}

@article {pmid38655401,
year = {2024},
author = {Shi, W and Li, Z and Wang, W and Liu, X and Wu, H and Chen, X and Zhou, X and Zhang, S},
title = {Dynamic gut microbiome-metabolome in cationic bovine serum albumin induced experimental immune-complex glomerulonephritis and effect of losartan and mycophenolate mofetil on microbiota modulation.},
journal = {Journal of pharmaceutical analysis},
volume = {14},
number = {4},
pages = {100931},
pmid = {38655401},
issn = {2214-0883},
abstract = {Dynamic changes in gut dysbiosis and metabolomic dysregulation are associated with immune-complex glomerulonephritis (ICGN). However, an in-depth study on this topic is currently lacking. Herein, we report an ICGN model to address this gap. ICGN was induced via the intravenous injection of cationized bovine serum albumin (c-BSA) into Sprague-Dawley (SD) rats for two weeks, after which mycophenolate mofetil (MMF) and losartan were administered orally. Two and six weeks after ICGN establishment, fecal samples were collected and 16S ribosomal DNA (rDNA) sequencing and untargeted metabolomic were conducted. Fecal microbiota transplantation (FMT) was conducted to determine whether gut normalization caused by MMF and losartan contributed to their renal protective effects. A gradual decline in microbial diversity and richness was accompanied by a loss of renal function. Approximately 18 genera were found to have significantly different relative abundances between the early and later stages, and Marvinbryantia and Allobaculum were markedly upregulated in both stages. Untargeted metabolomics indicated that the tryptophan metabolism was enhanced in ICGN, characterized by the overproduction of indole and kynurenic acid, while the serotonin pathway was reduced. Administration of losartan and MMF ameliorated microbial dysbiosis and reduced the accumulation of indoxyl conjugates in feces. FMT using feces from animals administered MMF and losartan improved gut dysbiosis by decreasing the Firmicutes/Bacteroidetes (F/B) ratio but did not improve renal function. These findings indicate that ICGN induces serous gut dysbiosis, wherein an altered tryptophan metabolism may contribute to its progression. MMF and losartan significantly reversed the gut microbial and metabolomic dysbiosis, which partially contributed to their renoprotective effects.},
}

@article {pmid38655340,
year = {2024},
author = {Ma, CY and Zhao, J and Zhou, JY},
title = {Microbiome profiling and Co-metabolism pathway analysis in cervical cancer patients with acute radiation enteritis.},
journal = {Heliyon},
volume = {10},
number = {8},
pages = {e29598},
pmid = {38655340},
issn = {2405-8440},
abstract = {BACKGROUND: Intestinal bacteria significantly contribute to the metabolism of intestinal epithelial tissues. As the occurrence and development of radiation enteritis (RE) depend on the "co-metabolism" microenvironment formed by the host and intestinal microbiota, which involves complex influencing factors and strong correlations, ordinary techniques struggle to fully explain the underlying mechanisms. However, given that it is based on systems biology, metabolomics analysis is well-suited to address these issues. This study aimed to analyze the metabolomic changes in urine, serum, and fecal samples during volumetric modulated arc therapy (VMAT) for cervical cancer and screen for characteristic metabolites of severe acute radiation enteritis (SARE) and RE.

METHODS: We enrolled 50 patients who received radiotherapy for cervical cancer. Urine, serum, and fecal samples of patients were collected at one day before radiotherapy and the second week, fourth week, and sixth week after the start of radiotherapy. Control group samples were collected during the baseline period. Differential metabolites were identified by metabolomics analysis; co-metabolic pathways were clarified. We used the mini-SOM library for incorporating characteristic metabolites, and established metabolite classification models for predicting SARE and RE.

RESULTS: Urine and serum sample data showed remarkable clustering effect; metabolomics data of the fecal supernatant were evidently disturbed. Patient sample analyses during VMAT revealed the following. Urine samples: Downregulation of the pyrimidine and riboflavin metabolism pathways as well as initial upregulation followed by downregulation of arginine and proline metabolism pathways and the arginine biosynthesis pathway. Fecal samples: Upregulation of linoleic acid and phenylalanine metabolic pathways and initial downregulation followed by upregulation of arachidonic acid (AA) metabolic pathways. Serum samples: Initial upregulation followed by downregulation of the arginine biosynthesis pathway and downregulation of glutathione, AA, and arginine and proline metabolic pathways.

CONCLUSION: Patients with cervical cancer exhibited characteristic metabolic pathways and characteristic metabolites predicting RE and SARE were screened out. An effective RE mini-SOM classification model was successfully established.},
}

@article {pmid38655049,
year = {2024},
author = {Kretzschmar, GC and Boldt, ABW and Targa, ADS},
title = {Editorial: The genetics and epigenetics of mental health.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1402495},
doi = {10.3389/fgene.2024.1402495},
pmid = {38655049},
issn = {1664-8021},
}