@article {pmid39045787,
year = {2024},
author = {Tayebwa, DS and Hyeroba, D and Dunn, CD and Dunay, E and Richard, JC and Biryomumaisho, S and Acai, JO and Goldberg, TL},
title = {Viruses of free-roaming and hunting dogs in Uganda show elevated prevalence, richness and abundance across a gradient of contact with wildlife.},
journal = {The Journal of general virology},
volume = {105},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002011},
pmid = {39045787},
issn = {1465-2099},
mesh = {Animals ; Dogs ; Uganda/epidemiology ; *Dog Diseases/virology/epidemiology/transmission ; Prevalence ; *Animals, Wild/virology ; Virome ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; Anelloviridae/genetics/isolation & purification/classification ; Humans ; Virus Diseases/epidemiology/veterinary/transmission/virology ; },
abstract = {Domestic dogs (Canis lupus familiaris) live with humans, frequently contact other animals and may serve as intermediary hosts for the transmission of viruses. Free-roaming dogs, which account for over 70% of the world's domestic dog population, may pose a particularly high risk in this regard. We conducted an epidemiological study of dog viromes in three locations in Uganda, representing low, medium and high rates of contact with wildlife, ranging from dogs owned specifically for traditional hunting in a biodiversity and disease 'hotspot' to pets in an affluent suburb. We quantified rates of contact between dogs and wildlife through owner interviews and conducted canine veterinary health assessments. We then applied broad-spectrum viral metagenomics to blood plasma samples, from which we identified 46 viruses, 44 of which were previously undescribed, in three viral families, Sedoreoviridae, Parvoviridae and Anelloviridae. All 46 viruses (100 %) occurred in the high-contact population of dogs compared to 63 % and 39 % in the medium- and low-contact populations, respectively. Viral prevalence ranged from 2.1 % to 92.0 % among viruses and was highest, on average, in the high-contact population (22.3 %), followed by the medium-contact (12.3 %) and low-contact (4.8 %) populations. Viral richness (number of viruses per dog) ranged from 0 to 27 and was markedly higher, on average, in the high-contact population (10.2) than in the medium-contact (5.7) or low-contact (2.3) populations. Viral richness was strongly positively correlated with the number of times per year that a dog was fed wildlife and negatively correlated with the body condition score, body temperature and packed cell volume. Viral abundance (cumulative normalized metagenomic read density) varied 124-fold among dogs and was, on average, 4.1-fold higher and 2.4-fold higher in the high-contact population of dogs than in the low-contact or medium-contact populations, respectively. Viral abundance was also strongly positively correlated with the number of times per year that a dog was fed wildlife, negatively correlated with packed cell volume and positively correlated with white blood cell count. These trends were driven by nine viruses in the family Anelloviridae, genus Thetatorquevirus, and by one novel virus in the family Sedoreoviridae, genus Orbivirus. The genus Orbivirus contains zoonotic viruses and viruses that dogs can acquire through ingestion of infected meat. Overall, our findings show that viral prevalence, richness and abundance increased across a gradient of contact between dogs and wildlife and that the health status of the dog modified viral infection. Other ecological, geographic and social factors may also have contributed to these trends. Our finding of a novel orbivirus in dogs with high wildlife contact supports the idea that free-roaming dogs may serve as intermediary hosts for viruses of medical importance to humans and other animals.},
}

Animals
Dogs
Uganda/epidemiology
*Dog Diseases/virology/epidemiology/transmission
Prevalence
*Animals, Wild/virology
Virome
Viruses/classification/isolation & purification/genetics
Metagenomics
Anelloviridae/genetics/isolation & purification/classification
Humans
Virus Diseases/epidemiology/veterinary/transmission/virology

@article {pmid39044909,
year = {2024},
author = {Moumen, B and Samba-Louaka, C and Kimpamboudi, VAM and Boumba, AM and Ngoma, HS and Samba-Louaka, A},
title = {Metagenomic data from gutter water in the city of Pointe-Noire, Republic of Congo.},
journal = {Data in brief},
volume = {55},
number = {},
pages = {110655},
pmid = {39044909},
issn = {2352-3409},
abstract = {After Amazonia, the Congo Basin represents the second-largest tropical rainforest area in the world. This basin harbours remarkable biodiversity, yet much of its microbiological diversity within its waters, soils, and populations remains largely unexplored and undiscovered. While many initiatives to characterize global biodiversity are being undertaken, few are conducted in Africa and none of them concern the Congo Basin specifically in urban areas. In this context, we assessed the microbial diversity present in gutter water in the city of Pointe-Noire, Congo. This town has interesting characteristics as the population density is high and it is located between the Atlantic Ocean and the forest of Mayombe in Central Africa. The findings illuminate the microbial composition of surface water in Pointe-Noire. The dataset allows the identification of putative new bacteria through the assembly of 81 meta-genome-assembled genomes. It also serves as a valuable primary resource for assessing the presence of antibiotic-resistant genes, offering a useful tool for monitoring risks by public health authorities.},
}

@article {pmid39044261,
year = {2024},
author = {Ma, S and Yin, Y and Guo, Y and Yao, C and Xu, S and Luo, Q and Yin, G and Wang, S and Wang, Q and Chen, H and Wang, R and Jin, L and Liang, G and Wang, H},
title = {The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {137},
pmid = {39044261},
issn = {2049-2618},
mesh = {Humans ; Male ; Female ; *DNA Viruses/isolation & purification/genetics ; Middle Aged ; *Virus Diseases/blood/virology ; Adult ; *Hematologic Diseases/complications/blood ; *RNA Viruses/isolation & purification ; Virome ; Aged ; Torque teno virus/isolation & purification/genetics ; Cohort Studies ; Herpesvirus 4, Human/genetics/isolation & purification ; Young Adult ; },
abstract = {BACKGROUND: Haematological patients exhibit immune system abnormalities that make them susceptible to viral infections. Understanding the relationship between the virome in the blood plasma of haematological patients and their clinical characteristic is crucial for disease management. We aimed to explore the presence of viral pathogens and identify close associations between viral infections and various clinical features.

RESULTS: A total of 21 DNA viruses and 6 RNA viruses from 12 virus families were identified from 1383 patients. Patients with haematological diseases exhibited significantly higher diversity, prevalence, and co-detection rates of viral pathogens. During fever episodes, pathogen detection was notably higher, with Epstein-Barr virus (EBV) and Mucorales infections being the most probable culprits for fever symptoms in non-haematological patients. The detection rate of torque teno virus (TTV) significantly increases in haematological patients after transplantation and during primary lung infections. Additionally, TTV-positive patients demonstrate significantly higher absolute neutrophil counts, while C-reactive protein and procalcitonin levels are notably lower. Furthermore, TTV, cytomegalovirus, and parvovirus B19 (B19V) were found to be more prevalent in non-neutropenic patients, while non-viral pathogenic infections, such as Gram-negative bacteria and Mucorales, were more common in neutropenic patients. Pegivirus C (HPgV-C) infection often occurred post-transplantation, regardless of neutropenia. Additionally, some viruses such as TTV, B19V, EBV, and HPgV-C showed preferences for age and seasonal infections.

CONCLUSIONS: Analysis of the plasma virome revealed the susceptibility of haematological patients to plasma viral infections at specific disease stages, along with the occurrence of mixed infections with non-viral pathogens. Close associations were observed between the plasma virome and various clinical characteristics, as well as clinical detection parameters. Understanding plasma virome aids in auxiliary clinical diagnosis and treatment, enabling early prevention to reduce infection rates in patients and improve their quality of life. Video Abstract.},
}

Humans
Male
Female
*DNA Viruses/isolation & purification/genetics
Middle Aged
*Virus Diseases/blood/virology
Adult
*Hematologic Diseases/complications/blood
*RNA Viruses/isolation & purification
Virome
Aged
Torque teno virus/isolation & purification/genetics
Cohort Studies
Herpesvirus 4, Human/genetics/isolation & purification
Young Adult

@article {pmid39044244,
year = {2024},
author = {Glendinning, L and Jia, X and Kebede, A and Oyola, SO and Park, JE and Park, W and Assiri, A and Holm, JB and Kristiansen, K and Han, J and Hanotte, O},
title = {Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {138},
pmid = {39044244},
issn = {2049-2618},
mesh = {Animals ; *Chickens/microbiology ; Ethiopia ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Cecum/microbiology ; Microbiota ; Biodiversity ; Phylogeny ; },
abstract = {BACKGROUND: Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.

RESULTS: Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.

CONCLUSIONS: The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.},
}

Animals
*Chickens/microbiology
Ethiopia
*Altitude
*Bacteria/classification/genetics/isolation & purification
Gastrointestinal Microbiome/genetics
Metagenome
Cecum/microbiology
Microbiota
Biodiversity
Phylogeny

@article {pmid39040604,
year = {2024},
author = {Hasan, Z and Netherland, M and Hasan, NA and Begum, N and Yasmin, M and Ahmed, S},
title = {An insight into the vaginal microbiome of infertile women in Bangladesh using metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1390088},
pmid = {39040604},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Metagenomics/methods ; *Infertility, Female/microbiology ; Adult ; *Microbiota/genetics ; Bangladesh ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Young Adult ; Lactobacillus/isolation & purification/genetics/classification ; Dysbiosis/microbiology ; Phylogeny ; },
abstract = {INTRODUCTION: The dysbiosis of vaginal microbiota is recognized as a potential underlying factor contributing to infertility in women. This study aimed to compare the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility.

METHODS: Metagenomic analysis was conducted on samples from 5 infertile and 5 fertile individuals using both amplicon 16S and metagenomics shotgun sequencing methods.

RESULTS AND DISCUSSION: In the infertile group, the bacterial community was primarily represented by three major bacterial genera: Lactobacillus (79.42%), Gardnerella (12.56%) and Prevotella (3.33%), whereas, the fertile group exhibited a more diverse composition with over 8 major bacterial genera, accompanied by significantly reduced abundance of Lactobacillus (48.79%) and Gardnerella (6.98%). At the species level, higher abundances of L. iners, L. gasseri and G. vaginalis were observed in the infertile group. Regarding the microbiome composition, only one fertile and two infertile subjects exhibited the healthiest Community State Types, CST-1, while CST-3 was observed among two infertile and one fertile subject, and CST-4 in three other fertile and one infertile subject. Overall, alpha diversity metrics indicated greater diversity and lower species richness in the control (fertile) group, while the infertile group displayed the opposite trend. However, beta-diversity analysis did not show distinct clustering of samples associated with any specific group; instead, it demonstrated CST-type specific clustering. Shotgun metagenomics further confirmed the dominance of Firmicutes, with a greater abundance of Lactobacillus species in the infertile group. Specifically, L. iners and G. vaginalis were identified as the most dominant and highly abundant in the infertile group. Fungi were only identified in the control group, dominated by Penicillium citrinum (62.5%). Metagenome-assembled genomes (MAGs) corroborated read-based taxonomic profiling, with the taxon L. johnsonii identified exclusively in disease samples. MAG identities shared by both groups include Shamonda orthobunyavirus, L. crispatus, Human endogenous retrovirus K113, L. iners, and G. vaginalis. Interestingly, the healthy microbiomes sequenced in this study contained two clusters, Penicillium and Staphylococcus haemolyticus, not found in the public dataset. In conclusion, this study suggests that lower species diversity with a higher abundance of L. iners, L. gasseri and G. vaginalis, may contribute to female infertility in our study datasets. However, larger sample sizes are necessary to further evaluate such association.},
}

Humans
Female
*Vagina/microbiology
*Metagenomics/methods
*Infertility, Female/microbiology
Adult
*Microbiota/genetics
Bangladesh
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenome
Young Adult
Lactobacillus/isolation & purification/genetics/classification
Dysbiosis/microbiology
Phylogeny

@article {pmid39039586,
year = {2024},
author = {Liang, JL and Feng, SW and Jia, P and Lu, JL and Yi, X and Gao, SM and Wu, ZH and Liao, B and Shu, WS and Li, JT},
title = {Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {136},
pmid = {39039586},
issn = {2049-2618},
support = {42177009//National Natural Science Foundation of China/ ; 41622106//National Natural Science Foundation of China/ ; 2023YFC3207300//National Key R&D Program of China/ ; },
mesh = {China ; *Soil Microbiology ; *Metagenome ; *Ecosystem ; *Giant Viruses/genetics/classification ; Soil/chemistry ; Phylogeny ; Genome, Viral/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood.

RESULTS: In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling.

CONCLUSIONS: These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses. Video Abstract.},
}

China
*Soil Microbiology
*Metagenome
*Ecosystem
*Giant Viruses/genetics/classification
Soil/chemistry
Phylogeny
Genome, Viral/genetics
Metagenomics

@article {pmid39039555,
year = {2024},
author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T},
title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {134},
pmid = {39039555},
issn = {2049-2618},
mesh = {*Bacteriophages/genetics/classification/physiology/isolation & purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; },
abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.

RESULTS: We uncovered distinct distribution patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as potentially host abundance- or phage/host ratio-driven phage population changes.

CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.},
}

*Bacteriophages/genetics/classification/physiology/isolation & purification
*Sewage/virology/microbiology
*Wastewater/virology/microbiology
*Bacteria/virology/genetics/classification
Biofilms
Metagenomics
Water Purification/methods
Microbiota

@article {pmid39039462,
year = {2024},
author = {Yan, L and Ye, B and Yang, M and Shan, Y and Yan, D and Fang, D and Zhang, K and Yu, Y},
title = {Gut microbiota and metabolic changes in children with idiopathic short stature.},
journal = {BMC pediatrics},
volume = {24},
number = {1},
pages = {468},
pmid = {39039462},
issn = {1471-2431},
mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Feces/microbiology ; Case-Control Studies ; Adolescent ; Body Height ; Growth Disorders/microbiology/metabolism ; Metabolomics/methods ; Metabolome ; },
abstract = {BACKGROUND: Idiopathic short stature (ISS) is characterized by short stature with unknown causes. Recent studies showed different gut microbiota flora and reduced fecal short-chain fatty acids in ISS children. However, the roles of the microbiome and metabolites in the pathogenesis of ISS remains largely unknown.

METHODS: We recruited 51 Chinese subjects, comprising 26 ISS children and 25 normal-height control individuals. Untargeted metabolomics was performed to explore the fecal metabolic profiles between groups. A shotgun metagenomic sequencing approach was used to investigate the microbiome at the strains level. Mediation analyses were done to reveal correlations between the height standard deviation (SD) value, the gut microbiome and metabolites.

RESULTS: We detected marked differences in the composition of fecal metabolites in the ISS group, particularly a significant increase in erucic acid and a decrease in spermidine, adenosine and L-5-Hydroxytryptophan, when compared to those of controls. We further identified specific groups of bacterial strains to be associated with the different metabolic profile. Through mediation analysis, 50 linkages were established. KEGG pathway analysis of microbiota and metabolites indicated nutritional disturbances. 13 selected features were able to accurately distinguish the ISS children from the controls (AUC = 0.933 [95%CI, 79.9-100%]) by receiver operating characteristic (ROC) analysis.

CONCLUSION: Our study suggests that the microbiome and the microbial-derived metabolites play certain roles in children's growth. These findings provide a new research direction for better understanding the mechanism(s) underlying ISS.},
}

Humans
*Gastrointestinal Microbiome
Child
Male
Female
*Feces/microbiology
Case-Control Studies
Adolescent
Body Height
Growth Disorders/microbiology/metabolism
Metabolomics/methods
Metabolome

@article {pmid39039075,
year = {2024},
author = {Stothart, MR and McLoughlin, PD and Medill, SA and Greuel, RJ and Wilson, AJ and Poissant, J},
title = {Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6012},
pmid = {39039075},
issn = {2041-1723},
support = {2016-06459//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 2019-04388//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 25046//Canada Foundation for Innovation (Fondation canadienne pour l'innovation)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; },
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Methane/metabolism ; Animals, Wild/microbiology ; Metagenome ; Fatty Acids, Volatile/metabolism ; Metagenomics/methods ; Male ; Female ; Canada ; },
abstract = {Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Methane/metabolism
Animals, Wild/microbiology
Metagenome
Fatty Acids, Volatile/metabolism
Metagenomics/methods
Male
Female
Canada

@article {pmid39038938,
year = {2024},
author = {Chuang, YF and Fan, KC and Su, YY and Wu, MF and Chiu, YL and Liu, YC and Lin, CC},
title = {Precision probiotics supplement strategy in aging population based on gut microbiome composition.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {4},
pages = {},
pmid = {39038938},
issn = {1477-4054},
support = {//Taiwan National Science and Technology Council/ ; MOST 110-2321-B-418//Ministry of Science and Technology/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare/ ; NYCU-FEMH 112DN11//FEMH-NYCU Joint Research Program/ ; },
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Gastrointestinal Microbiome ; Aged ; *Aging ; Female ; Male ; *Dietary Supplements ; Aged, 80 and over ; Middle Aged ; Lactobacillus/genetics ; Metagenomics/methods ; Bifidobacterium ; },
abstract = {With the increasing prevalence of age-related chronic diseases burdening healthcare systems, there is a pressing need for innovative management strategies. Our study focuses on the gut microbiota, essential for metabolic, nutritional, and immune functions, which undergoes significant changes with aging. These changes can impair intestinal function, leading to altered microbial diversity and composition that potentially influence health outcomes and disease progression. Using advanced metagenomic sequencing, we explore the potential of personalized probiotic supplements in 297 older adults by analyzing their gut microbiota. We identified distinctive Lactobacillus and Bifidobacterium signatures in the gut microbiota of older adults, revealing probiotic patterns associated with various population characteristics, microbial compositions, cognitive functions, and neuroimaging results. These insights suggest that tailored probiotic supplements, designed to match individual probiotic profile, could offer an innovative method for addressing age-related diseases and functional declines. Our findings enhance the existing evidence base for probiotic use among older adults, highlighting the opportunity to create more targeted and effective probiotic strategies. However, additional research is required to validate our results and further assess the impact of precision probiotics on aging populations. Future studies should employ longitudinal designs and larger cohorts to conclusively demonstrate the benefits of tailored probiotic treatments.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Gastrointestinal Microbiome
Aged
*Aging
Female
Male
*Dietary Supplements
Aged, 80 and over
Middle Aged
Lactobacillus/genetics
Metagenomics/methods
Bifidobacterium

@article {pmid39038883,
year = {2024},
author = {Han, PJ and Song, L and Wen, Z and Zhu, HY and Wei, YH and Wang, JW and Bai, M and Luo, LJ and Wang, JW and Chen, SX and You, XL and Han, DY and Bai, FY},
title = {Species-level understanding of the bacterial community in Daqu based on full-length 16S rRNA gene sequences.},
journal = {Food microbiology},
volume = {123},
number = {},
pages = {104566},
doi = {10.1016/j.fm.2024.104566},
pmid = {39038883},
issn = {1095-9998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Fermentation ; China ; Microbiota ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; Alcoholic Beverages/microbiology/analysis ; Food Microbiology ; Metagenome ; Fermented Foods/microbiology ; },
abstract = {Daqu is used as the fermentation starter of Baijiu and contributes diversified functional microbes for saccharifying grains and converting sugars into ethanol and aroma components in Baijiu products. Daqu is mainly classified into three types, namely low (LTD), medium (MTD) and high (HTD) temperature Daqu, according to the highest temperatures reached in their fermentation processes. In this study, we used the PacBio small-molecule real-time (SMRT) sequencing technology to determine the full-length 16 S rRNA gene sequences from the metagenomes of 296 samples of different types of Daqu collected from ten provinces in China, and revealed the bacterial diversity at the species level in the Daqu samples. We totally identified 310 bacteria species, including 78 highly abundant species (with a relative abundance >0.1% each) which accounted for 91.90% of the reads from all the Daqu samples. We also recognized the differentially enriched bacterial species in different types of Daqu, and in the Daqu samples with the same type but from different provinces. Specifically, Lactobacillales, Enterobacterales and Bacillaceae were significantly enriched in the LTD, MTD and HTD groups, respectively. The potential co-existence and exclusion relationships among the bacteria species involved in all the Daqu samples and in the LTD, MTD and HTD samples from a specific region were also identified. These results provide a better understanding of the bacterial diversity in different types of Daqu at the species level.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Fermentation
China
Microbiota
Phylogeny
DNA, Bacterial/genetics
Biodiversity
Alcoholic Beverages/microbiology/analysis
Food Microbiology
Metagenome
Fermented Foods/microbiology

@article {pmid39038849,
year = {2024},
author = {Lee, S and Portlock, T and Le Chatelier, E and Garcia-Guevara, F and Clasen, F and Oñate, FP and Pons, N and Begum, N and Harzandi, A and Proffitt, C and Rosario, D and Vaga, S and Park, J and von Feilitzen, K and Johansson, F and Zhang, C and Edwards, LA and Lombard, V and Gauthier, F and Steves, CJ and Gomez-Cabrero, D and Henrissat, B and Lee, D and Engstrand, L and Shawcross, DL and Proctor, G and Almeida, M and Nielsen, J and Mardinoglu, A and Moyes, DL and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Global compositional and functional states of the human gut microbiome in health and disease.},
journal = {Genome research},
volume = {34},
number = {6},
pages = {967-978},
doi = {10.1101/gr.278637.123},
pmid = {39038849},
issn = {1549-5469},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Metagenomics/methods ; Machine Learning ; Fusobacterium nucleatum/genetics ; Bacteria/classification/genetics ; },
abstract = {The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenome
*Metagenomics/methods
Machine Learning
Fusobacterium nucleatum/genetics
Bacteria/classification/genetics

@article {pmid39037634,
year = {2024},
author = {Elmagzoub, WA and Idris, SM and Elnaiem, MHE and Mukhtar, ME and Eltayeb, E and Bakhiet, SM and Okuni, JB and Ojok, L and El Sanousi, SM and El Wahed, AA and Gameel, AA and Eltom, KH},
title = {Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {9},
pages = {276},
pmid = {39037634},
issn = {1573-0972},
support = {Project number 404935781//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Cattle ; *Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics ; *Feces/microbiology ; *Paratuberculosis/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Cattle Diseases/microbiology ; *Milk/microbiology ; *DNA, Bacterial/genetics ; Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; },
abstract = {Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.},
}

Animals
Cattle
*Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics
*Feces/microbiology
*Paratuberculosis/microbiology
*RNA, Ribosomal, 16S/genetics
*Cattle Diseases/microbiology
*Milk/microbiology
*DNA, Bacterial/genetics
Gastrointestinal Microbiome
Female
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods

@article {pmid39035870,
year = {2024},
author = {Rabbachin, L and Nir, I and Waldherr, M and Vassallo, Y and Piñar, G and Graf, A and Kushmaro, A and Sterflinger, K},
title = {Diversity of fungi associated with petroglyph sites in the Negev Desert, Israel, and their potential role in bioweathering.},
journal = {Frontiers in fungal biology},
volume = {5},
number = {},
pages = {1400380},
pmid = {39035870},
issn = {2673-6128},
abstract = {The petroglyphs of the Negev Desert, Israel, are famous and valuable archaeological remains. Previous studies have investigated the microbial communities associated with petroglyphs and their potential role in stone deterioration; nevertheless, the role of fungi remains unclear. In this study, the fungal communities present on the stone and, as a comparison, in the surrounding environment (soil and air) at Negev petroglyph sites were analyzed by means of culture-dependent and -independent (metagenomic) techniques. The metagenomic results showed a high fungal biodiversity in the soil, and both approaches highlighted the prevalence of species producing melanized, large, thick-walled spores (mainly Alternaria spp.). From the air sampling, mostly Cladosporium spp. were retrieved. On the other hand, on the rock, the results seem to indicate a low presence of fungi, but with a rock-specialized mycobiota consisting of extremotolerant microcolonial fungi (MCF) (e.g., Vermiconidia and Coniosporium) and lichens (Flavoplaca). In addition, low proportions of cosmopolitan fungi were detected on the stone, but the comparison of the data clearly indicates that they are transients from the surrounding environment. The ability of the isolated strains to dissolve CaCO3 and therefore be a potential threat to the petroglyphs (limestone substrate) was tested, but only one strain resulted in positive acid production under laboratory conditions. Nevertheless, both lichens and MCF detected in this study are well-known stone deteriogens, which may have a significant impact on the petroglyph's deterioration.},
}

@article {pmid39034613,
year = {2024},
author = {Krigul, KL and Feeney, RH and Wongkuna, S and Aasmets, O and Holmberg, SM and Andreson, R and Puértolas-Balint, F and Pantiukh, K and Sootak, L and Org, T and Tenson, T and Org, E and Schroeder, BO},
title = {A history of repeated antibiotic usage leads to microbiota-dependent mucus defects.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2377570},
doi = {10.1080/19490976.2024.2377570},
pmid = {39034613},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Fecal Microbiota Transplantation ; *Mucus/metabolism/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification/metabolism ; Intestinal Mucosa/microbiology/metabolism/drug effects ; Male ; Female ; Feces/microbiology ; Adult ; Middle Aged ; Akkermansia ; Mice, Inbred C57BL ; Colon/microbiology ; Bacteroides fragilis/drug effects ; },
abstract = {Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Animals
*Anti-Bacterial Agents/pharmacology
Mice
*Fecal Microbiota Transplantation
*Mucus/metabolism/microbiology
*Bacteria/classification/genetics/drug effects/isolation & purification/metabolism
Intestinal Mucosa/microbiology/metabolism/drug effects
Male
Female
Feces/microbiology
Adult
Middle Aged
Akkermansia
Mice, Inbred C57BL
Colon/microbiology
Bacteroides fragilis/drug effects

@article {pmid39033279,
year = {2024},
author = {Trinh, P and Teichman, S and Roberts, MC and Rabinowitz, PM and Willis, AD},
title = {A cross-sectional comparison of gut metagenomes between dairy workers and community controls.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {708},
doi = {10.1186/s12864-024-10562-1},
pmid = {39033279},
issn = {1471-2164},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Metagenome ; Female ; Dairying ; Metagenomics/methods ; Adult ; Animals ; Middle Aged ; Bacteria/genetics/classification ; Farmers ; Male ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).

CONCLUSIONS: This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.},
}

Humans
*Gastrointestinal Microbiome/genetics
Cross-Sectional Studies
*Metagenome
Female
Dairying
Metagenomics/methods
Adult
Animals
Middle Aged
Bacteria/genetics/classification
Farmers
Male
Drug Resistance, Bacterial/genetics

@article {pmid39030648,
year = {2024},
author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE},
title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {50},
pmid = {39030648},
issn = {2524-6372},
support = {2016/23699-8; 2018/14892-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.},
}

@article {pmid39030599,
year = {2024},
author = {Xu, SY and Feng, XR and Zhao, W and Bi, YL and Diao, QY and Tu, Y},
title = {Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {131},
pmid = {39030599},
issn = {2049-2618},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Weaning ; Bacteria/classification/isolation & purification/metabolism/genetics ; Female ; Fermentation ; Metagenomics/methods ; Metabolomics ; Fatty Acids, Volatile/metabolism/analysis ; Weight Gain ; Butyrates/metabolism ; },
abstract = {BACKGROUND: The average daily gain (ADG) of preweaning calves significantly influences their adult productivity and reproductive performance. Gastrointestinal microbes are known to exert an impact on host phenotypes, including ADG. The aim of this study was to investigate the mechanisms by which gastrointestinal microbiome regulate ADG in preweaning calves and to further validate them by isolating ADG-associated rumen microbes in vitro.

RESULTS: Sixteen Holstein heifer calves were selected from a cohort with 106 calves and divided into higher ADG (HADG; n = 8) and lower ADG (LADG; n = 8) groups. On the day of weaning, samples of rumen contents, hindgut contents, and plasma were collected for rumen metagenomics, rumen metabolomics, hindgut metagenomics, hindgut metabolomics, and plasma metabolomics analyses. Subsequently, rumen contents of preweaning Holstein heifer calves from the same dairy farm were collected to isolate ADG-associated rumen microbes. The results showed that the rumen microbes, including Pyramidobacter sp. C12-8, Pyramidobacter sp. CG50-2, Pyramidobacter porci, unclassified_g_Pyramidobacter, Pyramidobacter piscolens, and Acidaminococcus fermentans, were enriched in the rumen of HADG calves (LDA > 2, P < 0.05). Enrichment of these microbes in HADG calves' rumen promoted carbohydrate degradation and volatile fatty acid production, increasing proportion of butyrate in the rumen and ultimately contributing to higher preweaning ADG in calves (P < 0.05). The presence of active carbohydrate degradation in the rumen was further suggested by the negative correlation of the rumen microbes P. piscolens, P. sp. C12-8 and unclassified_g_Pyramidobacter with the rumen metabolites D-fructose (R <  - 0.50, P < 0.05). Widespread positive correlations were observed between rumen microbes (such as P. piscolens, P. porci, and A. fermentans) and beneficial plasma metabolites (such as 1-pyrroline-5-carboxylic acid and 4-fluoro-L-phenylalanine), which were subsequently positively associated with the growth rate of HADG calves (R > 0.50, P < 0.05). We succeeded in isolating a strain of A. fermentans from the rumen contents of preweaning calves and named it Acidaminococcus fermentans P41. The in vitro cultivation revealed its capability to produce butyrate. In vitro fermentation experiments demonstrated that the addition of A. fermentans P41 significantly increased the proportion of butyrate in the rumen fluid (P < 0.05). These results further validated our findings. The relative abundance of Bifidobacterium pseudolongum in the hindgut of HADG calves was negatively correlated with hindgut 4-hydroxyglucobrassicin levels, which were positively correlated with plasma 4-hydroxyglucobrassicin levels, and plasma 4-hydroxyglucobrassicin levels were positively correlated with ADG (P < 0.05).

CONCLUSIONS: This study's findings unveil that rumen and hindgut microbes play distinctive roles in regulating the preweaning ADG of Holstein heifer calves. Additionally, the successful isolation of A. fermentans P41 not only validated our findings but also provided a valuable strain resource for modulating rumen microbes in preweaning calves. Video Abstract.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Gastrointestinal Microbiome
*Weaning
Bacteria/classification/isolation & purification/metabolism/genetics
Female
Fermentation
Metagenomics/methods
Metabolomics
Fatty Acids, Volatile/metabolism/analysis
Weight Gain
Butyrates/metabolism

@article {pmid39028528,
year = {2024},
author = {Han, Y and Zhang, Y and Yang, Z and Zhang, Q and He, X and Song, Y and Tian, L and Wu, H},
title = {Improving Aerobic Digestion of Food Waste by Adding a Personalized Microbial Inoculum.},
journal = {Current microbiology},
volume = {81},
number = {9},
pages = {277},
pmid = {39028528},
issn = {1432-0991},
support = {236Z3301G//Natural Science Foundation of Hebei Province/ ; B2020203005//Natural Science Foundation of Hebei Province/ ; 2021LGQN027//Cultivation Project for Basic Research and Innovation of YanShan University/ ; 236Z3604G//National Science Founbdation of Hebei Province/ ; 2023GJJG396//Hebei Education Department/ ; ZD2022088//China Hebei Education Department/ ; ZC2023041//China Hebei Education Department/ ; 2021LGQN018//Cultivation Project for Basic Research and Innovation of YanShan University/ ; },
mesh = {Aerobiosis ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Microbial Consortia ; Garbage ; China ; Refuse Disposal/methods ; Hydrolysis ; Metagenomics ; Food Loss and Waste ; },
abstract = {In the context of China's garbage classification policy, on-site aerobic food waste (FW) digestion is crucial for reducing transportation and disposal costs. The efficiency of this process is largely determined by the microbial community structure and its functions. Therefore, this study aimed to analyze the impact of a personalized microbial consortium (MCM) on the efficiency of aerobic FW digestion and to reveal the underlying mechanisms. An MCM, sourced from naturally degrading FW, was selected to enrich degrading bacteria with relatively high hydrolyzing ability. The functionality of the MCM was evaluated by tracing the successions of microbial communities, and comparing the differences in the forms of organic compounds, metabolic functions, and hydrolase activities. X-ray photoelectron spectroscopy demonstrated that the MCM metabolized faster, and produced more acidic metabolites. Metagenomic analysis indicated that FW inoculated with the personalized MCM increased abundance of Bacillaceae producing hydrolysis enzymes and promoted glycolysis metabolic pathways, enhancing energy generation for metabolism, compared to the commercial effective bacterial agent. This paper provides both theoretical and practical evidence for the improvement of biochemical processor of FW with the personalized MCM, which has promising application prospects and economic value.},
}

Aerobiosis
*Bacteria/classification/metabolism/genetics/isolation & purification
Microbial Consortia
Garbage
China
Refuse Disposal/methods
Hydrolysis
Metagenomics
Food Loss and Waste

@article {pmid39026261,
year = {2024},
author = {Lee, M and Kaul, A and Ward, JM and Zhu, Q and Richards, M and Wang, Z and González, A and Parks, CG and Beane Freeman, LE and Umbach, DM and Motsinger-Reif, AA and Knight, R and London, SJ},
title = {House dust metagenome and pulmonary function in a US farming population.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {129},
pmid = {39026261},
issn = {2049-2618},
support = {Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-CP010119B/CA/NCI NIH HHS/United States ; },
mesh = {*Dust/analysis ; Humans ; *Metagenome ; Female ; Male ; United States ; *Microbiota/genetics ; Middle Aged ; Lung/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Forced Expiratory Volume ; Agriculture ; Respiratory Function Tests ; Vital Capacity ; Metagenomics/methods ; },
abstract = {BACKGROUND: Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together.

RESULTS: Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait.

CONCLUSIONS: Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract.},
}

*Dust/analysis
Humans
*Metagenome
Female
Male
United States
*Microbiota/genetics
Middle Aged
Lung/microbiology
Adult
Bacteria/classification/genetics/isolation & purification
Forced Expiratory Volume
Agriculture
Respiratory Function Tests
Vital Capacity
Metagenomics/methods

@article {pmid39026166,
year = {2024},
author = {Jing, Z and Zheng, W and Jianwen, S and Hong, S and Xiaojian, Y and Qiang, W and Yunfeng, Y and Xinyue, W and Shuwen, H and Feimin, Z},
title = {Gut microbes on the risk of advanced adenomas.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {264},
pmid = {39026166},
issn = {1471-2180},
support = {No.2023KY1178//Zhejiang Medical and Health Technology Project/ ; No.2023KY1178//Zhejiang Medical and Health Technology Project/ ; No.2023HT078//China University Industry University Research Innovation Fund/ ; No.2023HT078//China University Industry University Research Innovation Fund/ ; No. 2023GY18//PublicWelfare Technology Application Research Program of Huzhou/ ; No. 2023GY18//PublicWelfare Technology Application Research Program of Huzhou/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Adenoma/microbiology/virology ; *Feces/microbiology/virology ; *Colorectal Neoplasms/microbiology/virology ; Male ; Middle Aged ; Female ; Viruses/isolation & purification/classification/genetics/pathogenicity ; High-Throughput Nucleotide Sequencing ; Aged ; Machine Learning ; },
abstract = {BACKGROUND: More than 90% of colorectal cancer (CRC) arises from advanced adenomas (AA) and gut microbes are closely associated with the initiation and progression of both AA and CRC.

OBJECTIVE: To analyze the characteristic microbes in AA.

METHODS: Fecal samples were collected from 92 AA and 184 negative control (NC). Illumina HiSeq X sequencing platform was used for high-throughput sequencing of microbial populations. The sequencing results were annotated and compared with NCBI RefSeq database to find the microbial characteristics of AA. R-vegan package was used to analyze α diversity and β diversity. α diversity included box diagram, and β diversity included Principal Component Analysis (PCA), principal co-ordinates analysis (PCoA), and non-metric multidimensional scaling (NMDS). The AA risk prediction models were constructed based on six kinds of machine learning algorithms. In addition, unsupervised clustering methods were used to classify bacteria and viruses. Finally, the characteristics of bacteria and viruses in different subtypes were analyzed.

RESULTS: The abundance of Prevotella sp900557255, Alistipes putredinis, and Megamonas funiformis were higher in AA, while the abundance of Lilyvirus, Felixounavirus, and Drulisvirus were also higher in AA. The Catboost based model for predicting the risk of AA has the highest accuracy (bacteria test set: 87.27%; virus test set: 83.33%). In addition, 4 subtypes (B1V1, B1V2, B2V1, and B2V2) were distinguished based on the abundance of gut bacteria and enteroviruses (EVs). Escherichia coli D, Prevotella sp900557255, CAG-180 sp000432435, Phocaeicola plebeiuA, Teseptimavirus, Svunavirus, Felixounavirus, and Jiaodavirus are the characteristic bacteria and viruses of 4 subtypes. The results of Catboost model indicated that the accuracy of prediction improved after incorporating subtypes. The accuracy of discovery sets was 100%, 96.34%, 100%, and 98.46% in 4 subtypes, respectively.

CONCLUSION: Prevotella sp900557255 and Felixounavirus have high value in early warning of AA. As promising non-invasive biomarkers, gut microbes can become potential diagnostic targets for AA, and the accuracy of predicting AA can be improved by typing.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification
*Adenoma/microbiology/virology
*Feces/microbiology/virology
*Colorectal Neoplasms/microbiology/virology
Male
Middle Aged
Female
Viruses/isolation & purification/classification/genetics/pathogenicity
High-Throughput Nucleotide Sequencing
Aged
Machine Learning

@article {pmid39024228,
year = {2024},
author = {Ravelo, AD and Ferm, P and Guo, Y and Omontese, BO and Morley, PS and Chen, C and Noyes, NR and Caixeta, LS},
title = {Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305674},
pmid = {39024228},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; Female ; *Milk/metabolism/microbiology ; *Lactation ; Phenotype ; Metabolome ; Microbiota ; Genomics/methods ; Metagenome ; Metabolomics/methods ; Multiomics ; },
abstract = {This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
Female
*Milk/metabolism/microbiology
*Lactation
Phenotype
Metabolome
Microbiota
Genomics/methods
Metagenome
Metabolomics/methods
Multiomics

@article {pmid39023095,
year = {2024},
author = {Zhang, P and Ma, S and Guo, R and Li, L and Guo, X and Chang, D and Li, S and Zhang, H and Fu, C and Yang, L and Zhang, Y and Jiang, J and Wang, T and Wang, J and Shi, H},
title = {Metagenomic analysis of the gut virome in patients with irritable bowel syndrome.},
journal = {Journal of medical virology},
volume = {96},
number = {7},
pages = {e29802},
doi = {10.1002/jmv.29802},
pmid = {39023095},
issn = {1096-9071},
mesh = {Humans ; *Irritable Bowel Syndrome/virology/microbiology ; *Virome ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Feces/virology/microbiology ; Viruses/classification/genetics/isolation & purification ; Adult ; Male ; Female ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between-sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss-like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS-enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS-associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management.},
}

Humans
*Irritable Bowel Syndrome/virology/microbiology
*Virome
*Gastrointestinal Microbiome/genetics
*Metagenomics
*Feces/virology/microbiology
Viruses/classification/genetics/isolation & purification
Adult
Male
Female
Middle Aged
Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid39022885,
year = {2024},
author = {Piontek, J and Hassenrück, C and Zäncker, B and Jürgens, K},
title = {Environmental control and metabolic strategies of organic-matter-responsive bacterioplankton in the Weddell Sea (Antarctica).},
journal = {Environmental microbiology},
volume = {26},
number = {7},
pages = {e16675},
doi = {10.1111/1462-2920.16675},
pmid = {39022885},
issn = {1462-2920},
support = {PI 784/3-1//Deutsche Forschungsgemeinschaft/ ; PI 784/4-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Seawater/microbiology ; Antarctic Regions ; *Gammaproteobacteria/metabolism/genetics ; *Phytoplankton/metabolism/genetics ; Carbon/metabolism ; Microbiota ; Plankton/metabolism/genetics/growth & development ; Metagenome ; Ecosystem ; Bacteroidetes/genetics/metabolism/growth & development ; Temperature ; },
abstract = {Heterotrophic microbial communities play a significant role in driving carbon fluxes in marine ecosystems. Despite their importance, these communities remain understudied in remote polar oceans, which are known for their substantial contribution to the biological drawdown of atmospheric carbon dioxide. Our research focused on understanding the environmental factors and genetic makeup of key bacterial players involved in carbon remineralization in the Weddell Sea, including its coastal polynyas. Our experiments demonstrated that the combination of labile organic matter supply and temperature increase synergistically boosted bacterial growth. This suggests that, besides low seawater temperature, carbon limitation also hinders heterotrophic bacterial activity. Through the analysis of metagenome-assembled genomes, we discovered distinct genomic adaptation strategies in Bacteroidia and Gammaproteobacteria, both of which respond to organic matter. Both natural phytoplankton blooms and experimental addition of organic matter favoured Bacteroidia, which possess a large number of gene copies and a wide range of functional membrane transporters, glycoside hydrolases, and aminopeptidases. In contrast, the genomes of organic-matter-responsive Gammaproteobacteria were characterized by high densities of transcriptional regulators and transporters. Our findings suggest that bacterioplankton in the Weddell Sea, which respond to organic matter, employ metabolic strategies similar to those of their counterparts in temperate oceans. These strategies enable efficient growth at extremely low seawater temperatures, provided that organic carbon limitation is alleviated.},
}

*Seawater/microbiology
Antarctic Regions
*Gammaproteobacteria/metabolism/genetics
*Phytoplankton/metabolism/genetics
Carbon/metabolism
Microbiota
Plankton/metabolism/genetics/growth & development
Metagenome
Ecosystem
Bacteroidetes/genetics/metabolism/growth & development
Temperature

@article {pmid39020289,
year = {2024},
author = {Pérez-Prieto, I and Vargas, E and Salas-Espejo, E and Lüll, K and Canha-Gouveia, A and Pérez, LA and Fontes, J and Salumets, A and Andreson, R and Aasmets, O and , and Whiteson, K and Org, E and Altmäe, S},
title = {Gut microbiome in endometriosis: a cohort study on 1000 individuals.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {294},
pmid = {39020289},
issn = {1741-7015},
mesh = {Humans ; *Endometriosis/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Adult ; Case-Control Studies ; Estonia/epidemiology ; Cohort Studies ; Middle Aged ; Metagenomics ; Dysbiosis/microbiology ; Young Adult ; },
abstract = {BACKGROUND: Endometriosis, defined as the presence of endometrial-like tissue outside of the uterus, is one of the most prevalent gynecological disorders. Although different theories have been proposed, its pathogenesis is not clear. Novel studies indicate that the gut microbiome may be involved in the etiology of endometriosis; nevertheless, the connection between microbes, their dysbiosis, and the development of endometriosis is understudied. This case-control study analyzed the gut microbiome in women with and without endometriosis to identify microbial targets involved in the disease.

METHODS: A subsample of 1000 women from the Estonian Microbiome cohort, including 136 women with endometriosis and 864 control women, was analyzed. Microbial composition was determined by shotgun metagenomics and microbial functional pathways were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Partitioning Around Medoids (PAM) algorithm was performed to cluster the microbial profile of the Estonian population. The alpha- and beta-diversity and differential abundance analyses were performed to assess the gut microbiome (species and KEGG orthologies (KO)) in both groups. Metagenomic reads were mapped to estrobolome-related enzymes' sequences to study potential microbiome-estrogen metabolism axis alterations in endometriosis.

RESULTS: Diversity analyses did not detect significant differences between women with and without endometriosis (alpha-diversity: all p-values > 0.05; beta-diversity: PERMANOVA, both R [2] < 0.0007, p-values > 0.05). No differential species or pathways were detected after multiple testing adjustment (all FDR p-values > 0.05). Sensitivity analysis excluding women at menopause (> 50 years) confirmed our results. Estrobolome-associated enzymes' sequence reads were not significantly different between groups (all FDR p-values > 0.05).

CONCLUSIONS: Our findings do not provide enough evidence to support the existence of a gut microbiome-dependent mechanism directly implicated in the pathogenesis of endometriosis. To the best of our knowledge, this is the largest metagenome study on endometriosis conducted to date.},
}

Humans
*Endometriosis/microbiology
Female
*Gastrointestinal Microbiome/physiology
Adult
Case-Control Studies
Estonia/epidemiology
Cohort Studies
Middle Aged
Metagenomics
Dysbiosis/microbiology
Young Adult

@article {pmid39019914,
year = {2024},
author = {Dong, Y and Chen, R and Graham, EB and Yu, B and Bao, Y and Li, X and You, X and Feng, Y},
title = {Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6013},
pmid = {39019914},
issn = {2041-1723},
support = {41977045//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; *Salt Stress ; *Microbiota/genetics/drug effects ; *Climate Change ; Salinity ; Soil/chemistry ; Metagenomics ; Phylogeny ; Biological Evolution ; Genome, Bacterial ; Metagenome ; },
abstract = {With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.},
}

*Soil Microbiology
*Carbon/metabolism
*Archaea/genetics/metabolism
*Bacteria/metabolism/genetics/classification
*Salt Stress
*Microbiota/genetics/drug effects
*Climate Change
Salinity
Soil/chemistry
Metagenomics
Phylogeny
Biological Evolution
Genome, Bacterial
Metagenome

@article {pmid39019886,
year = {2024},
author = {Dhariwal, A and Rajar, P and Salvadori, G and Åmdal, HA and Berild, D and Saugstad, OD and Fugelseth, D and Greisen, G and Dahle, U and Haaland, K and Petersen, FC},
title = {Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6024},
pmid = {39019886},
issn = {2041-1723},
mesh = {Humans ; *Nasopharynx/microbiology ; *Infant, Premature ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Infant, Newborn ; Prospective Studies ; *Hospitalization ; Female ; Male ; Metagenomics/methods ; Infant ; Serratia marcescens/drug effects/genetics ; Microbiota/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics/drug effects ; },
abstract = {Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8-10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.},
}

Humans
*Nasopharynx/microbiology
*Infant, Premature
*Anti-Bacterial Agents/pharmacology/therapeutic use
Infant, Newborn
Prospective Studies
*Hospitalization
Female
Male
Metagenomics/methods
Infant
Serratia marcescens/drug effects/genetics
Microbiota/drug effects/genetics
Drug Resistance, Bacterial/genetics
Drug Resistance, Microbial/genetics/drug effects

@article {pmid39017960,
year = {2024},
author = {Daddy Gaoh, S and Alusta, P and Lee, YJ and LiPuma, JJ and Hussong, D and Marasa, B and Ahn, Y},
title = {A Comparative Metagenomic Analysis of Specified Microorganisms in Groundwater for Non-Sterilized Pharmaceutical Products.},
journal = {Current microbiology},
volume = {81},
number = {9},
pages = {273},
pmid = {39017960},
issn = {1432-0991},
mesh = {*Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Groundwater/microbiology ; Microbiota/genetics ; Pharmaceutical Preparations ; Metagenome ; Water Microbiology ; },
abstract = {In pharmaceutical manufacturing, ensuring product safety involves the detection and identification of microorganisms with human pathogenic potential, including Burkholderia cepacia complex (BCC), Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma spp., some of which may be missed or not identified by traditional culture-dependent methods. In this study, we employed a metagenomic approach to detect these taxa, avoiding the limitations of conventional cultivation methods. We assessed the groundwater microbiome's taxonomic and functional features from samples collected at two locations in the spring and summer. All datasets comprised 436-557 genera with Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Cyanobacteria accounting for > 95% of microbial DNA sequences. The aforementioned species constituted less than 18.3% of relative abundance. Escherichia and Salmonella were mainly detected in Hot Springs, relative to Jefferson, while Clostridium and Pseudomonas were mainly found in Jefferson relative to Hot Springs. Multidrug resistance efflux pumps and BlaR1 family regulatory sensor-transducer disambiguation dominated in Hot Springs and in Jefferson. These initial results provide insight into the detection of specified microorganisms and could constitute a framework for the establishment of comprehensive metagenomic analysis for the microbiological evaluation of pharmaceutical-grade water and other non-sterile pharmaceutical products, ensuring public safety.},
}

*Metagenomics
*Bacteria/genetics/classification/isolation & purification
*Groundwater/microbiology
Microbiota/genetics
Pharmaceutical Preparations
Metagenome
Water Microbiology

@article {pmid39016466,
year = {2024},
author = {Zhang, P and Shi, H and Guo, R and Li, L and Guo, X and Yang, H and Chang, D and Cheng, Y and Zhao, G and Li, S and Zhong, Q and Zhang, H and Zhao, P and Fu, C and Song, Y and Yang, L and Wang, Y and Zhang, Y and Jiang, J and Wang, T and Zhao, J and Li, Y and Wang, B and Chen, F and Zhao, H and Wang, Y and Wang, J and Ma, S},
title = {Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer.},
journal = {Journal of medical virology},
volume = {96},
number = {7},
pages = {e29809},
doi = {10.1002/jmv.29809},
pmid = {39016466},
issn = {1096-9071},
mesh = {Humans ; *Pancreatic Neoplasms/virology/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Metagenomics/methods ; *Feces/virology/microbiology ; Viruses/isolation & purification/genetics/classification ; Metagenome ; Bacteria/isolation & purification/classification/genetics ; Middle Aged ; Male ; Female ; Aged ; Case-Control Studies ; },
abstract = {Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.},
}

Humans
*Pancreatic Neoplasms/virology/diagnosis/microbiology
*Gastrointestinal Microbiome/genetics
*Virome
*Metagenomics/methods
*Feces/virology/microbiology
Viruses/isolation & purification/genetics/classification
Metagenome
Bacteria/isolation & purification/classification/genetics
Middle Aged
Male
Female
Aged
Case-Control Studies

@article {pmid39015337,
year = {2024},
author = {Bashir, Z and Hugerth, LW and Krog, MC and Prast-Nielsen, S and Edfeldt, G and Boulund, F and Schacht, SR and Tetens, I and Engstrand, L and Schuppe-Koistinen, I and Fransson, E and Nielsen, HS},
title = {Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1324794},
pmid = {39015337},
issn = {2235-2988},
mesh = {Humans ; Female ; Adult ; Young Adult ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Adolescent ; *Depression/microbiology ; *Vagina/microbiology ; *Feces/microbiology ; *Stress, Psychological/microbiology ; Microbiota ; Denmark ; Healthy Volunteers ; Brain-Gut Axis/physiology ; Surveys and Questionnaires ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Despite mounting evidence of gut-brain involvement in psychiatric conditions, functional data remain limited, and analyses of other microbial niches, such as the vaginal microbiota, are lacking in relation to mental health. This aim of this study was to investigate if the connections between the gut microbiome and mental health observed in populations with a clinical diagnosis of mental illness extend to healthy women experiencing stress and depressive symptoms. Additionally, this study examined the functional pathways of the gut microbiota according to the levels of psychological symptoms. Furthermore, the study aimed to explore potential correlations between the vaginal microbiome and mental health parameters in young women without psychiatric diagnoses.

METHODS: In this cross-sectional study, 160 healthy Danish women (aged 18-40 years) filled out questionnaires with validated scales measuring symptoms of stress and depression and frequency of dietary intake. Fecal and vaginal microbiota samples were collected at the beginning of the menstrual cycle and vaginal samples were also collected at cycle day 8-12 and 18-22. Shotgun metagenomic profiling of the gut and vaginal microbiome was performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for functional profiling and 56 Gut Brain Modules were analyzed in the fecal samples.

RESULTS: The relative abundance in the gut of the genera Escherichia, Parabacteroides, and Shigella was higher in women with elevated depressive symptoms. Women with high perceived stress showed a tendency of increased abundance of Escherichia, Shigella, and Blautia. Amongst others, the potentially pathogenic genera, Escherichia and Shigella correlate with alterations in the neuroactive pathways such as the glutamatergic, GABAeric, dopaminergic, and Kynurenine pathways. Vaginosis symptoms were more prevalent in women reporting high levels of stress and depressive symptoms.

CONCLUSIONS: The findings of this study support the concept of a microbiota-associated effect on the neuroactive pathways even in healthy young women. This suggest, that targeting the gut microbiome could be a promising approach for future psychiatric interventions.},
}

Humans
Female
Adult
Young Adult
Cross-Sectional Studies
*Gastrointestinal Microbiome
Adolescent
*Depression/microbiology
*Vagina/microbiology
*Feces/microbiology
*Stress, Psychological/microbiology
Microbiota
Denmark
Healthy Volunteers
Brain-Gut Axis/physiology
Surveys and Questionnaires
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification

@article {pmid39014300,
year = {2024},
author = {Darabi, A and Sobhani, S and Aghdam, R and Eslahchi, C},
title = {AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {241},
pmid = {39014300},
issn = {1471-2105},
mesh = {*Metagenomics/methods ; *Algorithms ; Nucleotides/genetics ; High-Throughput Nucleotide Sequencing/methods ; Software ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Cluster Analysis ; Contig Mapping/methods ; Metagenome/genetics ; },
abstract = {BACKGROUND: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.

RESULTS: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.

CONCLUSION: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.

AVAILABILITY: A python package is available at: https://github.com/SayehSobhani/AFITBin .},
}

*Metagenomics/methods
*Algorithms
Nucleotides/genetics
High-Throughput Nucleotide Sequencing/methods
Software
Microbiota/genetics
Sequence Analysis, DNA/methods
Cluster Analysis
Contig Mapping/methods
Metagenome/genetics

@article {pmid39012105,
year = {2024},
author = {Wu, W-C and Pan, Y-F and Zhou, W-D and Liao, Y-Q and Peng, M-W and Luo, G-Y and Xin, G-Y and Peng, Y-N and An, T and Li, B and Luo, H and Barrs, VR and Beatty, JA and Holmes, EC and Zhao, W and Shi, M and Shu, Y},
title = {Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043924},
doi = {10.1128/msphere.00439-24},
pmid = {39012105},
issn = {2379-5042},
abstract = {UNLABELLED: Companion animals such as cats and dogs harbor diverse microbial communities that can potentially impact human health due to close and frequent contact. To better characterize their total infectomes and assess zoonotic risks, we characterized the overall infectomes of companion animals (cats and dogs) and evaluated their potential zoonotic risks. Meta-transcriptomic analyses were performed on 239 samples from cats and dogs collected across China, identifying 24 viral species, 270 bacterial genera, and two fungal genera. Differences in the overall microbiome and infectome composition were compared across different animal species (cats or dogs), sampling sites (rectal or oropharyngeal), and health status (healthy or diseased). Diversity analyses revealed that viral abundance was generally higher in diseased animals compared to healthy ones, while differences in microbial composition were mainly driven by sampling site, followed by animal species and health status. Disease association analyses validated the pathogenicity of known pathogens and suggested potential pathogenic roles of previously undescribed bacteria and newly discovered viruses. Cross-species transmission analyses identified seven pathogens shared between cats and dogs, such as alphacoronavirus 1, which was detected in both oropharyngeal and rectal swabs albeit with differential pathogenicity. Further analyses showed that some viruses, like alphacoronavirus 1, harbored multiple lineages exhibiting distinct pathogenicity, tissue, or host preferences. Ultimately, a systematic evolutionary screening identified 27 potential zoonotic pathogens in this sample set, with far more bacterial than viral species, implying potential health threats to humans. Overall, our meta-transcriptomic analysis reveals a landscape of actively transcribing microorganisms in major companion animals, highlighting key pathogens, those with the potential for cross-species transmission, and possible zoonotic threats.

IMPORTANCE: This study provides a comprehensive characterization of the entire community of infectious microbes (viruses, bacteria, and fungi) in companion animals like cats and dogs, termed the "infectome." By analyzing hundreds of samples from across China, the researchers identified numerous known and novel pathogens, including 27 potential zoonotic agents that could pose health risks to both animals and humans. Notably, some of these zoonotic pathogens were detected even in apparently healthy pets, highlighting the importance of surveillance. The study also revealed key microbial factors associated with respiratory and gastrointestinal diseases in pets, as well as potential cross-species transmission events between cats and dogs. Overall, this work sheds light on the complex microbial landscapes of companion animals and their potential impacts on animal and human health, underscoring the need for monitoring and management of these infectious agents.},
}

@article {pmid39010229,
year = {2024},
author = {Chang, T and Gavelis, GS and Brown, JM and Stepanauskas, R},
title = {Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {126},
pmid = {39010229},
issn = {2049-2618},
support = {827839//Simons Foundation/ ; 827839//Simons Foundation/ ; 827839//Simons Foundation/ ; 827839//Simons Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; OIA-1826734//National Science Foundation/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Bacteria/genetics/classification ; *Plankton/genetics/classification/microbiology ; Phylogeny ; Seawater/microbiology ; Chimerism ; Genome, Bacterial ; Metagenomics/methods ; Microbiota/genetics ; Genomics ; },
abstract = {BACKGROUND: Single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are the predominant sources of information about the coding potential of uncultured microbial lineages, but their strengths and limitations remain poorly understood. Here, we performed a direct comparison of two previously published collections of thousands of SAGs and MAGs obtained from the same, global environment.

RESULTS: We found that SAGs were less prone to chimerism and more accurately reflected the relative abundance and the pangenome content of microbial lineages inhabiting the epipelagic of the tropical and subtropical ocean, as compared to MAGs. SAGs were also better suited to link genome information with taxa discovered through 16S rRNA amplicon analyses. Meanwhile, MAGs had the advantage of more readily recovering genomes of rare lineages.

CONCLUSIONS: Our analyses revealed the relative strengths and weaknesses of the two most commonly used genome recovery approaches in environmental microbiology. These considerations, as well as the need for better tools for genome quality assessment, should be taken into account when designing studies and interpreting data that involve SAGs or MAGs. Video Abstract.},
}

*RNA, Ribosomal, 16S/genetics
*Metagenome
*Bacteria/genetics/classification
*Plankton/genetics/classification/microbiology
Phylogeny
Seawater/microbiology
Chimerism
Genome, Bacterial
Metagenomics/methods
Microbiota/genetics
Genomics

@article {pmid39009515,
year = {2024},
author = {Takeda, M and Doki, Y},
title = {[The Power of the Gut Microbiome: Exploring New Perspectives in Colorectal Cancer Therapy].},
journal = {Gan to kagaku ryoho. Cancer & chemotherapy},
volume = {51},
number = {6},
pages = {608-612},
pmid = {39009515},
issn = {0385-0684},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy ; *Gastrointestinal Microbiome ; Animals ; Dysbiosis/microbiology ; },
abstract = {The gut microbiome is involved in host physiology, including nutrition, metabolism, and immunity. It was recently known that dysbiosis of the gut microbiome has been implicated in several human diseases such as inflammatory bowel disease. It is altered by environmental factors such as diet, habit and lifestyle and has been directly and indirectly linked to the development and progression of colorectal cancer(CRC). Fusobacterium(F.)nucleatum, which causes periodontal disease, has been shown to play an important role in the initiation and development of CRC, although not as clearly as Helicobacter(H.) pylori in gastric cancer. Therefore, gut bacteria hold promise as a potential therapeutic approach to prevent or treat CRC. Although its clinical usefulness has not yet been demonstrated, future research such as metagenomics may open new avenues for CRC treatment with gut bacteria. Here, we reviewed the role of the gut microbial community in the development, progression, and prevention of colorectal carcinogenesis.},
}

Humans
*Colorectal Neoplasms/microbiology/therapy
*Gastrointestinal Microbiome
Animals
Dysbiosis/microbiology

@article {pmid39008123,
year = {2024},
author = {Núñez-Muñoz, LA and Sánchez-García, ME and Calderón-Pérez, B and De la Torre-Almaraz, R and Ruiz-Medrano, R and Xoconostle-Cázares, B},
title = {Metagenomic Analysis of Rhizospheric Bacterial Community of Citrus Trees Expressing Phloem-Directed Antimicrobials.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {93},
pmid = {39008123},
issn = {1432-184X},
support = {SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; CF-2023-G-231//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
mesh = {*Rhizosphere ; *Phloem/microbiology/metabolism ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; *Plant Diseases/microbiology ; *Citrus/microbiology ; Plants, Genetically Modified/microbiology/genetics ; Phylogeny ; Metagenomics ; Muramidase/metabolism/genetics ; Plant Proteins/genetics/metabolism ; beta-Defensins/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Infective Agents/pharmacology/metabolism ; Citrus sinensis/microbiology ; Plant Roots/microbiology ; },
abstract = {Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota.},
}

*Rhizosphere
*Phloem/microbiology/metabolism
*Soil Microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota
*Plant Diseases/microbiology
*Citrus/microbiology
Plants, Genetically Modified/microbiology/genetics
Phylogeny
Metagenomics
Muramidase/metabolism/genetics
Plant Proteins/genetics/metabolism
beta-Defensins/genetics
RNA, Ribosomal, 16S/genetics
Anti-Infective Agents/pharmacology/metabolism
Citrus sinensis/microbiology
Plant Roots/microbiology

@article {pmid39007947,
year = {2024},
author = {Nilsen, M and Nygaard, UC and Brodin, P and Carlsen, KCL and Fredheim, C and Haugen, G and Hedlin, G and Jonassen, CM and Jonsmoen, ULA and Lakshmikanth, T and Nordlund, B and Olin, A and Rehbinder, EM and Skjerven, HO and Snipen, L and Staff, AC and Söderhäll, C and Vettukattil, R and Rudi, K},
title = {Gut bacteria at 6 months of age are associated with immune cell status in 1-year-old children.},
journal = {Scandinavian journal of immunology},
volume = {99},
number = {4},
pages = {e13346},
doi = {10.1111/sji.13346},
pmid = {39007947},
issn = {1365-3083},
support = {//Arne Ingel's legat/ ; //Barnestifteslen at Oslo University Hospital/ ; //Forte/ ; //Fürst Medical Laboratory, Oslo, Norway/ ; //Health and Rehabilitation Norway/ ; //Karolinska Institutet/ ; //Norges Forskningsråd/ ; //Norwegian Association of Asthma and Allergy/ ; //Norwegian Society of Dermatology and Venerology/ ; //Oslo University Hospital/ ; //Region Stockholm (ALF-project and individual grants)/ ; //Roche/ ; //SFO-V Karolinska Institutet/ ; //Swedish Asthma and Allergy Association's Research Foundation/ ; //Swedish Order of Freemasons Foundation Barnhuset/ ; //Swedish Research council/ ; //Sykehuset Østfold/ ; //The Cancer- and Allergy Foundation/ ; //Delegation of the European Union to Norway, University of Oslo/ ; //The Foundation for Healthcare and Allergy Research in Sweden - Vårdalstiftelsen/ ; //The Fridtjof Nansen Institute/ ; //The Hesselman foundation/ ; //The Initiative for Clinical Therapy Research/ ; //The King Gustaf V 80th Birthday Foundation/ ; //The Kloster foundation/ ; //The Konsul Th C Bergh's Foundation/ ; //The Magnus Bergwall foundation/ ; //The Pediatric Research Foundation at Astrid Lindgren Children's Hospital/ ; //The Samaritan Foundation for Pediatric research/ ; //The Sven Jerring Foundation/ ; //The Swedish Heart-Lung Foundation/ ; //The Swedish Society of Medicine/ ; //Thermo-Fisher Uppsala, Sweden/ ; //Universitetet i Oslo/ ; },
mesh = {Humans ; Infant ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; *Feces/microbiology ; Infant, Newborn ; Bacteria/immunology/classification ; Fatty Acids, Volatile/metabolism ; Metagenome ; Prospective Studies ; },
abstract = {Age-related gut bacterial changes during infancy have been widely studied, but it remains still unknown how these changes are associated with immune cell composition. This study's aim was to explore if the temporal development of gut bacteria during infancy prospectively affects immune cell composition. Faecal bacteria and short-chain fatty acids were analysed from 67 PreventADALL study participants at four timepoints (birth to 12 months) using reduced metagenome sequencing and gas chromatography. Immune cell frequencies were assessed using mass cytometry in whole blood samples at 12 months. The infants clustered into four groups based on immune cell composition: clusters 1 and 2 showed a high relative abundance of naïve cells, cluster 3 exhibited increased abundance of classical- and non-classical monocytes and clusters 3 and 4 had elevated neutrophil levels. At all age groups, we did observe significant associations between the gut microbiota and immune cell clusters; however, these were generally from low abundant species. Only at 6 months of age we observed significant associations between abundant (>8%) species and immune cell clusters. Bifidobacterium adolescentis and Porphyromonadaceae are associated with cluster 1, while Bacteroides fragilis and Bifidobacterium longum are associated with clusters 3 and 4 respectively. These species have been linked to T-cell polarization and maturation. No significant correlations were found between short-chain fatty acids and immune cell composition. Our findings suggest that abundant gut bacteria at 6 months may influence immune cell frequencies at 12 months, highlighting the potential role of gut microbiota in shaping later immune cell composition.},
}

Humans
Infant
*Gastrointestinal Microbiome/immunology
Male
Female
*Feces/microbiology
Infant, Newborn
Bacteria/immunology/classification
Fatty Acids, Volatile/metabolism
Metagenome
Prospective Studies

@article {pmid39007592,
year = {2024},
author = {Zhang, G and Wang, H and Zhang, Z and Zhang, L and Guo, G and Yang, J and Yuan, F and Ju, F},
title = {Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {4},
pages = {},
pmid = {39007592},
issn = {1477-4054},
support = {WU2022A008//Center of Synthetic Biology and Integrated Bioengineering/ ; WU2022C030//Research Center for Industries of the Future/ ; 2024SSYS0032//'Pioneer' and 'Leading Goose' Key R&D Program of Zhejiang/ ; LR22D010001//Zhejiang Provincial Natural Science Foundation of China/ ; },
mesh = {*Deep Learning ; Humans ; Computational Biology/methods ; Microbiota/genetics ; Bacterial Proteins/genetics ; Drug Resistance, Microbial/genetics ; Software ; High-Throughput Nucleotide Sequencing/methods ; Virulence Factors/genetics ; },
abstract = {High-throughput DNA sequencing technologies decode tremendous amounts of microbial protein-coding gene sequences. However, accurately assigning protein functions to novel gene sequences remain a challenge. To this end, we developed FunGeneTyper, an extensible framework with two new deep learning models (i.e., FunTrans and FunRep), structured databases, and supporting resources for achieving highly accurate (Accuracy > 0.99, F1-score > 0.97) and fine-grained classification of antibiotic resistance genes (ARGs) and virulence factor genes. Using an experimentally confirmed dataset of ARGs comprising remote homologous sequences as the test set, our framework achieves by-far-the-best performance in the discovery of new ARGs from human gut (F1-score: 0.6948), wastewater (0.6072), and soil (0.5445) microbiomes, beating the state-of-the-art bioinformatics tools and sequence alignment-based (F1-score: 0.0556-0.5065) and domain-based (F1-score: 0.2630-0.5224) annotation approaches. Furthermore, our framework is implemented as a lightweight, privacy-preserving, and plug-and-play neural network module, facilitating its versatility and accessibility to developers and users worldwide. We anticipate widespread utilization of FunGeneTyper (https://github.com/emblab-westlake/FunGeneTyper) for precise classification of protein-coding gene functions and the discovery of numerous valuable enzymes. This advancement will have a significant impact on various fields, including microbiome research, biotechnology, metagenomics, and bioinformatics.},
}

*Deep Learning
Humans
Computational Biology/methods
Microbiota/genetics
Bacterial Proteins/genetics
Drug Resistance, Microbial/genetics
Software
High-Throughput Nucleotide Sequencing/methods
Virulence Factors/genetics

@article {pmid39006020,
year = {2024},
author = {Enagbonma, BJ and Fadiji, AE and Babalola, OO},
title = {Anthropogenic fertilization influences a shift in barley rhizosphere microbial communities.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17303},
pmid = {39006020},
issn = {2167-8359},
mesh = {*Hordeum/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Fertilizers/analysis ; Microbiota ; Bacteria/genetics/classification ; Soil/chemistry ; },
abstract = {BACKGROUND: Anthropogenic mediations contribute a significant role in stimulating positive reactions in soil-plant interactions; however, methodical reports on how anthropogenic activities impact soil microorganism-induced properties and soil health are still inadequate. In this study, we evaluated the influence of anthropogenic fertilization of farmland soil on barley rhizosphere microbial community structure and diversity, and the significant impacts on agro-ecosystem productivity. This will help validate the premise that soil amendment with prolonged synthetic fertilizers can lead to a significant reduction in bacterial abundance and diversity, while soils amended with organic fertilizers elicit the succession of the native soil microbial community and favor the growth of copiotrophic bacteria.

METHODS: The total metagenomic DNA was extracted from soils obtained from the barley rhizosphere under chemical fertilization (CB), organic fertilization (OB), and bulk soil (NB). Subsequently, these samples were sequenced using an amplicon-based sequencing approach, and the raw sequence dataset was examined using a metagenomic rast server (MG-RAST).

RESULTS: Our findings showed that all environments (CB, OB, and NB) shared numerous soil bacterial phyla but with different compositions. However, Bacteroidetes, Proteobacteria, and Actinobacteria predominated in the barley rhizosphere under chemical fertilization, organic fertilization, and bulk soils, respectively. Alpha and beta diversity analysis showed that the diversity of bacteria under organic barley rhizosphere was significantly higher and more evenly distributed than bacteria under chemical fertilization and bulk soil.

CONCLUSION: Understanding the impact of conventional and organic fertilizers on the structure, composition, and diversity of the rhizosphere microbiome will assist in soil engineering to enhance microbial diversity in the agroecosystem.},
}

*Hordeum/microbiology
*Rhizosphere
*Soil Microbiology
*Fertilizers/analysis
Microbiota
Bacteria/genetics/classification
Soil/chemistry

@article {pmid39005434,
year = {2024},
author = {Kosch, TA and Torres-Sánchez, M and Liedtke, HC and Summers, K and Yun, MH and Crawford, AJ and Maddock, ST and Ahammed, MS and Araújo, VLN and Bertola, LV and Bucciarelli, G and Carné, A and Carneiro, CM and Chan, KO and Chen, Y and Crottini, A and da Silva, JM and Denton, RD and Dittrich, C and Themudo, GE and Farquharson, KA and Forsdick, NJ and Gilbert, E and Jing, C and Katzenback, BA and Kotharambath, R and Levis, NA and Márquez, R and Mazepa, G and Mulder, KP and Müller, H and O'Connell, MJ and Orozco-terWengel, P and Palomar, G and Petzold, A and Pfennig, DW and Pfennig, KS and Reichert, MS and Robert, J and Scherz, MD and Siu-Ting, K and Snead, AA and Stöck, M and Stuckert, AMM and Stynoski, JL and Tarvin, RD and Valero, KCW and , },
title = {The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39005434},
issn = {2692-8205},
abstract = {Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.},
}

@article {pmid39005339,
year = {2024},
author = {Kananen, K and Veseli, I and Quiles Pérez, CJ and Miller, S and Eren, AM and Bradley, PH},
title = {Adaptive adjustment of significance thresholds produces large gains in microbial gene annotations and metabolic insights.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39005339},
issn = {2692-8205},
support = {R35 GM151155/GM/NIGMS NIH HHS/United States ; },
abstract = {Gene function annotations enable microbial ecologists to make inferences about metabolic potential from genomes and metagenomes. However, even tools that use the same database and general approach can differ markedly in the annotations they recover. We compare three popular methods for identifying KEGG Orthologs, applying them to genomes drawn from a range of bacterial families that occupy different host-associated and free-living biomes. Our results show that by adaptively tuning sequence similarity thresholds, sensitivity can be substantially improved while maintaining accuracy. We observe the largest improvements when few reference sequences exist for a given protein family, and when annotating genomes from non-model organisms (such as gut-dwelling Lachnospiraceae). Our results suggest that straightforward heuristic adjustments can broadly improve microbial metabolic predictions.},
}

@article {pmid39004662,
year = {2024},
author = {Kang, L and Song, Y and Mackelprang, R and Zhang, D and Qin, S and Chen, L and Wu, L and Peng, Y and Yang, Y},
title = {Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5920},
pmid = {39004662},
issn = {2041-1723},
support = {31988102 and 31825006//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Permafrost/microbiology ; Tibet ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; *Microbiota/genetics ; Bacteria/genetics/classification/metabolism ; Soil/chemistry ; Metagenome ; Ecosystem ; Climate Change ; Biodiversity ; Phylogeny ; },
abstract = {Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in microbial profiles remains limited. Here, we analyze microbial community structure and functional potential based on 16S rRNA gene amplicon sequencing and metagenomic data obtained from an ∼1000 km permafrost transect on the Tibetan Plateau. We find that microbial alpha diversity declines but beta diversity increases down the soil profile. Microbial assemblages are primarily governed by dispersal limitation and drift, with the importance of drift decreasing but that of dispersal limitation increasing with soil depth. Moreover, genes related to reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate reduction, and denitrification) are enriched in the subsurface and permafrost layers. In addition, microbial groups involved in alternative electron accepting processes are more diverse and contribute highly to community-level metabolic profiles in the subsurface and permafrost layers, likely reflecting the lower redox potential and more complicated trophic strategies for microorganisms in deeper soils. Overall, these findings provide comprehensive insights into large-scale stratigraphic profiles of microbial community structure and functional potentials in permafrost regions.},
}

*Permafrost/microbiology
Tibet
*Soil Microbiology
*RNA, Ribosomal, 16S/genetics
*Metagenomics
*Microbiota/genetics
Bacteria/genetics/classification/metabolism
Soil/chemistry
Metagenome
Ecosystem
Climate Change
Biodiversity
Phylogeny

@article {pmid39004260,
year = {2024},
author = {Tischer, M and Bleidorn, C},
title = {Further evidence of low infection frequencies of Wolbachia in soil arthropod communities.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {123},
number = {},
pages = {105641},
doi = {10.1016/j.meegid.2024.105641},
pmid = {39004260},
issn = {1567-7257},
abstract = {Endosymbiotic Alphaproteobacteria of the genus Wolbachia are exclusively transferred maternally from mother to offspring, but horizontal transfer across species boundaries seems to be frequent as well. However, the (ecological) mechanisms of how these bacteria are transferred between distantly related arthropod hosts remain unclear. Based on the observation that species that are part of the same ecological community often also share similar Wolbachia strains, host ecology has been hypothesized as an important factor enabling transmission and a key factor in explaining the global distribution of Wolbachia lineages. In this study, we focus on the diversity and abundance of Wolbachia strains in soil arthropods, a so far rather neglected community. We screened 82 arthropod morphotypes collected in the beech forest (dominated by Fagus sp.) soil in the area of Göttingen in central Germany for the presence of Wolbachia. By performing a PCR screen with Wolbachia-MLST markers (coxA, dnaA, fbpA, ftsZ, gatB, and hcpA), we found a rather low infection frequency of 12,2%. Additionally, we performed metagenomic screening of pooled individuals from the same sampling site and could not find evidence that this low infection frequency is an artefact due to PCR-primer bias. Phylogenetic analyses of the recovered Wolbachia strains grouped them in three known supergroups (A, B, and E), with the first report of Wolbachia in Protura (Hexapoda). Moreover, Wolbachia sequences from the pseudoscorpion Neobisium carcinoides cluster outside the currently known supergroup diversity. Our screening supports results from previous studies that the prevalence of Wolbachia infections seems to be lower in soil habitats than in above-ground terrestrial habitats. The reasons for this pattern are not completely understood but might stem from the low opportunity of physical contact and the prevalence of supergroups that are less suited for horizontal transfer.},
}

@article {pmid39003345,
year = {2024},
author = {Das, BK and Chakraborty, HJ and Kumar, V and Rout, AK and Patra, B and Das, SK and Behera, BK},
title = {Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16218},
pmid = {39003345},
issn = {2045-2322},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Wetlands ; Ecosystem ; Phylogeny ; Soil Microbiology ; India ; },
abstract = {The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world's largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.},
}

*Metagenomics/methods
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Metagenome
Wetlands
Ecosystem
Phylogeny
Soil Microbiology
India

@article {pmid39003315,
year = {2024},
author = {Knjaz, M and Baricevic, A and Tankovic, MS and Kuzat, N and Vlasicek, I and Grizancic, L and Podolsak, I and Pfannkuchen, M and Kogovsek, T and Pfannkuchen, DM},
title = {First regional reference database of northern Adriatic diatom transcriptomes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16209},
pmid = {39003315},
issn = {2045-2322},
support = {UIP -2020-02-7868//Hrvatska Zaklada za Znanost/ ; DOK-2021-02-5104//Hrvatska Zaklada za Znanost/ ; UIP-2014-09-6563//Hrvatska Zaklada za Znanost/ ; 871153//H2020 Excellent Science/ ; },
mesh = {*Diatoms/genetics/classification ; *Transcriptome ; Metagenomics/methods ; Gene Expression Profiling/methods ; Databases, Genetic ; },
abstract = {Marine microbial communities form the basis for the functioning of marine ecosystems and the conservation of biodiversity. With the application of metagenomics and metatranscriptomics in marine environmental studies, significant progress has been made in analysing the functioning of microbial communities as a whole. These molecular techniques are highly dependent on reliable, well-characterised, comprehensive and taxonomically diverse sequenced reference transcriptomes of microbial organisms. Here we present a set of 12 individual transcriptome assemblies derived from 6 representative diatom species from the northern Adriatic Sea grown under 2 environmentally relevant growth conditions (phosphate replete vs. phosphate deprived). After filtering the reads and assembly, an average number of 64,932 transcripts per assembly was obtained, of which an average of 8856 were assigned to functionally known proteins. Of all assigned transcripts, an average of 6483 proteins were taxonomically assigned to diatoms (Bacillariophyta). On average, a higher number of assigned proteins was detected in the transcriptome assemblies of diatoms grown under replete media condition. On average, 50% of the mapped proteins were shared between the two growth conditions. All recorded proteins in the dataset were classified into 24 COG categories, with approximately 25% belonging to the unknown function and the remaining 75% belonging to all other categories. The resulting diatom reference database for the northern Adriatic, focussing on the response to nutrient limitation as characteristic for the region and predicted for the future world oceans, provides a valuable resource for analysing environmental metatranscriptome and metagenome data. Each northern Adriatic transcriptome can also be used by itself as a reference database for the (meta)transcriptomes and gene expression studies of the associated species that will be generated in the future.},
}

*Diatoms/genetics/classification
*Transcriptome
Metagenomics/methods
Gene Expression Profiling/methods
Databases, Genetic

@article {pmid39002479,
year = {2024},
author = {Zeng, H and Wang, Y and Zhao, Z and Zhu, D and Xia, H and Wei, Y and Kuang, P and An, D and Chen, K and Li, R and Lei, Y and Sun, G},
title = {Travertine deposition rather than tourism activity is the primary contributor to the microplastic risks in alpine karst lakes.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135192},
doi = {10.1016/j.jhazmat.2024.135192},
pmid = {39002479},
issn = {1873-3336},
abstract = {Microplastics (MPs) are emerging as anthropogenic vectors to form plastisphere, facilitating microbiome colonization and pathogenic dissemination, thus contributing to environmental and health crises across various ecosystems. However, a knowledge gap persists regarding MPs risks and their driving factors in certain unique and vulnerable ecosystems, such as Karst travertine lakes, some of which are renowned World Natural Heritage Sites under ever-increasing tourism pressure. We hypothesized that tourism activities serve as the most important factor of MPs pollution, whereas intrinsic features, including travertine deposition can exacerbate potential environmental risks. Thus, metagenomic approaches were employed to investigate the geographical distribution of the microbiome, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their combined environmental risks in Jiuzhaigou and Huanglong, two famous tourism destinations in Southwest China. The plastisphere risks were higher in Huanglong, contradicting our hypothesis that Jiuzhaigou would face more crucial antibiotic risks due to its higher tourist activities. Specifically, the levels of Lipopolysaccharide Lewis and fosD increased by sevenfold and 20-fold, respectively, from upstream to downstream in Huanglong, whereas in Jiuzhaigou, no significant accrual was observed. Structural equation modeling results showed that travertine deposition was the primary contributor to MPs risks in alpine karstic lakes. Our findings suggest that tourism has low impact on MPs risks, possibly because of proper management, and that travertine deposition might act as an MPs hotspot, emphasizing the importance of considering the unique aspects of travertine lakes in mitigating MPs pollution and promoting the sustainable development of World Natural Heritage Sites.},
}

@article {pmid39000578,
year = {2024},
author = {Min, M and Egli, C and Sivamani, RK},
title = {The Gut and Skin Microbiome and Its Association with Aging Clocks.},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000578},
issn = {1422-0067},
mesh = {Humans ; *Skin/microbiology/metabolism ; *Aging ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; Epigenesis, Genetic ; Animals ; Biological Clocks ; },
abstract = {Aging clocks are predictive models of biological age derived from age-related changes, such as epigenetic changes, blood biomarkers, and, more recently, the microbiome. Gut and skin microbiota regulate more than barrier and immune function. Recent studies have shown that human microbiomes may predict aging. In this narrative review, we aim to discuss how the gut and skin microbiomes influence aging clocks as well as clarify the distinction between chronological and biological age. A literature search was performed on PubMed/MEDLINE databases with the following keywords: "skin microbiome" OR "gut microbiome" AND "aging clock" OR "epigenetic". Gut and skin microbiomes may be utilized to create aging clocks based on taxonomy, biodiversity, and functionality. The top contributing microbiota or metabolic pathways in these aging clocks may influence aging clock predictions and biological age. Furthermore, gut and skin microbiota may directly and indirectly influence aging clocks through the regulation of clock genes and the production of metabolites that serve as substrates or enzymatic regulators. Microbiome-based aging clock models may have therapeutic potential. However, more research is needed to advance our understanding of the role of microbiota in aging clocks.},
}

Humans
*Skin/microbiology/metabolism
*Aging
*Gastrointestinal Microbiome/physiology
*Microbiota
Epigenesis, Genetic
Animals
Biological Clocks

@article {pmid39000530,
year = {2024},
author = {Liu, Y and Kou, C and Chen, J and Li, Y and Li, J},
title = {The Response of the Gut Physiological Function and Microbiome of a Wild Freshwater Fish (Megalobrama terminalis) to Alterations in Reproductive Behavior.},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000530},
issn = {1422-0067},
support = {202201010762//Science and Technology Program of Guangzhou/ ; 2023TD10//Pearl river fishery resources investigation and evaluation innovation team project/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Reproduction ; Female ; Cyprinidae/microbiology/physiology/metabolism ; Fresh Water/microbiology ; Intestinal Mucosa/metabolism/microbiology ; },
abstract = {The fish gut microbiome is well known for its role in degrading nutrients to improve the host's digestion and absorption efficiency. In this study, we focused on the core physiological adaptability during the various reproductive stages of the black Amur bream (Megalobrama terminalis) to explore the interaction mechanisms among the fish host gut mucosal structure, gut enzyme activity, and gut microbial metabolism in the course of the host's reproductive cycle. Our findings showed that M. terminalis exhibited locomotion metabolic type (aids in sporting) in the reproductive stage, and a change to visceral metabolic type (aids in digestion) during non-reproductive and post-reproductive stage phases. The impact of metabolic type selection and energy demand during various reproductive stages on fish nutrition strategy and digestive function was substantial. Our resulted showed that mitochondria in intestinal epithelial cells of reproductive M. terminalis appeared autophagy phenomenon, and the digestive enzyme activities in the intestines of reproductive M. terminalis were lower than those in the non-reproductive and post-reproductive individuals. Moreover, these differences in nutrition strategy have a prominent impact on the gut microbiome of reproductive M. terminalis, compared to non-reproductive and post-reproductive samples. Our findings showed that reproductive females had lower levels of alpha diversity compared to non-reproductive and post-reproductive females. Our results also showed a greater functional variety and an increase in functional genes related to carbohydrate, lipid, amino acid, cofactors, and vitamin metabolic pathways in the NRS and PRS group. It is noteworthy that an enrichment of genes encoding putative enzymes implicated in the metabolism of taurine and hypotaurine was observed in the RS samples. Our findings illustrated that the stability and resilience of the gut bacterial community could be shaped in the wild fish host-microbiome interactions during reproductive life history.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Reproduction
Female
Cyprinidae/microbiology/physiology/metabolism
Fresh Water/microbiology
Intestinal Mucosa/metabolism/microbiology

@article {pmid38998029,
year = {2024},
author = {Guo, Y and Garber, PA and Yang, Y and Wang, S and Zhou, J},
title = {The Conservation Implications of the Gut Microbiome for Protecting the Critically Endangered Gray Snub-Nosed Monkey (Rhinopithecus brelichi).},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {13},
pages = {},
pmid = {38998029},
issn = {2076-2615},
support = {(2018[2780])//Investigation into the conservation genetics of the gray snub-nosed monkey/ ; (32070523)//Population genetics analysis of the isolated gray snub-nosed monkey/ ; },
abstract = {The gut microbiota plays a crucial role in regulating energy metabolism, facilitating nutrient absorption, and supporting immune function, thereby assisting the host in adapting to seasonal dietary changes. Here, we compare the gut microbiome composition of wild gray snub-nosed monkeys during winter (from October to December) and spring (from January to March) to understand differences in seasonal nutrient intake patterns. Snub-nosed monkeys are foregut fermenters and consume difficult-to-digest carbohydrates and lichen. To examine the digestive adaptations of gray snub-nosed monkeys, we collected 14 fresh fecal samples for DNA analysis during the winter and spring. Based on 16S rRNA sequencing, metagenomic sequencing, and functional metagenomic analyses, we identified that Firmicutes, Actinobacteria, Verrucomicrobia, and Bacteroidetes constitute a keystone bacterial group in the gut microbiota during winter and spring and are responsible for degrading cellulose. Moreover, the transition in dietary composition from winter to spring was accompanied by changes in gut microbiota composition, demonstrating adaptive responses to varying food sources and availability. In winter, the bacterial species of the genera Streptococcus were found in higher abundance. At the functional level, these bacteria are involved in fructose and mannose metabolism and galactose metabolism c-related pathways, which facilitate the breakdown of glycogen, starch, and fiber found in fruits, seeds, and mature leaves. During spring, there was an increased abundance of bacteria species from the Prevotella and Lactobacillus genera, which aid the digestion of protein-rich buds. Combined, these findings reveal how the gut microbiota adjusts to fluctuations in energy balance and nutrient intake across different seasons in this critically endangered species. Moreover, we also identified Pseudomonas in two samples; the presence of potential pathogens within the gut could pose a risk to other troop members. Our findings highlight the necessity of a conservation plan that focuses on protecting vegetation and implementing measures to prevent disease transmission for this critically endangered species.},
}

@article {pmid38997719,
year = {2024},
author = {Sun, Y and Gan, Z and Wang, X and Liu, J and Zhong, W and Zhang, Z and Zuo, J and Zhong, H and Huang, X and Yan, Z and Cao, Q},
title = {Integrative metagenomic, transcriptomic, and proteomic analysis reveal the microbiota-host interplay in early-stage lung adenocarcinoma among non-smokers.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {652},
pmid = {38997719},
issn = {1479-5876},
support = {220904094208//The Fifth Affiliated Hospital of Sun Yat-sen University Qingdong Cao's talent-attracting fund/ ; },
mesh = {Humans ; *Proteomics ; *Adenocarcinoma of Lung/microbiology/genetics ; *Lung Neoplasms/microbiology/pathology/genetics ; *Metagenomics/methods ; Male ; Female ; *Transcriptome/genetics ; *Microbiota/genetics ; Middle Aged ; Neoplasm Staging ; Dysbiosis/microbiology ; Gene Expression Profiling ; Host Microbial Interactions/genetics ; Aged ; },
abstract = {BACKGROUND: The incidence of early-stage lung adenocarcinoma (ES-LUAD) is steadily increasing among non-smokers. Previous research has identified dysbiosis in the gut microbiota of patients with lung cancer. However, the local microbial profile of non-smokers with ES-LUAD remains largely unknown. In this study, we systematically characterized the local microbial community and its associated features to enable early intervention.

METHODS: A prospective collection of ES-LUAD samples (46 cases) and their corresponding normal tissues adjacent to the tumor (41 cases), along with normal lung tissue samples adjacent to pulmonary bullae in patients with spontaneous pneumothorax (42 cases), were subjected to ultra-deep metagenomic sequencing, host transcriptomic sequencing, and proteomic sequencing. The obtained omics data were subjected to both individual and integrated analysis using Spearman correlation coefficients.

RESULTS: We concurrently detected the presence of bacteria, fungi, and viruses in the lung tissues. The microbial profile of ES-LUAD exhibited similarities to NAT but demonstrated significant differences from the healthy controls (HCs), characterized by an overall reduction in species diversity. Patients with ES-LUAD exhibited local microbial dysbiosis, suggesting the potential pathogenicity of certain microbial species. Through multi-omics correlations, intricate local crosstalk between the host and local microbial communities was observed. Additionally, we identified a significant positive correlation (rho > 0.6) between Methyloversatilis discipulorum and GOLM1 at both the transcriptional and protein levels using multi-omics data. This correlated axis may be associated with prognosis. Finally, a diagnostic model composed of six bacterial markers successfully achieved precise differentiation between patients with ES-LUAD and HCs.

CONCLUSIONS: Our study depicts the microbial spectrum in patients with ES-LUAD and provides evidence of alterations in lung microbiota and their interplay with the host, enhancing comprehension of the pathogenic mechanisms that underlie ES-LUAD. The specific model incorporating lung microbiota can serve as a potential diagnostic tool for distinguishing between ES-LUAD and HCs.},
}

Humans
*Proteomics
*Adenocarcinoma of Lung/microbiology/genetics
*Lung Neoplasms/microbiology/pathology/genetics
*Metagenomics/methods
Male
Female
*Transcriptome/genetics
*Microbiota/genetics
Middle Aged
Neoplasm Staging
Dysbiosis/microbiology
Gene Expression Profiling
Host Microbial Interactions/genetics
Aged

@article {pmid38997445,
year = {2024},
author = {He, C and Fucich, D and Sosa, A and Wang, H and Kan, J and Liu, J and Xu, Y and Jiao, N and Gonsior, M and Chen, F},
title = {Deep metagenomic sequencing unveils novel SAR202 lineages and their vertical adaptation in the ocean.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {853},
pmid = {38997445},
issn = {2399-3642},
support = {Award #1829888//Armenian National Science and Education Fund (Armenian National Science & Education Fund)/ ; },
mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; Oceans and Seas ; Metagenome ; Seawater/microbiology ; Phylogeny ; Genome, Bacterial ; Chloroflexi/genetics/classification ; Bermuda ; Adaptation, Physiological/genetics ; Microbiota/genetics ; },
abstract = {SAR202 bacteria in the Chloroflexota phylum are abundant and widely distributed in the ocean. Their genome coding capacities indicate their potential roles in degrading complex and recalcitrant organic compounds in the ocean. However, our understanding of their genomic diversity, vertical distribution, and depth-related metabolisms is still limited by the number of assembled SAR202 genomes. In this study, we apply deep metagenomic sequencing (180 Gb per sample) to investigate microbial communities collected from six representative depths at the Bermuda Atlantic Time Series (BATS) station. We obtain 173 SAR202 metagenome-assembled genomes (MAGs). Intriguingly, 154 new species and 104 new genera are found based on these 173 SAR202 genomes. We add 12 new subgroups to the current SAR202 lineages. The vertical distribution of 20 SAR202 subgroups shows their niche partitioning in the euphotic, mesopelagic, and bathypelagic oceans, respectively. Deep-ocean SAR202 bacteria contain more genes and exhibit more metabolic potential for degrading complex organic substrates than those from the euphotic zone. With deep metagenomic sequencing, we uncover many new lineages of SAR202 bacteria and their potential functions which greatly deepen our understanding of their diversity, vertical profile, and contribution to the ocean's carbon cycling, especially in the deep ocean.},
}

*Metagenomics/methods
*High-Throughput Nucleotide Sequencing
Oceans and Seas
Metagenome
Seawater/microbiology
Phylogeny
Genome, Bacterial
Chloroflexi/genetics/classification
Bermuda
Adaptation, Physiological/genetics
Microbiota/genetics

@article {pmid38997249,
year = {2024},
author = {Su, X and Huang, X and Zhang, Y and Yang, L and Wen, T and Yang, X and Zhu, G and Zhang, J and Tang, Y and Li, Z and Ding, J and Li, R and Pan, J and Chen, X and Huang, F and Rillig, MC and Zhu, YG},
title = {Nitrifying niche in estuaries is expanded by the plastisphere.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5866},
pmid = {38997249},
issn = {2041-1723},
support = {42021005//Science Fund for Creative Research Groups (Fund for Creative Research Groups)/ ; },
mesh = {*Nitrification ; *Estuaries ; *Seawater/microbiology ; *Bacteria/metabolism/genetics ; *Biofilms/growth & development ; Ecosystem ; Microbiota/physiology ; Metagenomics ; Phylogeny ; Nitrogen Cycle ; Nitrogen/metabolism ; Nitrogen Isotopes/metabolism ; },
abstract = {The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered global concerns. Recent geochemical evidence has pointed out its potential role in influencing nitrogen biogeochemistry. However, the biogeochemical significance of the plastisphere and its mechanisms regulating nitrogen cycling remain elusive. Using [15]N- and [13]C-labelling coupled with metagenomics and metatranscriptomics, here we unveil that the plastisphere likely acts as an underappreciated nitrifying niche in estuarine ecosystems, exhibiting a 0.9 ~ 12-fold higher activity of bacteria-mediated nitrification compared to surrounding seawater and other biofilms (stone, wood and glass biofilms). The shift of active nitrifiers from O2-sensitive nitrifiers in the seawater to nitrifiers with versatile metabolisms in the plastisphere, combined with the potential interspecific cooperation of nitrifying substrate exchange observed among the plastisphere nitrifiers, collectively results in the unique nitrifying niche. Our findings highlight the plastisphere as an emerging nitrifying niche in estuarine environment, and deepen the mechanistic understanding of its contribution to marine biogeochemistry.},
}

*Nitrification
*Estuaries
*Seawater/microbiology
*Bacteria/metabolism/genetics
*Biofilms/growth & development
Ecosystem
Microbiota/physiology
Metagenomics
Phylogeny
Nitrogen Cycle
Nitrogen/metabolism
Nitrogen Isotopes/metabolism

@article {pmid38995889,
year = {2024},
author = {Melchior, PP and Reiss, E and Payne, Z and Vuong, N and Hovorka, K and Lindsay, HL and Diaz, GR and Gaire, T and Noyes, N},
title = {Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0306602},
pmid = {38995889},
issn = {1932-6203},
mesh = {*Seasons ; *Sarraceniaceae/microbiology ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Nitrogen/metabolism ; Bacteria/genetics/classification/isolation & purification ; Nitrogen Fixation ; Oxidoreductases/genetics/metabolism ; },
abstract = {The insectivorous Northern Pitcher Plant, Sarracenia purpurea, recruits a dynamic biotic community in the rainwater collected by its pitcher-shaped leaves. Insect capture and degradation within the pitcher fluid (phytotelma) has been well documented as a mechanism for supplementing the plant's nitrogen, phosphorous, and micronutrient requirements. Metagenomic studies have shown a diverse microbiome in this phytotelm environment, including taxa that contribute metabolically to prey digestion. In this investigation, we used high-throughput 16S rDNA sequencing and bioinformatics to analyze the S. purpurea phytotelm bacteriome as it changes through the growing season (May-September) in plants from the north-central region of the species' native range. Additionally, we used molecular techniques to detect and quantify bacterial nitrogenase genes (nifH) in all phytotelm samples to explore the hypothesis that diazotrophy is an additional mechanism of supplying biologically available nitrogen to S. purpurea. The results of this study indicate that while prokaryote diversity remains relatively stable in plants at different locations within our region, diversity changes significantly as the growing season progresses. Furthermore, nifH genes were detected at biologically significant concentrations in one hundred percent of samples, suggesting that nitrogen fixation may be an important contributor to the S. purpurea nutrient budget.},
}

*Seasons
*Sarraceniaceae/microbiology
Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Nitrogen/metabolism
Bacteria/genetics/classification/isolation & purification
Nitrogen Fixation
Oxidoreductases/genetics/metabolism

@article {pmid38995542,
year = {2024},
author = {Van Den Bossche, T and Verschaffelt, P and Vande Moortele, T and Dawyndt, P and Martens, L and Mesuere, B},
title = {Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2836},
number = {},
pages = {183-215},
pmid = {38995542},
issn = {1940-6029},
mesh = {*Proteomics/methods ; *Software ; *Microbiota/genetics ; *Biodiversity ; Humans ; Computational Biology/methods ; Metagenomics/methods ; },
abstract = {Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be , has emerged as a valuable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.},
}

*Proteomics/methods
*Software
*Microbiota/genetics
*Biodiversity
Humans
Computational Biology/methods
Metagenomics/methods

@article {pmid38995243,
year = {2024},
author = {Leech, SM and Borg, DJ and Rae, KM and Kumar, S and Clifton, VL and Dekker Nitert, M},
title = {Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics.},
journal = {Microbial genomics},
volume = {10},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001269},
pmid = {38995243},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; *Anti-Bacterial Agents/administration & dosage ; Pregnancy ; *Cesarean Section ; Adult ; Infant ; *Feces/microbiology ; *Delivery, Obstetric ; Peripartum Period ; Infant, Newborn ; Male ; Antibiotic Prophylaxis ; Longitudinal Studies ; },
abstract = {Background. Previous research has shown that delivery mode can shape infant gut microbiome composition. However, mothers delivering by caesarean section routinely receive prophylactic antibiotics prior to delivery, resulting in antibiotic exposure to the infant via the placenta. Previously, only a small number of studies have examined the effect of delivery mode versus antibiotic exposure on the infant gut microbiome with mixed findings.Objective. We aimed to determine the effect of delivery mode compared to antibiotic use during labour and delivery on the infant and maternal gut microbiome at 6 weeks post-partum.Methodology. Twenty-five mother-infant dyads were selected from the longitudinal Queensland Family Cohort Study. The selected dyads comprised nine vaginally delivered infants without antibiotics, seven vaginally delivered infants exposed to antibiotics and nine infants born by caesarean section with routine maternal prophylactic antibiotics. Shotgun-metagenomic sequencing of DNA from stool samples collected at 6 weeks post-partum from mother and infant was used to assess microbiome composition.Results. Caesarean section infants exhibited decreases in Bacteroidetes (ANCOM-BC q<0.0001, MaAsLin 2 q=0.041), changes to several functional pathways and altered beta diversity (R [2]=0.056, P=0.029), while minimal differences due to antibiotic exposure were detected. For mothers, caesarean delivery (P=0.0007) and antibiotic use (P=0.016) decreased the evenness of the gut microbiome at 6 weeks post-partum without changing beta diversity. Several taxa in the maternal microbiome were altered in association with antibiotic use, with few differentially abundant taxa associated with delivery mode.Conclusion. For infants, delivery mode appears to have a larger effect on gut microbiome composition at 6 weeks post-partum than intrapartum antibiotic exposure. For mothers, both delivery mode and intrapartum antibiotic use have a small effect on gut microbiome composition at 6 weeks post-partum.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
*Anti-Bacterial Agents/administration & dosage
Pregnancy
*Cesarean Section
Adult
Infant
*Feces/microbiology
*Delivery, Obstetric
Peripartum Period
Infant, Newborn
Male
Antibiotic Prophylaxis
Longitudinal Studies

@article {pmid38995144,
year = {2024},
author = {Arikan, M and Muth, T},
title = {gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {38995144},
issn = {2047-217X},
support = {//Türkiye Bilimsel ve Teknolojik Araştirma Kurumu/ ; },
mesh = {*Microbiota ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Software ; *Computational Biology/methods ; *Proteomics/methods ; Humans ; Metagenome ; Multiomics ; },
abstract = {BACKGROUND: In recent years, omics technologies have offered an exceptional chance to gain a deeper insight into the structural and functional characteristics of microbial communities. As a result, there is a growing demand for user-friendly, reproducible, and versatile bioinformatic tools that can effectively harness multi-omics data to provide a holistic understanding of microbiomes. Previously, we introduced gNOMO, a bioinformatic pipeline tailored to analyze microbiome multi-omics data in an integrative manner. In response to the evolving demands within the microbiome field and the growing necessity for integrated multi-omics data analysis, we have implemented substantial enhancements to the gNOMO pipeline.

RESULTS: Here, we present gNOMO2, a comprehensive and modular pipeline that can seamlessly manage various omics combinations, ranging from 2 to 4 distinct omics data types, including 16S ribosomal RNA (rRNA) gene amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics. Furthermore, gNOMO2 features a specialized module for processing 16S rRNA gene amplicon sequencing data to create a protein database suitable for metaproteomics investigations. Moreover, it incorporates new differential abundance, integration, and visualization approaches, enhancing the toolkit for a more insightful analysis of microbiomes. The functionality of these new features is showcased through the use of 4 microbiome multi-omics datasets encompassing various ecosystems and omics combinations. gNOMO2 not only replicated most of the primary findings from these studies but also offered further valuable perspectives.

CONCLUSIONS: gNOMO2 enables the thorough integration of taxonomic and functional analyses in microbiome multi-omics data, offering novel insights in both host-associated and free-living microbiome research. gNOMO2 is available freely at https://github.com/muzafferarikan/gNOMO2.},
}

*Microbiota
*Metagenomics/methods
*RNA, Ribosomal, 16S/genetics
*Software
*Computational Biology/methods
*Proteomics/methods
Humans
Metagenome
Multiomics

@article {pmid38990940,
year = {2024},
author = {Zomer, A and Ingham, CJ and von Meijenfeldt, FAB and Escobar Doncel, Á and van de Kerkhof, GT and Hamidjaja, R and Schouten, S and Schertel, L and Müller, KH and Catón, L and Hahnke, RL and Bolhuis, H and Vignolini, S and Dutilh, BE},
title = {Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {29},
pages = {e2309757121},
pmid = {38990940},
issn = {1091-6490},
support = {40-43500-98-4102/435004516//ZonMw (Netherlands Organisation for Health Research and Development)/ ; 860125//EC | HORIZON EUROPE Framework Programme (Horizon Europe)/ ; 2110570//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 722842//EC | HORIZON EUROPE Framework Programme (Horizon Europe)/ ; P2ZHP2_183998/SNSF_/Swiss National Science Foundation/Switzerland ; SNSF3//Isaac Newton Trust/ ; SNSF 40B1-0_198708/SNSF_/Swiss National Science Foundation/Switzerland ; 865694//EC | European Research Council (ERC)/ ; 101001637//EC | European Research Council (ERC)/ ; BB/V00364X/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Genome, Bacterial ; Phenotype ; Color ; Bacteria/genetics/metabolism ; Proteobacteria/genetics/metabolism ; Phylogeny ; Metagenome ; Genome-Wide Association Study ; Bacteroidetes/genetics/metabolism ; },
abstract = {Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.},
}

*Genome, Bacterial
Phenotype
Color
Bacteria/genetics/metabolism
Proteobacteria/genetics/metabolism
Phylogeny
Metagenome
Genome-Wide Association Study
Bacteroidetes/genetics/metabolism

@article {pmid38990824,
year = {2024},
author = {Schaible, GA and Jay, ZJ and Cliff, J and Schulz, F and Gauvin, C and Goudeau, D and Malmstrom, RR and Ruff, SE and Edgcomb, V and Hatzenpichler, R},
title = {Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells.},
journal = {PLoS biology},
volume = {22},
number = {7},
pages = {e3002638},
pmid = {38990824},
issn = {1545-7885},
support = {P30 GM140963/GM/NIGMS NIH HHS/United States ; },
mesh = {*In Situ Hybridization, Fluorescence ; Metagenome ; Microbial Consortia/genetics ; Genome, Bacterial ; Bacteria/genetics/metabolism ; Genetic Variation ; Phylogeny ; },
abstract = {Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.},
}

*In Situ Hybridization, Fluorescence
Metagenome
Microbial Consortia/genetics
Genome, Bacterial
Bacteria/genetics/metabolism
Genetic Variation
Phylogeny

@article {pmid38989650,
year = {2024},
author = {Shi, Z and Long, X and Zhang, C and Chen, Z and Usman, M and Zhang, Y and Zhang, S and Luo, G},
title = {Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants.},
journal = {Environmental science & technology},
volume = {58},
number = {29},
pages = {13010-13022},
doi = {10.1021/acs.est.4c04109},
pmid = {38989650},
issn = {1520-5851},
mesh = {*Biofuels ; *Bacteria ; Food ; Microbiota ; Anaerobiosis ; Viruses ; Food Loss and Waste ; },
abstract = {Anaerobic digestion (AD) is commonly used in food waste treatment. Prokaryotic microbial communities in AD of food waste have been comprehensively studied. The role of viruses, known to affect microbial dynamics and metabolism, remains largely unexplored. This study employed metagenomic analysis and recovered 967 high-quality viral bins within food waste and digestate derived from 8 full-scale biogas plants. The diversity of viral communities was higher in digestate. In silico predictions linked 20.8% of viruses to microbial host populations, highlighting possible virus predators of key functional microbes. Lineage-specific virus-host ratio varied, indicating that viral infection dynamics might differentially affect microbial responses to the varying process parameters. Evidence for virus-mediated gene transfer was identified, emphasizing the potential role of viruses in controlling the microbiome. AD altered the specific process parameters, potentially promoting a shift in viral lifestyle from lysogenic to lytic. Viruses encoding auxiliary metabolic genes (AMGs) were involved in microbial carbon and nutrient cycling, and most AMGs were transcriptionally expressed in digestate, meaning that viruses with active functional states were likely actively involved in AD. These findings provided a comprehensive profile of viral and bacterial communities and expanded knowledge of the interactions between viruses and hosts in food waste and digestate.},
}

*Biofuels
*Bacteria
Food
Microbiota
Anaerobiosis
Viruses
Food Loss and Waste

@article {pmid38989465,
year = {2024},
author = {Nanetti, E and Scicchitano, D and Palladino, G and Interino, N and Corlatti, L and Pedrotti, L and Zanetti, F and Pagani, E and Esposito, E and Brambilla, A and Grignolio, S and Marotti, I and Turroni, S and Fiori, J and Rampelli, S and Candela, M},
title = {The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.},
journal = {iScience},
volume = {27},
number = {7},
pages = {110194},
pmid = {38989465},
issn = {2589-0042},
abstract = {Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.},
}

@article {pmid38986506,
year = {2024},
author = {Popov, IV and Koopmans, B and Venema, K},
title = {Modulation of human gut microbiota by linear and branched fructooligosaccharides in an in vitro colon model (TIM-2).},
journal = {Journal of applied microbiology},
volume = {135},
number = {7},
pages = {},
doi = {10.1093/jambio/lxae170},
pmid = {38986506},
issn = {1365-2672},
support = {//Grassa/ ; HEFI-1//Dutch Province of Limburg/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/pharmacology/metabolism ; Humans ; *Bacteria/genetics/classification/metabolism/isolation & purification/drug effects ; *Colon/microbiology/metabolism ; *RNA, Ribosomal, 16S/genetics ; Lolium/microbiology ; Cichorium intybus ; Feces/microbiology ; },
abstract = {AIMS: This study aimed to compare the effects of linear and branched fructooligosaccharides (FOS) extracted from chicory and grass (Lolium perenne), respectively on human microbiota composition, diversity, and metabolism.

METHODS AND RESULTS: To test the effects of linear and branched FOS on human microbiota we used the artificial in vitro human colon model (TIM-2). Microbiota composition and diversity were assessed by V3-V4 16S rRNA metagenomic sequencing, followed by differential taxa abundance and alpha/beta diversity analyses. SCFA/BCFA production was evaluated by gas chromatography-mass spectrometry. As a result, branched FOS had the most beneficial effects on microbial diversity and metabolite production. Also, branched FOS significantly increased the abundance of commensal bacteria associated with maintaining healthy gut functions and controlling inflammation, such as Butyricicoccus, Erysipelotrichaceae, Phascolarctobacterium, and Sutterella. Linear FOS also significantly increased the abundance of some other commensal gut bacteria (Anaerobutyricum, Lachnospiraceae, Faecalibacterium), but there were no differences in diversity metrics compared to the control.

CONCLUSIONS: The study revealed that branched FOS had the most beneficial effects compared to the linear FOS in vitro, concerning microbiota modulation, and metabolite production, making this a good candidate for further studies in food biotechnology.},
}

*Gastrointestinal Microbiome/drug effects
*Oligosaccharides/pharmacology/metabolism
Humans
*Bacteria/genetics/classification/metabolism/isolation & purification/drug effects
*Colon/microbiology/metabolism
*RNA, Ribosomal, 16S/genetics
Lolium/microbiology
Cichorium intybus
Feces/microbiology

@article {pmid38984661,
year = {2024},
author = {Zhao, JT and Zhang, Y and Wang, XW and Zou, PY and Zhao, Z and Mei, H and Liu, YX and Su, NY and Zhu, YJ and Wang, B and Wei, YL and Chen, DF and Lan, CH},
title = {Long-term effects of fecal microbiota transplantation on gut microbiota after Helicobacter pylori eradication with bismuth quadruple therapy: A randomized controlled trial.},
journal = {Helicobacter},
volume = {29},
number = {4},
pages = {e13079},
doi = {10.1111/hel.13079},
pmid = {38984661},
issn = {1523-5378},
support = {82072253//National Natural Science Foundation of China/ ; 2022jstg020//Chongqing Appropriate Health Technology Promotion/ ; },
mesh = {Humans ; *Helicobacter Infections/therapy/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Middle Aged ; *Helicobacter pylori/drug effects ; Adult ; *Anti-Bacterial Agents/therapeutic use ; Prospective Studies ; *Bismuth/therapeutic use ; Drug Therapy, Combination ; China ; Amoxicillin/therapeutic use ; Clarithromycin/therapeutic use ; Treatment Outcome ; Aged ; Feces/microbiology ; },
abstract = {BACKGROUND: Eradicating Helicobacter pylori infection by bismuth quadruple therapy (BQT) is effective. However, the effect of BQT and subsequent fecal microbiota transplant (FMT) on the gut microbiota is less known.

MATERIALS AND METHODS: This prospective randomized controlled trial was conducted at a tertiary hospital in China from January 2019 to October 2020, with the primary endpoints the effect of BQT on the gut microbiota and the effect of FMT on the gut microbiota after bismuth quadruple therapy eradication therapy. A 14-day BQT with amoxicillin and clarithromycin was administered to H. pylori-positive subjects, and after eradication therapy, patients received a one-time FMT or placebo treatment. We then collected stool samples to assess the effects of 14-day BQT and FMT on the gut microbiota. 16 s rDNA and metagenomic sequencing were used to analyze the structure and function of intestinal flora. We also used Gastrointestinal Symptom Rating Scale (GSRS) to evaluate gastrointestinal symptom during treatment.

RESULTS: A total of 30 patients were recruited and 15 were assigned to either FMT or placebo groups. After eradication therapy, alpha-diversity was decreased in both groups. At the phylum level, the abundance of Bacteroidetes and Firmicutes decreased, while Proteobacteria increased. At the genus level, the abundance of beneficial bacteria decreased, while pathogenic bacteria increased. Eradication therapy reduced some resistance genes abundance while increased the resistance genes abundance linked to Escherichia coli. While they all returned to baseline by Week 10. Besides, the difference was observed in Week 10 by the diarrhea score between two groups. Compared to Week 2, the GSRS total score and diarrhea score decreased in Week 3 only in FMT group.

CONCLUSIONS: The balance of intestinal flora in patients can be considerably impacted by BQT in the short term, but it has reverted back to baseline by Week 10. FMT can alleviate gastrointestinal symptoms even if there was no evidence it promoted restoration of intestinal flora.},
}

Humans
*Helicobacter Infections/therapy/microbiology/drug therapy
*Gastrointestinal Microbiome/drug effects
*Fecal Microbiota Transplantation/methods
Male
Female
Middle Aged
*Helicobacter pylori/drug effects
Adult
*Anti-Bacterial Agents/therapeutic use
Prospective Studies
*Bismuth/therapeutic use
Drug Therapy, Combination
China
Amoxicillin/therapeutic use
Clarithromycin/therapeutic use
Treatment Outcome
Aged
Feces/microbiology

@article {pmid38983956,
year = {2024},
author = {Jin, LX and Fang, YP and Xia, CM and Cai, TW and Li, QQ and Wang, YY and Yan, HF and Chen, X},
title = {Helicobacter pylori infection alters gastric microbiota structure and biological functions in patients with gastric ulcer or duodenal ulcer.},
journal = {World journal of gastroenterology},
volume = {30},
number = {24},
pages = {3076-3085},
pmid = {38983956},
issn = {2219-2840},
mesh = {Humans ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/isolation & purification/genetics ; *Duodenal Ulcer/microbiology/diagnosis ; Male ; Female ; Middle Aged ; *Gastric Mucosa/microbiology/pathology ; *Gastrointestinal Microbiome ; *Stomach Ulcer/microbiology ; Adult ; Case-Control Studies ; Aged ; Metagenomics/methods ; Duodenum/microbiology ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection is closely associated with gastrointestinal diseases. Our preliminary studies have indicated that H. pylori infection had a significant impact on the mucosal microbiome structure in patients with gastric ulcer (GU) or duodenal ulcer (DU).

AIM: To investigate the contributions of H. pylori infection and the mucosal microbiome to the pathogenesis and progression of ulcerative diseases.

METHODS: Patients with H. pylori infection and either GU or DU, and healthy individuals without H. pylori infection were included. Gastric or duodenal mucosal samples was obtained and subjected to metagenomic sequencing. The compositions of the microbial communities and their metabolic functions in the mucosal tissues were analyzed.

RESULTS: Compared with that in the healthy individuals, the gastric mucosal microbiota in the H. pylori-positive patients with GU was dominated by H. pylori, with significantly reduced biodiversity. The intergroup differential functions, which were enriched in the H. pylori-positive GU patients, were all derived from H. pylori, particularly those concerning transfer RNA queuosine-modification and the synthesis of demethylmenaquinones or menaquinones. A significant enrichment of the uibE gene was detected in the synthesis pathway. There was no significant difference in microbial diversity between the H. pylori-positive DU patients and healthy controls.

CONCLUSION: H. pylori infection significantly alters the gastric microbiota structure, diversity, and biological functions, which may be important contributing factors for GU.},
}

Humans
*Helicobacter Infections/microbiology
*Helicobacter pylori/isolation & purification/genetics
*Duodenal Ulcer/microbiology/diagnosis
Male
Female
Middle Aged
*Gastric Mucosa/microbiology/pathology
*Gastrointestinal Microbiome
*Stomach Ulcer/microbiology
Adult
Case-Control Studies
Aged
Metagenomics/methods
Duodenum/microbiology
Dysbiosis/microbiology

@article {pmid38982403,
year = {2024},
author = {Yao, G and Zhao, Z and Yang, C and Zuo, B and Sun, Z and Wang, J and Zhang, H},
title = {Evaluating the probiotic effects of spraying lactiplantibacillus plantarum P-8 in neonatal piglets.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {253},
pmid = {38982403},
issn = {1471-2180},
support = {2021ZD0014//Inner Mongolia Science and Technology Major Project/ ; 2019CG027//Inner Mongolia Autonomous Region Science and Technology Achievement Transformation Project/ ; },
mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; Swine ; *Animals, Newborn ; *Gastrointestinal Microbiome/drug effects ; Lactobacillus plantarum ; Fermentation ; Antioxidants/metabolism/administration & dosage/pharmacology ; Feces/microbiology ; },
abstract = {BACKGROUND: Gut microbes play an important role in the growth and health of neonatal piglets. Probiotics can promote the healthy growth of neonatal piglets by regulating their gut microbes. The study investigated the effects of spraying Lactiplantibacillus plantarum P-8 (L. plantarum P-8) fermentation broth on the growth performance and gut microbes of neonatal piglets.

RESULTS: The animals were randomly divided into probiotics groups (109 neonatal piglets) and control groups (113 neonatal piglets). The probiotics group was sprayed with L. plantarum P-8 fermented liquid from 3 day before the expected date of the sow to the 7-day-old of piglets, while the control group was sprayed with equal dose of PBS. Average daily gain (ADG), immune and antioxidant status and metagenome sequencing were used to assess the changes in growth performance and gut microbiota of neonatal piglets. The results showed that L. plantarum P-8 treatment significantly improved the average daily gain (P < 0.05) of neonatal piglets. L. plantarum P-8 increased the activities of CAT and SOD but reduced the levels of IL-2 and IL-6, effectively regulating the antioxidant capacity and immunity in neonatal piglets. L. plantarum P-8 adjusted the overall structure of gut microflora improving gut homeostasis to a certain extent, and significantly increased the relative abundance of gut beneficial bacteria such as L. mucosae and L. plantarum.

CONCLUSION: Spraying L. plantarum P-8 can be a feasible and effective probiotic intervention not only improving the growth of neonatal piglets, regulating the antioxidant capacity and immunity of neonatal piglets, but also improving the gut homeostasis to a certain extent.},
}

Animals
*Probiotics/administration & dosage/pharmacology
Swine
*Animals, Newborn
*Gastrointestinal Microbiome/drug effects
Lactobacillus plantarum
Fermentation
Antioxidants/metabolism/administration & dosage/pharmacology
Feces/microbiology

@article {pmid38981836,
year = {2024},
author = {Núñez-Montero, K and Leal, K and Rojas-Villalta, D and Castro, M and Larronde, C and Wagenknecht, L and Contreras, MJ},
title = {16s gene metagenomic characterization in healthy stallion semen.},
journal = {Research in veterinary science},
volume = {176},
number = {},
pages = {105354},
doi = {10.1016/j.rvsc.2024.105354},
pmid = {38981836},
issn = {1532-2661},
mesh = {Animals ; Horses/microbiology ; Male ; *Semen/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; Microbiota ; DNA, Bacterial/genetics ; },
abstract = {Studies on the bacterial composition of seminal samples have primarily focused on species isolated from semen and their effects on fertility and reproductive health. Culture-independent techniques, such as 16S rRNA gene sequencing and shotgun metagenomics, have revolutionized our ability to identify unculturable bacteria, which comprise >90% of the microbiome. These techniques allow for comprehensive analysis of microbial communities in seminal samples, shedding light on their interactions and roles. In this study, we characterized the taxonomic diversity of seminal microbial communities in healthy stallions using 16S rRNA gene sequencing. Semen samples were collected from four stallions during the reproductive season, and DNA was extracted for sequencing. The results revealed a diverse array of bacterial taxa, with Firmicutes, Bacteroidota, and Proteobacteria being predominant phyla. At the family and genus levels, significant variations were observed among individuals, with individual variability in microbial richness and diversity standing out. Moreover, each stallion showed a distinct microbial fingerprint, indicating the presence of a characteristic microbial core for each stallion. These results underscore the importance of considering individual microbial profiles in understanding reproductive health and fertility outcomes.},
}

Animals
Horses/microbiology
Male
*Semen/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification/isolation & purification
Metagenomics
Microbiota
DNA, Bacterial/genetics

@article {pmid38977718,
year = {2024},
author = {Wei, Y and Li, J and Zhu, B and Hu, Q and Lan, M and Zhou, J and Luo, J and Zhu, W and Lai, Y and Long, E and Zhou, L},
title = {Metagenomic comparison of intestinal microbiota between normal and liver fibrotic rhesus macaques (Macaca mulatta).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {15677},
pmid = {38977718},
issn = {2045-2322},
support = {2022JDZH0014//Science & Technology Department of Sichuan Province/ ; },
mesh = {Animals ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome/genetics ; *Liver Cirrhosis/microbiology/genetics/pathology ; Male ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Liver fibrosis is an important pathological process in chronic liver disease and cirrhosis. Recent studies have found a close association between intestinal microbiota and the development of liver fibrosis. To determine whether there are differences in the intestinal microbiota between rhesus macaques with liver fibrosis (MG) and normal rhesus macaques (MN), fecal samples were collected from 8 male MG and 12 male MN. The biological composition of the intestinal microbiota was then detected using 16S rRNA gene sequencing. The results revealed statistically significant differences in ASVs and Chao1 in the alpha-diversity and the beta-diversity of intestinal microbiota between MG and MN. Both groups shared Prevotella and Lactobacillus as common dominant microbiota. However, beneficial bacteria such as Lactobacillus were significantly less abundant in MG (P = 0.02). Predictive functional analysis using PICRUSt2 gene prediction revealed that MG exhibited a higher relative abundance of functions related to substance transport and metabolic pathways. This study may provide insight into further exploration of the mechanisms by which intestinal microbiota affect liver fibrosis and its potential future use in treating liver fibrosis.},
}

Animals
*Macaca mulatta/microbiology
*Gastrointestinal Microbiome/genetics
*Liver Cirrhosis/microbiology/genetics/pathology
Male
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Feces/microbiology
Metagenome
Bacteria/genetics/classification/isolation & purification

@article {pmid38977664,
year = {2024},
author = {Zachariasen, T and Russel, J and Petersen, C and Vestergaard, GA and Shah, S and Atienza Lopez, P and Passali, M and Turvey, SE and Sørensen, SJ and Lund, O and Stokholm, J and Brejnrod, A and Thorsen, J},
title = {MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5734},
pmid = {38977664},
issn = {2041-1723},
mesh = {*Phylogeny ; *Metagenomics/methods ; *Metagenome/genetics ; Humans ; *Microbiota/genetics ; Software ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; },
abstract = {Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with functional profiling of assembled genomes. To define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. Here, we present MAGinator, a freely available tool, tailored for profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes and genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences.},
}

*Phylogeny
*Metagenomics/methods
*Metagenome/genetics
Humans
*Microbiota/genetics
Software
Bacteria/genetics/classification
Genome, Bacterial/genetics

@article {pmid38972064,
year = {2024},
author = {Lee, S and Lee, I},
title = {Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2375679},
pmid = {38972064},
issn = {1949-0984},
mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Metagenome ; Case-Control Studies ; Crohn Disease/microbiology/diagnosis ; Colorectal Neoplasms/diagnosis/microbiology ; Bacteria/genetics/classification/isolation & purification ; Algorithms ; Gastrointestinal Diseases/diagnosis/microbiology ; },
abstract = {The gut microbiome, linked significantly to host diseases, offers potential for disease diagnosis through machine learning (ML) pipelines. These pipelines, crucial in modeling diseases using high-dimensional microbiome data, involve selecting profile modalities, data preprocessing techniques, and classification algorithms, each impacting the model accuracy and generalizability. Despite whole metagenome shotgun sequencing (WMS) gaining popularity for human gut microbiome profiling, a consensus on the optimal methods for ML pipelines in disease diagnosis using WMS data remains elusive. Addressing this gap, we comprehensively evaluated ML methods for diagnosing Crohn's disease and colorectal cancer, using 2,553 fecal WMS samples from 21 case-control studies. Our study uncovered crucial insights: gut-specific, species-level taxonomic features proved to be the most effective for profiling; batch correction was not consistently beneficial for model performance; compositional data transformations markedly improved the models; and while nonlinear ensemble classification algorithms typically offered superior performance, linear models with proper regularization were found to be more effective for diseases that are linearly separable based on microbiome data. An optimal ML pipeline, integrating the most effective methods, was validated for generalizability using holdout data. This research offers practical guidelines for constructing reliable disease diagnostic ML models with fecal WMS data.},
}

Humans
*Machine Learning
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Metagenome
Case-Control Studies
Crohn Disease/microbiology/diagnosis
Colorectal Neoplasms/diagnosis/microbiology
Bacteria/genetics/classification/isolation & purification
Algorithms
Gastrointestinal Diseases/diagnosis/microbiology

@article {pmid38972056,
year = {2024},
author = {Villani, A and Fontana, A and Panebianco, C and Ferro, C and Copetti, M and Pavlovic, R and Drago, D and Fiorentini, C and Terracciano, F and Bazzocchi, F and Canistro, G and Pisati, F and Maiello, E and Latiano, TP and Perri, F and Pazienza, V},
title = {A powerful machine learning approach to identify interactions of differentially abundant gut microbial subsets in patients with metastatic and non-metastatic pancreatic cancer.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2375483},
pmid = {38972056},
issn = {1949-0984},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome ; *Machine Learning ; *Bacteria/classification/genetics/isolation & purification ; *Neoplasm Metastasis ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Feces/microbiology ; Aged ; Metagenomics ; },
abstract = {Pancreatic cancer has a dismal prognosis, as it is often diagnosed at stage IV of the disease and is characterized by metastatic spread. Gut microbiota and its metabolites have been suggested to influence the metastatic spread by modulating the host immune system or by promoting angiogenesis. To date, the gut microbial profiles of metastatic and non-metastatic patients need to be explored. Taking advantage of the 16S metagenomic sequencing and the PEnalized LOgistic Regression Analysis (PELORA) we identified clusters of bacteria with differential abundances between metastatic and non-metastatic patients. An overall increase in Gram-negative bacteria in metastatic patients compared to non-metastatic ones was identified using this method. Furthermore, to gain more insight into how gut microbes can predict metastases, a machine learning approach (iterative Random Forest) was performed. Iterative Random Forest analysis revealed which microorganisms were characterized by a different level of relative abundance between metastatic and non-metastatic patients and established a functional relationship between the relative abundance and the probability of having metastases. At the species level, the following bacteria were found to have the highest discriminatory power: Anaerostipes hadrus, Coprobacter secundus, Clostridium sp. 619, Roseburia inulinivorans, Porphyromonas and Odoribacter at the genus level, and Rhodospirillaceae, Clostridiaceae and Peptococcaceae at the family level. Finally, these data were intertwined with those from a metabolomics analysis on fecal samples of patients with or without metastasis to better understand the role of gut microbiota in the metastatic process. Artificial intelligence has been applied in different areas of the medical field. Translating its application in the field of gut microbiota analysis may help fully exploit the potential information contained in such a large amount of data aiming to open up new supportive areas of intervention in the management of cancer.},
}

Humans
*Pancreatic Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome
*Machine Learning
*Bacteria/classification/genetics/isolation & purification
*Neoplasm Metastasis
Male
Female
RNA, Ribosomal, 16S/genetics
Middle Aged
Feces/microbiology
Aged
Metagenomics

@article {pmid38971804,
year = {2024},
author = {Huang, X and Zeng, J and Li, S and Chen, J and Wang, H and Li, C and Zhang, S},
title = {16S rRNA, metagenomics and 2bRAD-M sequencing to decode human thanatomicrobiome.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {736},
pmid = {38971804},
issn = {2052-4463},
support = {82371896//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072123//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; *Microbiota ; *Cadaver ; },
abstract = {Microorganisms are essential in the decomposition of corpses and play a significant role in forensic science. However, previous studies have primarily focused on animal remains, specifically the gut, skin, and burial environment. Insufficient research has been conducted on the microbiota of human cadavers, especially in cases of advanced decomposition and additional tissues, resulting in a lack of relevant reference data. In this study, the microbiota of eight cadavers at different stages of decomposition were detected using 16S rRNA, metagenomic sequencing and 2bRAD-M sequencing. Nine different sites, including oral and nasal cavities, heart, liver, spleen, lung, kidney, muscle and gut, were analysed and the efficacy of these methods was evaluated. The results showed that 16S rRNA sequencing was the most cost-effective method for the study of cadavers in the early stages of decomposition, whereas for cadaveric tissues in the late stages of decomposition, 2bRAD-M could overcome host contamination more effectively than metagenomic sequencing. This paves the way for new opportunities in data retrieval and promotes in-depth investigations into the microbiota.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Metagenomics
*Microbiota
*Cadaver

@article {pmid38970783,
year = {2024},
author = {Wang, X and Sun, J and Zhang, X and Chen, W and Cao, J and Hu, H},
title = {Metagenomics reveals unique gut mycobiome biomarkers in psoriasis.},
journal = {Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)},
volume = {30},
number = {7},
pages = {e13822},
pmid = {38970783},
issn = {1600-0846},
mesh = {Humans ; *Psoriasis/microbiology/blood ; Female ; *Mycobiome ; Adult ; Male ; *Biomarkers/blood ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; Middle Aged ; Machine Learning ; Feces/microbiology ; Young Adult ; Aspergillus ; },
abstract = {PURPOSE: In present, the diagnosis of psoriasis is mainly based on the patient's typical clinical manifestations, dermoscopy and skin biopsy, and unlike other immune diseases, psoriasis lacks specific indicators in the blood. Therefore, we are required to search novel biomarkers for the diagnosis of psoriasis.

METHODS: In this study, we analyzed the composition and the differences of intestinal fungal communities composition between psoriasis patients and healthy individuals in order to find the intestinal fungal communities associated with the diagnosis of psoriasis. We built a machine learning model and identified potential microbial markers for the diagnosis of psoriasis.

RESULTS: The results of AUROC (area under ROC) showed that Aspergillus puulaauensis (AUROC = 0.779), Kazachstania africana (AUROC = 0.750) and Torulaspora delbrueckii (AUROC = 0.745) had high predictive ability (AUROC > 0.7) for predicting psoriasis, While Fusarium keratoplasticum (AUROC = 0.670) was relatively lower (AUROC < 0.7).

CONCLUSION: The strategy based on the prediction of intestinal fungal communities provides a new idea for the diagnosis of psoriasis and is expected to become an auxiliary diagnostic method for psoriasis.},
}

Humans
*Psoriasis/microbiology/blood
Female
*Mycobiome
Adult
Male
*Biomarkers/blood
*Gastrointestinal Microbiome
*Metagenomics/methods
Middle Aged
Machine Learning
Feces/microbiology
Young Adult
Aspergillus

@article {pmid38970126,
year = {2024},
author = {Zuppi, M and Vatanen, T and Wilson, BC and Golovina, E and Portlock, T and Cutfield, WS and Vickers, MH and O'Sullivan, JM},
title = {Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {122},
pmid = {38970126},
issn = {2049-2618},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; *Bacteriophages/physiology/classification/isolation & purification/genetics ; *Feces/microbiology/virology ; *Obesity/therapy/microbiology ; Double-Blind Method ; Female ; Adolescent ; Male ; Bacteria/classification/virology/genetics ; Metagenomics/methods ; Treatment Outcome ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a therapeutic intervention used to treat diseases associated with the gut microbiome. In the human gut microbiome, phages have been implicated in influencing human health, with successful engraftment of donor phages correlated with FMT treatment efficacy. The impact that gastrointestinal phages exert on human health has primarily been connected to their ability to modulate the bacterial communities in the gut. Nonetheless, how FMT affects recipients' phage populations, and in turn, how this influences the gut environment, is not yet fully understood. In this study, we investigated the effects of FMT on the phageome composition of participants within the Gut Bugs Trial (GBT), a double-blind, randomized, placebo-controlled trial that investigated the efficacy of FMT in treating obesity and comorbidities in adolescents. Stool samples collected from donors at the time of treatment and recipients at four time points (i.e., baseline and 6 weeks, 12 weeks, and 26 weeks post-intervention), underwent shotgun metagenomic sequencing. Phage sequences were identified and characterized in silico to examine evidence of phage engraftment and to assess the extent of FMT-induced alterations in the recipients' phageome composition.

RESULTS: Donor phages engrafted stably in recipients following FMT, composing a significant proportion of their phageome for the entire course of the study (33.8 ± 1.2% in females and 33.9 ± 3.7% in males). Phage engraftment varied between donors and donor engraftment efficacy was positively correlated with their phageome alpha diversity. FMT caused a shift in recipients' phageome toward the donors' composition and increased phageome alpha diversity and variability over time.

CONCLUSIONS: FMT significantly altered recipients' phage and, overall, microbial populations. The increase in microbial diversity and variability is consistent with a shift in microbial population dynamics. This proposes that phages play a critical role in modulating the gut environment and suggests novel approaches to understanding the efficacy of FMT in altering the recipient's microbiome.

TRIAL REGISTRATION: The Gut Bugs Trial was registered with the Australian New Zealand Clinical Trials Registry (ACTR N12615001351505). Trial protocol: the trial protocol is available at https://bmjopen.bmj.com/content/9/4/e026174 . Video Abstract.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome
*Bacteriophages/physiology/classification/isolation & purification/genetics
*Feces/microbiology/virology
*Obesity/therapy/microbiology
Double-Blind Method
Female
Adolescent
Male
Bacteria/classification/virology/genetics
Metagenomics/methods
Treatment Outcome

@article {pmid38970122,
year = {2024},
author = {Yan, W and Wang, D and Wang, Y and Wang, C and Chen, X and Liu, L and Wang, Y and Li, YY and Kamagata, Y and Nobu, MK and Zhang, T},
title = {Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {121},
pmid = {38970122},
issn = {2049-2618},
support = {T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; T21-705/20-N//the Hong Kong Theme-based Research Scheme/ ; },
mesh = {*Methane/metabolism ; *Carbon/metabolism ; *Metagenomics/methods ; Bioreactors/microbiology ; Metagenome ; Bacteria/genetics/metabolism/classification ; Phylogeny ; Anaerobiosis ; Transcriptome ; Genome, Bacterial ; Microbiota ; Gene Expression Profiling ; },
abstract = {BACKGROUND: Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry.

RESULTS: In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role.

CONCLUSION: Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.},
}

*Methane/metabolism
*Carbon/metabolism
*Metagenomics/methods
Bioreactors/microbiology
Metagenome
Bacteria/genetics/metabolism/classification
Phylogeny
Anaerobiosis
Transcriptome
Genome, Bacterial
Microbiota
Gene Expression Profiling

@article {pmid38969657,
year = {2024},
author = {Łopucki, R and Sajnaga, E and Kalwasińska, A and Klich, D and Kitowski, I and Stępień-Pyśniak, D and Christensen, H},
title = {Green spaces contribute to structural resilience of the gut microbiota in urban mammals.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {15508},
pmid = {38969657},
issn = {2045-2322},
mesh = {Animals ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Cities ; Murinae/microbiology ; Ecosystem ; Mammals/microbiology ; Bacteria/classification/genetics ; },
abstract = {The gut microbiome of wild animals is subject to various environmental influences, including those associated with human-induced alterations to the environment. We investigated how the gut microbiota of a synurbic rodent species, the striped field mouse (Apodemus agrarius), change in cities of varying sizes, seeking the urban microbiota signature for this species. Fecal samples for analysis were collected from animals living in non-urbanized areas and green spaces of different-sized cities (Poland). Metagenomic 16S rRNA gene sequencing and further bioinformatics analyses were conducted. Significant differences in the composition of gut microbiomes among the studied populations were found. However, the observed changes were dependent on local habitat conditions, without strong evidence of a correlation with the size of the urbanized area. The results suggest that ecological detachment from a more natural, non-urban environment does not automatically lead to the development of an "urban microbiome" model in the studied rodent. The exposure to the natural environment in green spaces may serve as a catalyst for microbiome transformations, providing a previously underestimated contribution to the maintenance of native gut microbial communities in urban mammals.},
}

Animals
*Gastrointestinal Microbiome
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
Cities
Murinae/microbiology
Ecosystem
Mammals/microbiology
Bacteria/classification/genetics

@article {pmid38968121,
year = {2024},
author = {Lee, J and Wellenstein, K and Rahnavard, A and Nelson, AT and Holter, MM and Cummings, BP and Yeliseyev, V and Castoldi, A and Clish, CB and Bry, L and Siegel, D and Kahn, BB},
title = {Beneficial metabolic effects of PAHSAs depend on the gut microbiota in diet-induced obese mice but not in chow-fed mice.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {28},
pages = {e2318691121},
pmid = {38968121},
issn = {1091-6490},
support = {1K01DK114162-01A1//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK106210//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; R01 DK106210/DK/NIDDK NIH HHS/United States ; K01 DK114162/DK/NIDDK NIH HHS/United States ; P30DK57521//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; P30 DK057521/DK/NIDDK NIH HHS/United States ; n/a//JPB Foundation (JPBF)/ ; P30 DK034854/DK/NIDDK NIH HHS/United States ; 5P30DK057521-19//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
mesh = {Animals ; Male ; Female ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Obesity/metabolism/microbiology/etiology ; *Diet, High-Fat/adverse effects ; *Insulin Resistance ; Mice, Inbred C57BL ; Stearic Acids/metabolism ; Palmitic Acid/metabolism ; Feces/microbiology ; Mice, Obese ; },
abstract = {Dietary lipids play an essential role in regulating the function of the gut microbiota and gastrointestinal tract, and these luminal interactions contribute to mediating host metabolism. Palmitic Acid Hydroxy Stearic Acids (PAHSAs) are a family of lipids with antidiabetic and anti-inflammatory properties, but whether the gut microbiota contributes to their beneficial effects on host metabolism is unknown. Here, we report that treating chow-fed female and male germ-free (GF) mice with PAHSAs improves glucose tolerance, but these effects are lost upon high fat diet (HFD) feeding. However, transfer of feces from PAHSA-treated, but not vehicle-treated, chow-fed conventional mice increases insulin sensitivity in HFD-fed GF mice. Thus, the gut microbiota is necessary for, and can transmit, the insulin-sensitizing effects of PAHSAs in HFD-fed GF male mice. Analyses of the cecal metagenome and lipidome of PAHSA-treated mice identified multiple lipid species that associate with the gut commensal Bacteroides thetaiotaomicron (Bt) and with insulin sensitivity resulting from PAHSA treatment. Supplementing live, and to some degree, heat-killed Bt to HFD-fed female mice prevented weight gain, reduced adiposity, improved glucose tolerance, fortified the colonic mucus barrier and reduced systemic inflammation compared to HFD-fed controls. These effects were not observed in HFD-fed male mice. Furthermore, ovariectomy partially reversed the beneficial Bt effects on host metabolism, indicating a role for sex hormones in mediating the Bt probiotic effects. Altogether, these studies highlight the fact that PAHSAs can modulate the gut microbiota and that the microbiota is necessary for the beneficial metabolic effects of PAHSAs in HFD-fed mice.},
}

Animals
Male
Female
Mice
*Gastrointestinal Microbiome/drug effects
*Obesity/metabolism/microbiology/etiology
*Diet, High-Fat/adverse effects
*Insulin Resistance
Mice, Inbred C57BL
Stearic Acids/metabolism
Palmitic Acid/metabolism
Feces/microbiology
Mice, Obese

@article {pmid38966974,
year = {2024},
author = {Wu, EH and Qiao, L},
title = {[Microbial metaproteomics--From sample processing to data acquisition and analysis].},
journal = {Se pu = Chinese journal of chromatography},
volume = {42},
number = {7},
pages = {658-668},
pmid = {38966974},
issn = {1872-2059},
mesh = {Databases, Protein ; Mass Spectrometry/methods ; Metagenomics/methods ; Microbiota ; *Proteomics/methods ; },
abstract = {Microorganisms are closely associated with human diseases and health. Understanding the composition and function of microbial communities requires extensive research. Metaproteomics has recently become an important method for throughout and in-depth study of microorganisms. However, major challenges in terms of sample processing, mass spectrometric data acquisition, and data analysis limit the development of metaproteomics owing to the complexity and high heterogeneity of microbial community samples. In metaproteomic analysis, optimizing the preprocessing method for different types of samples and adopting different microbial isolation, enrichment, extraction, and lysis schemes are often necessary. Similar to those for single-species proteomics, the mass spectrometric data acquisition modes for metaproteomics include data-dependent acquisition (DDA) and data-independent acquisition (DIA). DIA can collect comprehensive peptide information from a sample and holds great potential for future development. However, data analysis for DIA is challenged by the complexity of metaproteome samples, which hinders the deeper coverage of metaproteomes. The most important step in data analysis is the construction of a protein sequence database. The size and completeness of the database strongly influence not only the number of identifications, but also analyses at the species and functional levels. The current gold standard for metaproteome database construction is the metagenomic sequencing-based protein sequence database. A public database-filtering method based on an iterative database search has been proven to have strong practical value. The peptide-centric DIA data analysis method is a mainstream data analysis strategy. The development of deep learning and artificial intelligence will greatly promote the accuracy, coverage, and speed of metaproteomic analysis. In terms of downstream bioinformatics analysis, a series of annotation tools that can perform species annotation at the protein, peptide, and gene levels has been developed in recent years to determine the composition of microbial communities. The functional analysis of microbial communities is a unique feature of metaproteomics compared with other omics approaches. Metaproteomics has become an important component of the multi-omics analysis of microbial communities, and has great development potential in terms of depth of coverage, sensitivity of detection, and completeness of data analysis.},
}

Databases, Protein
Mass Spectrometry/methods
Metagenomics/methods
Microbiota
*Proteomics/methods

@article {pmid38965579,
year = {2024},
author = {Dong, Y and Chen, WH and Zhao, XM},
title = {VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {177},
pmid = {38965579},
issn = {1474-760X},
support = {T2225015//National Natural Science Foundation of China/ ; 61932008//National Natural Science Foundation of China/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; ZDYF2024SHFZ058//Hainan Province Science and Technology Special Fund/ ; 2023YFF1204800//National Key R&D Program of China/ ; 2020YFA0712403//National Key R&D Program of China/ ; LG-TKN-202203-01//Lingang Laboratory & National Key Laboratory of Human Factors Engineering Joint Grant/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metagenome ; Viruses/genetics ; Feces/virology ; Metagenomics/methods ; Software ; Colorectal Neoplasms/virology/genetics ; },
abstract = {Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. VirRep combines a context-aware encoder and an evolution-aware encoder to improve sequence representation by incorporating k-mer patterns and sequence homologies. Benchmarking on both simulated and real datasets with varying viral proportions demonstrates that VirRep outperforms state-of-the-art methods. When applied to fecal metagenomes from a colorectal cancer cohort, VirRep identifies 39 high-quality viral species associated with the disease, many of which cannot be detected by existing methods.},
}

Humans
*Gastrointestinal Microbiome
*Metagenome
Viruses/genetics
Feces/virology
Metagenomics/methods
Software
Colorectal Neoplasms/virology/genetics

@article {pmid38965317,
year = {2024},
author = {de Freitas, STF and Silva, FG and Bessa, LA and de Souza, UJB and Augusto, DSS and de Faria, GS and Vitorino, LC},
title = {Low microbial diversity, yeast prevalence, and nematode-trapping fungal presence in fungal colonization and leaf microbiome of Serjania erecta.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {15456},
pmid = {38965317},
issn = {2045-2322},
mesh = {*Plant Leaves/microbiology/parasitology ; Animals ; *Nematoda/microbiology ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; Endophytes/genetics/isolation & purification ; Yeasts/classification/isolation & purification/genetics ; Metagenomics/methods ; Biodiversity ; },
abstract = {Medicinal plant microbiomes undergo selection due to secondary metabolite presence. Resident endophytic/epiphytic microorganisms directly influence plant's bioactive compound synthesis. Hypothesizing low microbial diversity in Serjania erecta leaves, we assessed leaf colonization by epiphytic and endophytic fungi. Given its traditional medicinal importance, we estimated diversity in the endophytic fungal microbiome. Analyses included scanning electron microscopy (SEM), isolation of cultivable species, and metagenomics. Epiphytic fungi interacted with S. erecta leaf tissues, horizontally transmitted via stomata/trichome bases, expressing traits for nematode trapping. Cultivable endophytic fungi, known for phytopathogenic habits, didn't induce dysbiosis symptoms. This study confirms low leaf microbiome diversity in S. erecta, with a tendency towards more fungal species, likely due to antibacterial secondary metabolite selection. The classification of Halicephalobus sp. sequence corroborated the presence of nematode eggs on the epidermal surface of S. erecta by SEM. In addition, we confirmed the presence of methanogenic archaea and a considerable number of methanotrophs of the genus Methylobacterium. The metagenomic study of endophytic fungi highlighted plant growth-promoting yeasts, mainly Malassezia, Leucosporidium, Meyerozyma, and Hannaella. Studying endophytic fungi and S. erecta microbiomes can elucidate their impact on beneficial bioactive compound production, on the other hand, it is possible that the bioactive compounds produced by this plant can recruit specific microorganisms, impacting the biological system.},
}

*Plant Leaves/microbiology/parasitology
Animals
*Nematoda/microbiology
*Microbiota
*Fungi/classification/genetics/isolation & purification
Endophytes/genetics/isolation & purification
Yeasts/classification/isolation & purification/genetics
Metagenomics/methods
Biodiversity

@article {pmid38964511,
year = {2024},
author = {Davido, B and Watson, AR and de Truchis, P and Galazzo, G and Dinh, A and Batista, R and Terveer, EM and Lawrence, C and Michelon, H and Jobard, M and Saleh-Mghir, A and Kuijper, EJ and Caballero, S},
title = {Bacterial diversity and specific taxa are associated with decolonization of carbapenemase-producing enterobacterales after fecal microbiota transplantation.},
journal = {The Journal of infection},
volume = {89},
number = {2},
pages = {106216},
doi = {10.1016/j.jinf.2024.106216},
pmid = {38964511},
issn = {1532-2742},
mesh = {Humans ; *Fecal Microbiota Transplantation ; Male ; Female ; Middle Aged ; Prospective Studies ; Adult ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Aged ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae Infections/therapy/microbiology ; beta-Lactamases/genetics ; Carrier State/microbiology/therapy ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification ; Biodiversity ; },
abstract = {OBJECTIVES: We evaluated the effect of fecal microbiota transplantation (FMT) on the clearance of carbapenemase-producing Enterobacterales (CPE) carriage.

METHODS: We performed a prospective, multi-center study, conducted among patients who received a single dose of FMT from one of four healthy donors. The primary endpoint was complete clearance of CPE carriage two weeks after FMT with a secondary endpoint at three months. Shotgun metagenomic sequencing was performed to assess gut microbiota composition of donors and recipients before and after FMT.

RESULTS: Twenty CPE-colonized patients were included in the study, where post-FMT 20% (n = 4/20) of patients met the primary endpoint and 40% (n = 8/20) of patients met the secondary endpoint. Kaplan-Meier curves between patients with FMT intervention and the control group (n = 82) revealed a similar rate of decolonization between groups. Microbiota composition analyses revealed that response to FMT was not donor-dependent. Responders had a significantly lower relative abundance of CPE species pre-FMT than non-responders, and 14 days post-FMT responders had significantly higher bacterial species richness and alpha diversity compared to non-responders (p < 0.05). Responder fecal samples were also enriched in specific species, with significantly higher relative abundances of Faecalibacterium prausnitzii, Parabacteroides distasonis, Collinsella aerofaciens, Alistipes finegoldii and Blautia_A sp900066335 (q<0.01) compared to non-responders.

CONCLUSION: FMT administration using the proposed regimen did not achieve statistical significance for complete CPE decolonization but was correlated with the relative abundance of specific bacterial taxa, including CPE species.},
}

Humans
*Fecal Microbiota Transplantation
Male
Female
Middle Aged
Prospective Studies
Adult
*Gastrointestinal Microbiome
*Feces/microbiology
Aged
Bacterial Proteins/genetics/metabolism
Enterobacteriaceae Infections/therapy/microbiology
beta-Lactamases/genetics
Carrier State/microbiology/therapy
Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification
Biodiversity

@article {pmid38961767,
year = {2024},
author = {Xing, Y and Liu, Y and Sha, S and Zhang, Y and Dou, Y and Liu, C and Xu, M and Zhao, L and Wang, J and Wang, Y and Ma, X and Yan, Q and Kong, X},
title = {Multikingdom characterization of gut microbiota in patients with rheumatoid arthritis and rheumatoid arthritis-associated interstitial lung disease.},
journal = {Journal of medical virology},
volume = {96},
number = {7},
pages = {e29781},
doi = {10.1002/jmv.29781},
pmid = {38961767},
issn = {1096-9071},
support = {//Dalian Key Laboratory for Autoantibody Testing/ ; JCH22023017//Interdisciplinary Research Cooperation Project Team Funding of Dalian Medical University/ ; 82225048//National Natural Science Foundation of China/ ; XJ2023001102//The cultivating scientific research project of the Second Hopital of Dalian Medical University/ ; //Liaoning Province Key Clinical Specialized (Department of Rheumatology, the Second Affiliated Hospital of Dalian Medical University) Funds/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung Diseases, Interstitial/microbiology/virology ; *Arthritis, Rheumatoid/complications/microbiology ; *Feces/microbiology/virology ; Female ; Male ; Middle Aged ; *Bacteria/classification/isolation & purification/genetics ; Aged ; Virome ; Mycobiome ; Adult ; Viruses/classification/isolation & purification/genetics ; Fungi/isolation & purification/classification ; },
abstract = {Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a serious and common extra-articular disease manifestation. Patients with RA-ILD experience reduced bacterial diversity and gut bacteriome alterations. However, the gut mycobiome and virome in these patients have been largely neglected. In this study, we performed whole-metagenome shotgun sequencing on fecal samples from 30 patients with RA-ILD, and 30 with RA-non-ILD, and 40 matched healthy controls. The gut bacteriome and mycobiome were explored using a reference-based approach, while the gut virome was profiled based on a nonredundant viral operational taxonomic unit (vOTU) catalog. The results revealed significant alterations in the gut microbiomes of both RA-ILD and RA-non-ILD groups compared with healthy controls. These alterations encompassed changes in the relative abundances of 351 bacterial species, 65 fungal species, and 4,367 vOTUs. Bacteria such as Bifidobacterium longum, Dorea formicigenerans, and Collinsella aerofaciens were enriched in both patient groups. Ruminococcus gnavus (RA-ILD), Gemmiger formicilis, and Ruminococcus bromii (RA-non-ILD) were uniquely enriched. Conversely, Faecalibacterium prausnitzii, Bacteroides spp., and Roseburia inulinivorans showed depletion in both patient groups. Mycobiome analysis revealed depletion of certain fungi, including Saccharomyces cerevisiae and Candida albicans, in patients with RA compared with healthy subjects. Notably, gut virome alterations were characterized by an increase in Siphoviridae and a decrease in Myoviridae, Microviridae, and Autographiviridae in both patient groups. Hence, multikingdom gut microbial signatures showed promise as diagnostic indicators for both RA-ILD and RA-non-ILD. Overall, this study provides comprehensive insights into the fecal virome, bacteriome, and mycobiome landscapes of RA-ILD and RA-non-ILD gut microbiota, thereby offering potential biomarkers for further mechanistic and clinical research.},
}

Humans
*Gastrointestinal Microbiome
*Lung Diseases, Interstitial/microbiology/virology
*Arthritis, Rheumatoid/complications/microbiology
*Feces/microbiology/virology
Female
Male
Middle Aged
*Bacteria/classification/isolation & purification/genetics
Aged
Virome
Mycobiome
Adult
Viruses/classification/isolation & purification/genetics
Fungi/isolation & purification/classification

@article {pmid38961596,
year = {2024},
author = {Mehra, P and Kumar, A},
title = {Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology.},
journal = {Cell biochemistry and function},
volume = {42},
number = {5},
pages = {e4063},
doi = {10.1002/cbf.4063},
pmid = {38961596},
issn = {1099-0844},
support = {//National Institute of Immunology/ ; },
mesh = {Humans ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; *Neoplasms/metabolism ; Metabolomics ; Metagenomics ; },
abstract = {The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.},
}

Humans
*Feces/microbiology/chemistry
*Gastrointestinal Microbiome
*Neoplasms/metabolism
Metabolomics
Metagenomics

@article {pmid38961134,
year = {2024},
author = {Montgomery, TL and Wang, Q and Mirza, A and Dwyer, D and Wu, Q and Dowling, CA and Martens, JWS and Yang, J and Krementsov, DN and Mao-Draayer, Y},
title = {Identification of commensal gut microbiota signatures as predictors of clinical severity and disease progression in multiple sclerosis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {15292},
pmid = {38961134},
issn = {2045-2322},
support = {R01 NS097596/NS/NINDS NIH HHS/United States ; UM1 AI144298/AI/NIAID NIH HHS/United States ; UM1-AI144298-01//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; UM1-AI110557-05//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Multiple Sclerosis/microbiology/pathology ; *Disease Progression ; Male ; Female ; Adult ; Longitudinal Studies ; Feces/microbiology ; Middle Aged ; Severity of Illness Index ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system and a leading cause of neurological disability in young adults. Clinical presentation and disease course are highly heterogeneous. Typically, disease progression occurs over time and is characterized by the gradual accumulation of disability. The risk of developing MS is driven by complex interactions between genetic and environmental factors, including the gut microbiome. How the commensal gut microbiota impacts disease severity and progression over time remains unknown. In a longitudinal study, disability status and associated clinical features in 58 MS patients were tracked over 4.2 ± 0.98 years, and the baseline fecal gut microbiome was characterized via 16S amplicon sequencing. Progressor status, defined as patients with an increase in Expanded Disability Status Scale (EDSS), were correlated with features of the gut microbiome to determine candidate microbiota associated with risk of MS disease progression. We found no overt differences in microbial community diversity and overall structure between MS patients exhibiting disease progression and non-progressors. However, a total of 41 bacterial species were associated with worsening disease, including a marked depletion in Akkermansia, Lachnospiraceae, and Oscillospiraceae, with an expansion of Alloprevotella, Prevotella-9, and Rhodospirillales. Analysis of the metabolic potential of the inferred metagenome from taxa associated with progression revealed enrichment in oxidative stress-inducing aerobic respiration at the expense of microbial vitamin K2 production (linked to Akkermansia), and a depletion in SCFA metabolism (linked to Oscillospiraceae). Further, as a proof of principle, statistical modeling demonstrated that microbiota composition and clinical features were sufficient to predict disease progression. Additionally, we found that constipation, a frequent gastrointestinal comorbidity among MS patients, exhibited a divergent microbial signature compared with progressor status. These results demonstrate a proof of principle for the utility of the gut microbiome for predicting disease progression in MS in a small well-defined cohort. Further, analysis of the inferred metagenome suggested that oxidative stress, vitamin K2, and SCFAs are associated with progression, warranting future functional validation and mechanistic study.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Multiple Sclerosis/microbiology/pathology
*Disease Progression
Male
Female
Adult
Longitudinal Studies
Feces/microbiology
Middle Aged
Severity of Illness Index
RNA, Ribosomal, 16S/genetics

@article {pmid38960615,
year = {2024},
author = {Mac Aogáin, M and Dicker, AJ and Mertsch, P and Chotirmall, SH},
title = {Infection and the microbiome in bronchiectasis.},
journal = {European respiratory review : an official journal of the European Respiratory Society},
volume = {33},
number = {173},
pages = {},
pmid = {38960615},
issn = {1600-0617},
mesh = {*Bronchiectasis/microbiology/immunology ; Humans ; *Microbiota ; *Dysbiosis ; *Host-Pathogen Interactions ; Lung/microbiology ; Animals ; Risk Factors ; Bacteria/genetics/classification ; Respiratory Tract Infections/microbiology/immunology ; Prognosis ; },
abstract = {Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.},
}

*Bronchiectasis/microbiology/immunology
Humans
*Microbiota
*Dysbiosis
*Host-Pathogen Interactions
Lung/microbiology
Animals
Risk Factors
Bacteria/genetics/classification
Respiratory Tract Infections/microbiology/immunology
Prognosis

@article {pmid38959253,
year = {2024},
author = {Wang, Y and Bi, S and Li, X and Zhong, Y and Qi, D},
title = {Perturbations in gut microbiota composition in schizophrenia.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0306582},
pmid = {38959253},
issn = {1932-6203},
mesh = {*Schizophrenia/microbiology ; Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Case-Control Studies ; Metagenomics/methods ; Metagenome ; },
abstract = {Schizophrenia is a severe, complex and long-term psychiatric disorder with unclear etiology. Gut microbes influence the central nervous system via the gut-brain axis. Consequently, investigations of the relationship between gut microbes and schizophrenia are warranted. This study involved 29 patients with schizophrenia and 30 age-matched normal controls. After 16S rRNA gene sequencing and whole-genome shotgun metagenomic sequencing, we analyzed microbial diversity, composition, and function. According to 16S rRNA and metagenomic gene sequencing results, patients with schizophrenia had higher abundances of Clostridium and Megasphaera. Functional analysis showed that sphingolipid, phosphonates and phosphinates, as well as glutamine metabolism were associated with the occurrence and development of schizophrenia. Our data suggest that the gut microbiota exerts an effect on patients with schizophrenia, providing valuable insights into the potential regulation of in the context of this disorder.},
}

*Schizophrenia/microbiology
Humans
*Gastrointestinal Microbiome
Male
Female
Adult
*RNA, Ribosomal, 16S/genetics
Middle Aged
Case-Control Studies
Metagenomics/methods
Metagenome

@article {pmid38957477,
year = {2024},
author = {Bredon, M and Danne, C and Pham, HP and Ruffié, P and Bessede, A and Rolhion, N and Creusot, L and Brot, L and Alonso, I and Langella, P and Derosa, L and Cortot, AB and Routy, B and Zitvogel, L and Segata, N and Sokol, H},
title = {Faecalibaterium prausnitzii strain EXL01 boosts efficacy of immune checkpoint inhibitors.},
journal = {Oncoimmunology},
volume = {13},
number = {1},
pages = {2374954},
pmid = {38957477},
issn = {2162-402X},
mesh = {*Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Animals ; Humans ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Faecalibacterium prausnitzii/drug effects ; Female ; Carcinoma, Non-Small-Cell Lung/drug therapy/immunology/pathology ; Melanoma/drug therapy/immunology/pathology ; Feces/microbiology ; Male ; Lung Neoplasms/drug therapy/immunology/pathology ; Cell Line, Tumor ; Mice, Inbred C57BL ; },
abstract = {Gut microbiota impacts responses to immune checkpoint inhibitors (ICI). A high level of Faecalibacterium prausnitzii have been associated with a positive response to ICI in multiple cancer types. Here, based on fecal shotgun metagenomics data, we show in two independent cohorts of patients with non-small cell lung cancer and advanced melanoma that a high level of F. prausnitzii at baseline is positively associated with a better clinical response to ICI. In MCA205 tumor-bearing mice, administration of F. prausnitzii strain EXL01, already in clinical development for Inflammatory Bowel Disease, restores the anti-tumor response to ICI in the context of antibiotic-induced microbiota perturbation at clinical and tumor transcriptomics level. In vitro, EXL01 strain enhances T cell activation in the presence of ICI. Interestingly, oral administration of EXL01 strain did not induce any change in fecal microbiota diversity or composition, suggesting a direct effect on immune cells in the small intestine. F. prausnitzii strain EXL01 will be evaluated as an adjuvant to ICI in multiple cancers in the near future.},
}

*Immune Checkpoint Inhibitors/pharmacology/therapeutic use
Animals
Humans
Mice
*Gastrointestinal Microbiome/drug effects
*Faecalibacterium prausnitzii/drug effects
Female
Carcinoma, Non-Small-Cell Lung/drug therapy/immunology/pathology
Melanoma/drug therapy/immunology/pathology
Feces/microbiology
Male
Lung Neoplasms/drug therapy/immunology/pathology
Cell Line, Tumor
Mice, Inbred C57BL

@article {pmid38956049,
year = {2024},
author = {Kifle, BA and Sime, AM and Gemeda, MT and Woldesemayat, AA},
title = {Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {15096},
pmid = {38956049},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Multigene Family ; *Secondary Metabolism/genetics ; *Metagenome ; Farms ; Bacteria/genetics/classification/metabolism ; Ethiopia ; Phylogeny ; },
abstract = {Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the "biosynthesis process". Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.},
}

*Soil Microbiology
*Metagenomics/methods
*Microbiota/genetics
*Multigene Family
*Secondary Metabolism/genetics
*Metagenome
Farms
Bacteria/genetics/classification/metabolism
Ethiopia
Phylogeny

@article {pmid38955825,
year = {2024},
author = {Pan, H and Wattiez, R and Gillan, D},
title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.},
journal = {Current microbiology},
volume = {81},
number = {8},
pages = {257},
pmid = {38955825},
issn = {1432-0991},
support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; },
mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; Computational Biology/methods ; },
abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.},
}

*Soil Microbiology
*Proteomics/methods
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota
Fungi/classification/genetics/metabolism/isolation & purification
Soil/chemistry
Computational Biology/methods

@article {pmid38955276,
year = {2024},
author = {Gaire, TN and Odland, C and Zhang, B and Slizovskiy, I and Jorgenson, B and Wehri, T and Meneguzzi, M and Wass, B and Schuld, J and Hanson, D and Doster, E and Singer, J and Cannon, J and Asmus, A and Ray, T and Dee, S and Nerem, J and Davies, P and Noyes, NR},
title = {Slaughtering processes impact microbial communities and antimicrobial resistance genes of pig carcasses.},
journal = {The Science of the total environment},
volume = {946},
number = {},
pages = {174394},
doi = {10.1016/j.scitotenv.2024.174394},
pmid = {38955276},
issn = {1879-1026},
mesh = {Animals ; *Abattoirs ; Swine ; *Microbiota/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; },
abstract = {Several steps in the abattoir can influence the presence of microbes and associated resistance genes (ARGs) on the animal carcasses used for further meat processing. We investigated how these processes influence the resistome-microbiome of groups of pigs with different on-farm antimicrobial exposure status, from the moment they entered the abattoir until the end of carcass processing. Using a targeted enrichment metagenomic approach, we identified 672 unique ARGs conferring resistance to 43 distinct AMR classes from pooled skin (N = 42) and carcass swabs (N = 63) collected sequentially before, during, and after the slaughter process and food safety interventions. We observed significant variations in the resistome and microbial profiles of pigs before and after slaughter, as well as a significant decline in ARG counts, diversity, and microbial DNA load during slaughter and carcass processing, irrespective of prior antimicrobial treatments on the farm. These results suggest that existing interventions in the abattoir are effective in reducing not only the pathogen load but also the overall bacterial burden, including ARGs on pork carcasses. Concomitant with reductions in microbial and ARG counts, we observed an increase in the relative abundance of non-drug-specific ARGs, such as those conferring resistance to metals and biocides, and in particular mercury. Using a strict colocalization procedure, we found that most mercury ARGs were associated with genomes from the Pseudomonadaceae and Enterobacteriaceae families. Collectively, these findings demonstrate that slaughter and processing practices within the abattoir can shape the microbial and ARG profiles of pork carcasses during the transition from living muscle to meat.},
}

Animals
*Abattoirs
Swine
*Microbiota/drug effects/genetics
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects

@article {pmid38955186,
year = {2024},
author = {Wang, S and Liu, Y and Tam, WH and Ching, JYL and Xu, W and Yan, S and Qin, B and Lin, L and Peng, Y and Zhu, J and Cheung, CP and Ip, KL and Wong, YM and Cheong, PK and Yeung, YL and Kan, WHB and Leung, TF and Leung, TY and Chang, EB and Rubin, DT and Claud, EC and Wu, WKK and Tun, HM and Chan, FKL and Ng, SC and Zhang, L},
title = {Maternal gestational diabetes mellitus associates with altered gut microbiome composition and head circumference abnormalities in male offspring.},
journal = {Cell host & microbe},
volume = {32},
number = {7},
pages = {1192-1206.e5},
doi = {10.1016/j.chom.2024.06.005},
pmid = {38955186},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome ; Female ; Humans ; *Diabetes, Gestational/microbiology ; Pregnancy ; Male ; Infant ; *Feces/microbiology ; Head/microbiology ; Adult ; Infant, Newborn ; Clostridium/growth & development ; Prenatal Exposure Delayed Effects/microbiology ; },
abstract = {The impact of gestational diabetes mellitus (GDM) on maternal or infant microbiome trajectory remains poorly understood. Utilizing large-scale longitudinal fecal samples from 264 mother-baby dyads, we present the gut microbiome trajectory of the mothers throughout pregnancy and infants during the first year of life. GDM mothers had a distinct microbiome diversity and composition during the gestation period. GDM leaves fingerprints on the infant's gut microbiome, which are confounded by delivery mode. Further, Clostridium species positively correlate with a larger head circumference at month 12 in male offspring but not females. The gut microbiome of GDM mothers with male fetuses displays depleted gut-brain modules, including acetate synthesis I and degradation and glutamate synthesis II. The gut microbiome of female infants of GDM mothers has higher histamine degradation and dopamine degradation. Together, our integrative analysis indicates that GDM affects maternal and infant gut composition, which is associated with sexually dimorphic infant head growth.},
}

*Gastrointestinal Microbiome
Female
Humans
*Diabetes, Gestational/microbiology
Pregnancy
Male
Infant
*Feces/microbiology
Head/microbiology
Adult
Infant, Newborn
Clostridium/growth & development
Prenatal Exposure Delayed Effects/microbiology

@article {pmid38951915,
year = {2024},
author = {Koci, O and Russell, RK and Shaikh, MG and Edwards, C and Gerasimidis, K and Ijaz, UZ},
title = {CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {117},
pmid = {38951915},
issn = {2049-2618},
support = {NE/L011956/1//NERC Environmental Bioinformatics Centre/ ; BB/T010657/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; Metagenome ; Crohn Disease/microbiology/genetics ; },
abstract = {BACKGROUND: Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.

RESULTS: In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case-control relationships.

CONCLUSIONS: CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn's disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract.},
}

*Metagenomics/methods
Humans
*Software
Microbiota/genetics
Gastrointestinal Microbiome/genetics
Computational Biology/methods
Metagenome
Crohn Disease/microbiology/genetics

@article {pmid38951816,
year = {2024},
author = {Qiu, H and Kan, C and Han, F and Luo, Y and Qu, N and Zhang, K and Ma, Y and Hou, N and Wu, D and Sun, X and Shi, J},
title = {Metagenomic and metabolomic analysis showing the adverse risk-benefit trade-off of the ketogenic diet.},
journal = {Lipids in health and disease},
volume = {23},
number = {1},
pages = {207},
pmid = {38951816},
issn = {1476-511X},
support = {ZR2022QH013//Natural Science Foundation of Shandong Province of China/ ; ZR2021QD132//Natural Science Foundation of Shandong Province of China/ ; 202003060400//Shandong Province Medical and Health Science and Technology Development Project/ ; 82170865//National Natural Science Foundation of China/ ; tsqn202211365//Taishan Scholars Project of Shandong Province/ ; 2022YB033//Education, Teaching and Research Projects of Weifang Medical University/ ; },
mesh = {*Diet, Ketogenic/adverse effects ; Animals ; *Gastrointestinal Microbiome ; Male ; Mice ; *Obesity/metabolism/microbiology/etiology ; *Diet, High-Fat/adverse effects ; *Metagenomics/methods ; Metabolomics/methods ; Dysbiosis/microbiology/metabolism ; Mice, Inbred C57BL ; Metabolome ; Body Weight ; },
abstract = {BACKGROUND: Ketogenic diets are increasingly popular for addressing obesity, but their impacts on the gut microbiota and metabolome remain unclear. This paper aimed to investigate how a ketogenic diet affects intestinal microorganisms and metabolites in obesity.

METHODS: Male mice were provided with one of the following dietary regimens: normal chow, high-fat diet, ketogenic diet, or high-fat diet converted to ketogenic diet. Body weight and fat mass were measured weekly using high-precision electronic balances and minispec body composition analyzers. Metagenomics and non-targeted metabolomics data were used to analyze differences in intestinal contents.

RESULTS: Obese mice on the ketogenic diet exhibited notable improvements in weight and body fat. However, these were accompanied by a significant decrease in intestinal microbial diversity, as well as an increase in Firmicutes abundance and a 247% increase in the Firmicutes/Bacteroidetes ratio. The ketogenic diet also altered multiple metabolic pathways in the gut, including glucose, lipid, energy, carbohydrate, amino acid, ketone body, butanoate, and methane pathways, as well as bacterial secretion and colonization pathways. These changes were associated with increased intestinal inflammation and dysbiosis in obese mice. Furthermore, the ketogenic diet enhanced the secretion of bile and the synthesis of aminoglycoside antibiotics in obese mice, which may impair the gut microbiota and be associated with intestinal inflammation and immunity.

CONCLUSIONS: The study suggest that the ketogenic diet had an unfavorable risk-benefit trade-off and may compromise metabolic homeostasis in obese mice.},
}

*Diet, Ketogenic/adverse effects
Animals
*Gastrointestinal Microbiome
Male
Mice
*Obesity/metabolism/microbiology/etiology
*Diet, High-Fat/adverse effects
*Metagenomics/methods
Metabolomics/methods
Dysbiosis/microbiology/metabolism
Mice, Inbred C57BL
Metabolome
Body Weight

@article {pmid38951807,
year = {2024},
author = {Li, W and Cheng, L and He, X and He, G and Liu, Y and Sang, Z and Wang, Y and Shao, M and Xiong, T and Xu, H and Zhao, J},
title = {Gut fungi of black-necked cranes (Grus nigricollis) respond to dietary changes during wintering.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {232},
pmid = {38951807},
issn = {1471-2180},
support = {NO. 202101BA070001-060//Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities Association/ ; },
mesh = {Animals ; *Seasons ; *Fungi/classification/genetics/isolation & purification ; *Diet ; *Gastrointestinal Microbiome ; *Birds/microbiology ; Gastrointestinal Tract/microbiology ; DNA, Fungal/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Migratory birds exhibit heterogeneity in foraging strategies during wintering to cope with environmental and migratory pressures, and gut bacteria respond to changes in host diet. However, less is known about the dynamics of diet and gut fungi during the wintering period in black-necked cranes (Grus nigricollis).

RESULTS: In this work, we performed amplicon sequencing of the trnL-P6 loop and ITS1 regions to characterize the dietary composition and gut fungal composition of black-necked cranes during wintering. Results indicated that during the wintering period, the plant-based diet of black-necked cranes mainly consisted of families Poaceae, Solanaceae, and Polygonaceae. Among them, the abundance of Solanaceae, Polygonaceae, Fabaceae, and Caryophyllaceae was significantly higher in the late wintering period, which also led to a more even consumption of various food types by black-necked cranes during this period. The diversity of gut fungal communities and the abundance of core fungi were more conserved during the wintering period, primarily dominated by Ascomycota and Basidiomycota. LEfSe analysis (P < 0.05, LDA > 2) found that Pyxidiophora, Pseudopeziza, Sporormiella, Geotrichum, and Papiliotrema were significantly enriched in early winter, Ramularia and Dendryphion were significantly enriched in mid-winter, Barnettozyma was significantly abundant in late winter, and Pleuroascus was significantly abundant in late winter. Finally, mantel test revealed a significant correlation between winter diet and gut fungal.

CONCLUSIONS: This study revealed the dynamic changes in the food composition and gut fungal community of black-necked cranes during wintering in Dashanbao. In the late wintering period, their response to environmental and migratory pressures was to broaden their diet, increase the intake of non-preferred foods, and promote a more balanced consumption ratio of various foods. Balanced food composition played an important role in stabilizing the structure of the gut fungal community. While gut fungal effectively enhanced the host's food utilization rate, they may also faced potential risks of introducing pathogenic fungi. Additionally, we recongnized the limitations of fecal testing in studying the composition of animal gut fungal, as it cannot effectively distinguished between fungal taxa from food or soil inadvertently ingested and intestines. Future research on functions such as cultivation and metagenomics may further elucidate the role of fungi in the gut ecosystem.},
}

Animals
*Seasons
*Fungi/classification/genetics/isolation & purification
*Diet
*Gastrointestinal Microbiome
*Birds/microbiology
Gastrointestinal Tract/microbiology
DNA, Fungal/genetics
Phylogeny

@article {pmid38948211,
year = {2024},
author = {Kallapura, G and Prakash, AS and Sankaran, K and Manjappa, P and Chaudhary, P and Ambhore, S and Dhar, D},
title = {Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: a prospective, open label, controlled, randomized, comparative, proof of concept study.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17583},
pmid = {38948211},
issn = {2167-8359},
mesh = {Humans ; Male ; *Hypertension/diet therapy/microbiology ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Prospective Studies ; *Diabetes Mellitus, Type 2/diet therapy/microbiology ; *Hyperglycemia/diet therapy/microbiology ; *Precision Medicine/methods ; Inflammation/diet therapy ; Proof of Concept Study ; Glycated Hemoglobin/metabolism/analysis ; Aged ; Hyperlipidemias/diet therapy/blood/microbiology ; Adult ; C-Reactive Protein/analysis/metabolism ; },
abstract = {BACKGROUND: Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks[®]-a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated.

METHODS: A total of 30 participants with type 2 diabetes and hyperlipidaemia were recruited for this study. The microbiome profile of the 15 participants (test arm) was evaluated using whole genome shotgun metagenomics and personalized nutritional recommendations based on their microbiota profile were provided. The remaining 15 participants (control arm) were provided with diabetic nutritional guidance for 3 months. Clinical and anthropometric parameters such as HbA1c, systolic/diastolic pressure, c-reactive protein levels and microbiota composition were measured and compared during the study.

RESULTS: The test arm (microbiome-based nutrition) showed a statistically significant decrease in HbA1c level from 8.30 (95% confidence interval (CI), [7.74-8.85]) to 6.67 (95% CI [6.2-7.05]), p < 0.001 after 90 days. The test arm also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130 mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure (p < 0.05), after the microbiome-based personalized dietary intervention. The intervention led to a minimum two-fold (Log2 fold change increase in species like Phascolarctobacterium succinatutens, Bifidobacterium angulatum, and Levilactobacillus brevis which might have a beneficial role in the current context and a similar decrease in species like Alistipes finegoldii, and Sutterella faecalis which have been earlier shown to have some negative effects in the host. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters.},
}

Humans
Male
*Hypertension/diet therapy/microbiology
Female
Middle Aged
*Gastrointestinal Microbiome
Prospective Studies
*Diabetes Mellitus, Type 2/diet therapy/microbiology
*Hyperglycemia/diet therapy/microbiology
*Precision Medicine/methods
Inflammation/diet therapy
Proof of Concept Study
Glycated Hemoglobin/metabolism/analysis
Aged
Hyperlipidemias/diet therapy/blood/microbiology
Adult
C-Reactive Protein/analysis/metabolism

@article {pmid38947127,
year = {2024},
author = {Li, Y and Qi, X and Wang, Q and He, Y and Li, Z and Cen, X and Wei, L},
title = {Comprehensive analysis of key host gene-microbe networks in the cecum tissues of the obese rabbits induced by a high-fat diet.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1407051},
pmid = {38947127},
issn = {2235-2988},
mesh = {Animals ; Rabbits ; *Diet, High-Fat/adverse effects ; *Cecum/microbiology/metabolism ; *Obesity/metabolism/microbiology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Gene Regulatory Networks ; Male ; Gene Expression Profiling ; },
abstract = {The Cecum is a key site for cellulose digestion in nutrient metabolism of intestine, but its mechanisms of microbial and gene interactions has not been fully elucidated during pathogenesis of obesity. Therefore, the cecum tissues of the New Zealand rabbits and their contents between the high-fat diet-induced group (Ob) and control group (Co) were collected and analyzed using multi-omics. The metagenomic analysis indicated that the relative abundances of Corallococcus_sp._CAG:1435 and Flavobacteriales bacterium species were significantly lower, while those of Akkermansia glycaniphila, Clostridium_sp._CAG:793, Mycoplasma_sp._CAG:776, Mycoplasma_sp._CAG:472, Clostridium_sp._CAG:609, Akkermansia_sp._KLE1605, Clostridium_sp._CAG:508, and Firmicutes_bacterium_CAG:460 species were significantly higher in the Ob as compared to those in Co. Transcriptomic sequencing results showed that the differentially upregulated genes were mainly enriched in pathways, including calcium signaling pathway, PI3K-Akt signaling pathway, and Wnt signaling pathway, while the differentially downregulated genes were mainly enriched in pathways of NF-kappaB signaling pathway and T cell receptor signaling pathway. The comparative analysis of metabolites showed that the glycine, serine, and threonine metabolism and cysteine and methionine metabolism were the important metabolic pathways between the two groups. The combined analysis showed that CAMK1, IGFBP6, and IGFBP4 genes were highly correlated with Clostridium_sp._CAG:793, and Akkermansia_glycaniphila species. Thus, the preliminary study elucidated the microbial and gene interactions in cecum of obese rabbit and provided a basis for further studies in intestinal intervention for human obesity.},
}

Animals
Rabbits
*Diet, High-Fat/adverse effects
*Cecum/microbiology/metabolism
*Obesity/metabolism/microbiology
*Gastrointestinal Microbiome
Host Microbial Interactions
Metagenomics
Bacteria/classification/genetics/metabolism/isolation & purification
Gene Regulatory Networks
Male
Gene Expression Profiling

@article {pmid38944892,
year = {2024},
author = {Bhat, AH and Tak, H and Ganai, BA and Malik, IM and Bambou, JC},
title = {Beyond parasitism: Exploring the microbial profile of Haemonchus contortus and its predilection site (abomasum) in Kashmir Merino sheep.},
journal = {Veterinary parasitology},
volume = {330},
number = {},
pages = {110243},
doi = {10.1016/j.vetpar.2024.110243},
pmid = {38944892},
issn = {1873-2550},
mesh = {Animals ; Sheep ; *Haemonchus/physiology ; *Sheep Diseases/parasitology/microbiology ; *Haemonchiasis/veterinary/parasitology ; *Abomasum/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Host-Parasite Interactions ; India ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Gastrointestinal helminth infection, particularly by Haemonchus contortus, poses significant challenges to sheep farming worldwide. While anthelmintic drugs have been traditional control measures, the emergence of resistance calls for alternative strategies. Understanding the interaction between parasites, host, and their microbiome is crucial for management of helminth infection. This study intricately explores the interactions between microbial communities in Kashmir Merino sheep infected with H. contortus, to understand the complex interplay between host, parasite, and their microbiome. Sheep abomasal contents and H. contortus were collected from infected and control groups, processed for DNA extraction, and subjected to metagenomic sequencing of the 16 S rRNA gene. Downstream analysis unveils distinct microbial patterns, where Proteobacteria were dominant in H. contortus, while Bacteroidota and Firmicutes prevailed in the sheep abomasum. The revelation of unique genera and shifts in diversity indices underscored helminth-induced disruptions in the host. Beta diversity analysis further showed significant variations in bacterial profiles, providing insights into the intricate host, parasite, and microbiome dynamics. Additionally, this study elucidated the presence of pathogenic bacteria within H. contortus, accentuating their potential role in exacerbating sheep health issues. This finding underscores the complexity of the host-parasite-microbiome interaction showing helminth-induced microbiome alterations of the host.},
}

Animals
Sheep
*Haemonchus/physiology
*Sheep Diseases/parasitology/microbiology
*Haemonchiasis/veterinary/parasitology
*Abomasum/parasitology/microbiology
RNA, Ribosomal, 16S/genetics
Microbiota
Host-Parasite Interactions
India
Bacteria/classification/genetics/isolation & purification

@article {pmid38943206,
year = {2024},
author = {Larzul, C and Estellé, J and Borey, M and Blanc, F and Lemonnier, G and Billon, Y and Thiam, MG and Quinquis, B and Galleron, N and Jardet, D and Lecardonnel, J and Plaza Oñate, F and Rogel-Gaillard, C},
title = {Driving gut microbiota enterotypes through host genetics.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {116},
pmid = {38943206},
issn = {2049-2618},
support = {Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics ; Metagenomics/methods ; Prevotella/genetics/classification ; Ruminococcus/genetics ; Treponema/genetics ; },
abstract = {BACKGROUND: Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits.

RESULTS: We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively.

CONCLUSION: We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/genetics
Swine/microbiology
*Feces/microbiology
Bacteria/classification/genetics
Metagenomics/methods
Prevotella/genetics/classification
Ruminococcus/genetics
Treponema/genetics

@article {pmid38943070,
year = {2024},
author = {Laux, M and Ciapina, LP and de Carvalho, FM and Gerber, AL and Guimarães, APC and Apolinário, M and Paes, JES and Jonck, CR and de Vasconcelos, ATR},
title = {Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {228},
pmid = {38943070},
issn = {1471-2180},
support = {Process number: 2018/00190-8//Petrobras/ ; 307145/2021-2//CNPq/ ; E-26/210.012/ 2020 and E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Wetlands ; Phylogeny ; Heterotrophic Processes ; Carbon Cycle ; Carbon/metabolism ; Methane/metabolism ; Autotrophic Processes ; Metabolic Networks and Pathways/genetics ; },
abstract = {BACKGROUND: Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

RESULTS: Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified.

CONCLUSION: The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.},
}

*Microbiota/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
*Wetlands
Phylogeny
Heterotrophic Processes
Carbon Cycle
Carbon/metabolism
Methane/metabolism
Autotrophic Processes
Metabolic Networks and Pathways/genetics

@article {pmid38942886,
year = {2024},
author = {Fo, X and Pei, ML and Liu, PJ and Zhu, F and Zhang, Y and Mu, X},
title = {Metagenomic analysis revealed the association between gut microbiota and different ovary responses to controlled ovarian stimulation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14930},
pmid = {38942886},
issn = {2045-2322},
support = {2022SF-471//Shaanxi Science and Technology/ ; },
mesh = {Female ; *Gastrointestinal Microbiome ; Animals ; Humans ; *Metagenomics/methods ; Adult ; Mice ; *Ovulation Induction/methods ; Ovary/microbiology ; Pregnancy ; Feces/microbiology ; Fertilization in Vitro/methods ; },
abstract = {The aim of this study was to assess the correlation between gut microbial taxonomy and various ovarian responses to controlled ovarian stimulation. A total of 22 IVF cycles with a follicle-to-oocyte index (FOI) < 0.5 and 25 IVF cycles with FOI ≥ 0.5 were included in this study. Baseline demographic characteristics were compared between the two groups. Metagenomic sequencing was performed to analyze fecal microbial community profiles. Mice were used to evaluate the effect of Bifidobacterium_longum on ovarian response to stimulation. Compared with FOI < 0.5 group, women in group with FOI ≥ 0.5 had significant more oocytes retrieved (p < 0.01). Prevotella_copri, Bateroides_vulgatus, Escherichia_coli and Bateroides_stercoris were more abundant in FOI < 0.5 group while Bifidobacterium_longum, Faecalibacterium_prausnitzii, Ruminococcus_gnavus and Bifidobacterium_pseudocatenula were more abundant in FOI ≥ 0.5 group. After adjusting for women's age and BMI, Pearson correlation analysis indicated alteration of gut microbiome was related with serum E2, FSH, number of oocytes retrieved and clinical pregnancy rate. Animal study showed ovarian response will be improved after Bifidobacterium_longum applied. An increased abundance of Bacteroidetes and Prevotella copri, as well as a decreased abundance of Bifidobacterium longum, have been found to be associated with poor ovarian responsiveness. Changes in gut microbiomes have been observed to be correlated with certain clinical characteristics. The potential enhancement of ovarian response may be facilitated by the integration of Bifidobacterium longum.},
}