@article {pmid38675943,
year = {2024},
author = {Bandoo, RA and Kraberger, S and Varsani, A},
title = {Two Novel Geminiviruses Identified in Bees (Apis mellifera and Nomia sp.).},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/v16040602},
pmid = {38675943},
issn = {1999-4915},
mesh = {Animals ; Bees/virology ; *Geminiviridae/genetics/classification/isolation & purification ; *Genome, Viral ; *Phylogeny ; Metagenomics ; DNA, Viral/genetics ; },
abstract = {Members of the Geminviridae family are circular single-stranded DNA plant-infecting viruses, some of which impact global food production. Geminiviruses are vectored by sap-feeding insects such as leafhoppers, treehoppers, aphids, and whiteflies. Additionally, geminivirus sequences have also been identified in other insects such as dragonflies, mosquitoes, and stingless bees. As part of a viral metagenomics study on honeybees and solitary bees (Nomia sp.), two geminivirus genomes were identified. These represent a novel citlodavirus (from honeybees collected from Westmoreland, Jamaica) and a mastrevirus-like genome (from a solitary bee collected from Tempe, Arizona, USA). The novel honeybee-derived citlodavirus genome shares ~61 to 69% genome-wide nucleotide pairwise identity with other citlodavirus genome sequences and is most closely related to the passion fruit chlorotic mottle virus identified in Brazil. Whereas the novel solitary bee-derived mastrevirus-like genome shares ~55 to 61% genome-wide nucleotide identity with other mastreviruses and is most closely related to tobacco yellow dwarf virus identified in Australia, based on pairwise identity scores of the full genome, replication-associated protein, and capsid protein sequences. Previously, two geminiviruses in the Begomovirus genus were identified in samples of stingless bee (Trigona spp.) samples. Here, we identify viruses that represent two new species of geminiviruses from a honeybee and a solitary bee, which continues to demonstrate that plant pollinators can be utilized for the identification of plant-infecting DNA viruses in ecosystems.},
}

Animals
Bees/virology
*Geminiviridae/genetics/classification/isolation & purification
*Genome, Viral
*Phylogeny
Metagenomics
DNA, Viral/genetics

@article {pmid38675877,
year = {2024},
author = {Zhao, H and Yang, M and Fan, X and Gui, Q and Yi, H and Tong, Y and Xiao, W},
title = {A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/v16040535},
pmid = {38675877},
issn = {1999-4915},
support = {32071570//National Natural Science Foundation of China/ ; 202303AP140004//the Science and Technology Planning Project in Key Areas of Yunnan Province/ ; },
mesh = {*Metagenomics ; *Wastewater/virology/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Sewage/virology/microbiology ; Humans ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; Bacteriophages/genetics/isolation & purification/classification ; Virome/genetics ; Water Purification ; Animals ; },
abstract = {The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.},
}

*Metagenomics
*Wastewater/virology/microbiology
*Bacteria/genetics/classification/isolation & purification
*Sewage/virology/microbiology
Humans
*Viruses/genetics/classification/isolation & purification
Metagenome
Bacteriophages/genetics/isolation & purification/classification
Virome/genetics
Water Purification
Animals

@article {pmid38675851,
year = {2024},
author = {Luqman, M and Duhan, N and Temeeyasen, G and Selim, M and Jangra, S and Mor, SK},
title = {Geographical Expansion of Avian Metapneumovirus Subtype B: First Detection and Molecular Characterization of Avian Metapneumovirus Subtype B in US Poultry.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/v16040508},
pmid = {38675851},
issn = {1999-4915},
mesh = {Animals ; *Metapneumovirus/genetics/classification/isolation & purification ; *Paramyxoviridae Infections/veterinary/virology/epidemiology ; *Poultry Diseases/virology/epidemiology ; *Phylogeny ; *Turkeys/virology ; *Genome, Viral ; United States/epidemiology ; Chickens/virology ; Poultry/virology ; Metagenomics ; Disease Outbreaks/veterinary ; },
abstract = {Avian metapneumovirus (aMPV), classified within the Pneumoviridae family, wreaks havoc on poultry health. It typically causes upper respiratory tract and reproductive tract infections, mainly in turkeys, chickens, and ducks. Four subtypes of AMPV (A, B, C, D) and two unclassified subtypes have been identified, of which subtypes A and B are widely distributed across the world. In January 2024, an outbreak of severe respiratory disease occurred on turkey and chicken farms across different states in the US. Metagenomics sequencing of selected tissue and swab samples confirmed the presence of aMPV subtype B. Subsequently, all samples were screened using an aMPV subtype A and B multiplex real-time RT-PCR kit. Of the 221 farms, 124 (56%) were found to be positive for aMPV-B. All samples were negative for subtype A. Six whole genomes were assembled, five from turkeys and one from chickens; all six assembled genomes showed 99.29 to 99.98% nucleotide identity, indicating a clonal expansion event for aMPV-B within the country. In addition, all six sequences showed 97.74 to 98.58% nucleotide identity with previously reported subtype B sequences, e.g., VCO3/60616, Hungary/657/4, and BR/1890/E1/19. In comparison to these two reference strains, the study sequences showed unique 49-62 amino acid changes across the genome, with maximum changes in glycoprotein (G). One unique AA change from T (Threonine) to I (Isoleucine) at position 153 in G protein was reported only in the chicken aMPV sequence, which differentiated it from turkey sequences. The twelve unique AA changes along with change in polarity of the G protein may indicate that these unique changes played a role in the adaptation of this virus in the US poultry. This is the first documented report of aMPV subtype B in US poultry, highlighting the need for further investigations into its genotypic characterization, pathogenesis, and evolutionary dynamics.},
}

Animals
*Metapneumovirus/genetics/classification/isolation & purification
*Paramyxoviridae Infections/veterinary/virology/epidemiology
*Poultry Diseases/virology/epidemiology
*Phylogeny
*Turkeys/virology
*Genome, Viral
United States/epidemiology
Chickens/virology
Poultry/virology
Metagenomics
Disease Outbreaks/veterinary

@article {pmid38675747,
year = {2024},
author = {Zhang, LN and Tan, JT and Ng, HY and Liao, YS and Zhang, RQ and Chan, KH and Hung, IF and Lam, TT and Cheung, KS},
title = {Association between Gut Microbiota Composition and Long-Term Vaccine Immunogenicity following Three Doses of CoronaVac.},
journal = {Vaccines},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/vaccines12040365},
pmid = {38675747},
issn = {2076-393X},
support = {COVID1903010//Food and Health Bureau, The Government of HKSAR/ ; },
abstract = {BACKGROUND: Neutralizing antibody level wanes with time after COVID-19 vaccination. We aimed to study the relationship between baseline gut microbiota and immunogenicity after three doses of CoronaVac.

METHODS: This was a prospective cohort study recruiting three-dose CoronaVac recipients from two centers in Hong Kong. Blood samples were collected at baseline and one year post-first dose for virus microneutralization (vMN) assays to determine neutralization titers. The primary outcome was high immune response (defined as with vMN titer ≥ 40). Shotgun DNA metagenomic sequencing of baseline fecal samples identified potential bacterial species and metabolic pathways using Linear Discriminant Analysis Effect Size (LEfSe) analysis. Univariate and multivariable logistic regression models were used to identify high response predictors.

RESULTS: In total, 36 subjects were recruited (median age: 52.7 years [IQR: 47.9-56.4]; male: 14 [38.9%]), and 18 had low immune response at one year post-first dose vaccination. Eubacterium rectale (log10LDA score = 4.15, p = 0.001; relative abundance of 1.4% vs. 0, p = 0.002), Collinsella aerofaciens (log10LDA score = 3.31, p = 0.037; 0.39% vs. 0.18%, p = 0.038), and Streptococcus salivarius (log10LDA score = 2.79, p = 0.021; 0.05% vs. 0.02%, p = 0.022) were enriched in low responders. The aOR of high immune response with E. rectale, C. aerofaciens, and S. salivarius was 0.03 (95% CI: 9.56 × 10[-4]-0.32), 0.03 (95% CI: 4.47 × 10[-4]-0.59), and 10.19 (95% CI: 0.81-323.88), respectively. S. salivarius had a positive correlation with pathways enriched in high responders like incomplete reductive TCA cycle (log10LDA score = 2.23). C. aerofaciens similarly correlated with amino acid biosynthesis-related pathways. These pathways all showed anti-inflammation functions.

CONCLUSION: E. rectale,C. aerofaciens, and S. salivarius correlated with poorer long-term immunogenicity following three doses of CoronaVac.},
}

@article {pmid38675716,
year = {2024},
author = {Chudan, S and Kurakawa, T and Nishikawa, M and Nagai, Y and Tabuchi, Y and Ikushiro, S and Furusawa, Y},
title = {Beneficial Effects of Dietary Fiber in Young Barley Leaf on Gut Microbiota and Immunity in Mice.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {8},
pages = {},
doi = {10.3390/molecules29081897},
pmid = {38675716},
issn = {1420-3049},
support = {20K05929//Japan Society for the Promotion of Science/ ; n/a//Takeda Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Hordeum/chemistry ; *Dietary Fiber/pharmacology ; *Plant Leaves/chemistry ; Mice ; Retinal Dehydrogenase/metabolism ; Butyrates/metabolism ; Feces/microbiology ; },
abstract = {The health benefits of young barley leaves, rich in dietary fiber, have been studied for several decades; however, their beneficial effects on the intestinal microenvironment remain to be elucidated. To investigate the effects of young barley leaf-derived dietary fiber (YB) on the gut microbiota and immunity, mice were fed an AIN-93G diet containing cellulose or YB and subjected to subsequent analysis. The population of MHC-II-positive conventional dendritic cells (cDCs) and CD86 expression in the cDCs of Peyer's patches were elevated in the YB-fed mice. MHC-II and CD86 expression was also elevated in the bone marrow-derived DCs treated with YB. 16S-based metagenomic analysis revealed that the gut microbiota composition was markedly altered by YB feeding. Among the gut microbiota, Lachnospiraceae, mainly comprising butyrate-producing NK4A136 spp., were overrepresented in the YB-fed mice. In fact, fecal butyrate concentration was also augmented in the YB-fed mice, which coincided with increased retinaldehyde dehydrogenase (RALDH) activity in the CD103[+] cDCs of the mesenteric lymph nodes. Consistent with elevated RALDH activity, the population of colonic IgA[+] plasma cells was higher in the YB-fed mice than in the parental control mice. In conclusion, YB has beneficial effects on the gut microbiota and intestinal immune system.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Hordeum/chemistry
*Dietary Fiber/pharmacology
*Plant Leaves/chemistry
Mice
Retinal Dehydrogenase/metabolism
Butyrates/metabolism
Feces/microbiology

@article {pmid38674803,
year = {2024},
author = {Arteaga-Muller, GY and Flores-Treviño, S and Bocanegra-Ibarias, P and Robles-Espino, D and Garza-González, E and Fabela-Valdez, GC and Camacho-Ortiz, A},
title = {Changes in the Progression of Chronic Kidney Disease in Patients Undergoing Fecal Microbiota Transplantation.},
journal = {Nutrients},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/nu16081109},
pmid = {38674803},
issn = {2072-6643},
mesh = {Humans ; *Renal Insufficiency, Chronic/therapy/microbiology ; *Fecal Microbiota Transplantation ; Male ; Female ; *Disease Progression ; Middle Aged ; Double-Blind Method ; *Gastrointestinal Microbiome ; Aged ; *Feces/microbiology ; Dysbiosis/therapy ; Treatment Outcome ; Adult ; Creatinine/blood ; },
abstract = {Chronic kidney disease (CKD) is a progressive loss of renal function in which gut dysbiosis is involved. Fecal microbiota transplantation (FMT) may be a promising alternative for restoring gut microbiota and treating CKD. This study evaluated the changes in CKD progression in patients treated with FMT. Patients with diabetes and/or hypertension with CKD clinical stages 2, 3, and 4 in this single-center, double-blind, randomized, placebo-controlled clinical trial (NCT04361097) were randomly assigned to receive either FMT or placebo capsules for 6 months. Laboratory and stool metagenomic analyses were performed. A total of 28 patients were included (15 FMT and 13 placebo). Regardless of CKD stages, patients responded similarly to FMT treatment. More patients (53.8%) from the placebo group progressed to CKD than the FMT group (13.3%). The FMT group maintained stable renal function parameters (serum creatinine and urea nitrogen) compared to the placebo group. Adverse events after FMT treatment were mild or moderate gastrointestinal symptoms. The abundance of Firmicutes and Actinobacteria decreased whereas Bacteroidetes, Proteobacteria and Roseburia spp. increased in the FMT group. CKD patients showed less disease progression after FMT administration. The administration of oral FMT in patients with CKD is a safe strategy, does not represent a risk, and has potential benefits.},
}

Humans
*Renal Insufficiency, Chronic/therapy/microbiology
*Fecal Microbiota Transplantation
Male
Female
*Disease Progression
Middle Aged
Double-Blind Method
*Gastrointestinal Microbiome
Aged
*Feces/microbiology
Dysbiosis/therapy
Treatment Outcome
Adult
Creatinine/blood

@article {pmid38674796,
year = {2024},
author = {Chang, WL and Chen, YE and Tseng, HT and Cheng, CF and Wu, JH and Hou, YC},
title = {Gut Microbiota in Patients with Prediabetes.},
journal = {Nutrients},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/nu16081105},
pmid = {38674796},
issn = {2072-6643},
support = {TCRD-TPE-109-RT-10//Taipei Tzu Chi Hospital/ ; TCRD-TPE-111-65//Taipei Tzu Chi Hospital/ ; TCRD-TPE-112-RT-9//Taipei Tzu Chi Hospital/ ; TCRD-TPE-108-38//Taipei Tzu Chi Hospital/ ; },
mesh = {Humans ; *Prediabetic State/microbiology ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Male ; Female ; *Feces/microbiology ; Aged ; Young Adult ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dietary Fiber/administration & dosage ; },
abstract = {Prediabetes is characterized by abnormal glycemic levels below the type 2 diabetes threshold, and effective control of blood glucose may prevent the progression to type 2 diabetes. While the association between the gut microbiota, glucose metabolism, and insulin resistance in diabetic patients has been established in previous studies, there is a lack of research regarding these aspects in prediabetic patients in Asia. We aim to investigate the composition of the gut microbiota in prediabetic patients and their differences compared to healthy individuals. In total, 57 prediabetic patients and 60 healthy adult individuals aged 18 to 65 years old were included in this study. Biochemistry data, fecal samples, and 3 days of food records were collected. Deoxyribonucleic acid extraction and next-generation sequencing via 16S ribosomal ribonucleic acid metagenomic sequencing were conducted to analyze the relationship between the gut microbiota and dietary habits. Prediabetic patients showed a lower microbial diversity than healthy individuals, with 9 bacterial genera being less abundant and 14 others more abundant. Prediabetic patients who consumed a low-carbohydrate (LC) diet exhibited higher diversity in the gut microbiota than those who consumed a high-carbohydrate diet. A higher abundance of Coprococcus was observed in the prediabetic patients on an LC diet. Compared to healthy individuals, the gut microbiota of prediabetic patients was significantly different, and adopting an LC diet with high dietary fiber consumption may positively impact the gut microbiota. Future studies should aim to understand the relationship between the gut microbiota and glycemic control in the Asian population.},
}

Humans
*Prediabetic State/microbiology
*Gastrointestinal Microbiome
Middle Aged
Adult
Male
Female
*Feces/microbiology
Aged
Young Adult
Adolescent
RNA, Ribosomal, 16S/genetics
Blood Glucose/metabolism
Diabetes Mellitus, Type 2/microbiology
Bacteria/classification/genetics/isolation & purification
Dietary Fiber/administration & dosage

@article {pmid38674771,
year = {2024},
author = {Gómez, F and Rodríguez, N and Rodríguez-Manfredi, JA and Escudero, C and Carrasco-Ropero, I and Martínez, JM and Ferrari, M and De Angelis, S and Frigeri, A and Fernández-Sampedro, M and Amils, R},
title = {Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040829},
pmid = {38674771},
issn = {2076-2607},
abstract = {This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade.},
}

@article {pmid38674713,
year = {2024},
author = {Iani, FCM and de Campos, GM and Adelino, TER and da Silva, AS and Kashima, S and Alcantara, LCJ and Sampaio, SC and Giovanetti, M and Elias, MC and Slavov, SN},
title = {Metagenomic Analysis for Diagnosis of Hemorrhagic Fever in Minas Gerais, Brazil.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040769},
pmid = {38674713},
issn = {2076-2607},
support = {2017/23205-8; 2021/11944-6; 2022/00910-6; 2022/10278-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Viral hemorrhagic fever poses a significant public health challenge due to its severe clinical presentation and high mortality rate. The diagnostic process is hindered by similarity of symptoms across different diseases and the broad spectrum of pathogens that can cause hemorrhagic fever. In this study, we applied viral metagenomic analysis to 43 serum samples collected by the Public Health Laboratory (Fundação Ezequiel Dias, FUNED) in Minas Gerais State, Brazil, from patients diagnosed with hemorrhagic fever who had tested negative for the standard local hemorrhagic disease testing panel. This panel includes tests for Dengue virus (DENV) IgM, Zika virus IgM, Chikungunya virus IgM, yellow fever IgM, Hantavirus IgM, Rickettsia rickettsii IgM/IgG, and Leptospira interrogans IgM, in addition to respective molecular tests for these infectious agents. The samples were grouped into 18 pools according to geographic origin and analyzed through next-generation sequencing on the NextSeq 2000 platform. Bioinformatic analysis revealed a prevalent occurrence of commensal viruses across all pools, but, notably, a significant number of reads corresponding to the DENV serotype 2 were identified in one specific pool. Further verification via real-time PCR confirmed the presence of DENV-2 RNA in an index case involving an oncology patient with hemorrhagic fever who had initially tested negative for anti-DENV IgM antibodies, thereby excluding this sample from initial molecular testing. The complete DENV-2 genome isolated from this patient was taxonomically classified within the cosmopolitan genotype that was recently introduced into Brazil. These findings highlight the critical role of considering the patient's clinical condition when deciding upon the most appropriate testing procedures. Additionally, this study showcases the potential of viral metagenomics in pinpointing the viral agents behind hemorrhagic diseases. Future research is needed to assess the practicality of incorporating metagenomics into standard viral diagnostic protocols.},
}

@article {pmid38674701,
year = {2024},
author = {Li, C and Han, G and Huang, L and Lu, Y and Xia, Y and Zhang, N and Liu, Q and Xu, J},
title = {Metagenomic Analyses Reveal Gut Microbial Profiles of Cnaphalocrocis medinalis Driven by the Infection of Baculovirus CnmeGV.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040757},
pmid = {38674701},
issn = {2076-2607},
support = {BK20191216//the Natural science Foundation of Jiangsu Province/ ; NAES069AM04 and NAES-EE-041//the National Agricultural Basic Long-Term Scientific and Technological Work/ ; CX(22)1009//the Jiangsu Agricultural Science and Technology Innovation Fund/ ; YZ2021049 and YZ2021034//Yangzhou Science and Technology Project/ ; },
abstract = {The composition of microbiota in the digestive tract gut is essential for insect physiology, homeostasis, and pathogen infection. Little is known about the interactions between microbiota load and oral infection with baculoviruses. CnmeGV is an obligative baculovirus to Cnaphalocrocis medinalis. We investigated the impact of CnmeGV infection on the structure of intestinal microbes of C. medinalis during the initial infection stage. The results revealed that the gut microbiota profiles were dynamically driven by pathogen infection of CnmeGV. The numbers of all the OTU counts were relatively higher at the early and later stages, while the microbial diversity significantly increased early but dropped sharply following the infection. The compositional abundance of domain bacteria Firmicutes developed substantially higher. The significantly enriched and depleted species can be divided into four groups at the species level. Fifteen of these species were ultimately predicted as the biomarkers of CnmeGV infection. CnmeGV infection induces significant enrichment of alterations in functional genes related to metabolism and the immune system, encompassing processes such as carbohydrate, amino acid, cofactor, and vitamin metabolism. Finally, the study may provide an in-depth analysis of the relationship between host microbiota, baculovirus infection, and pest control of C. medinalis.},
}

@article {pmid38674691,
year = {2024},
author = {Deryabin, D and Lazebnik, C and Vlasenko, L and Karimov, I and Kosyan, D and Zatevalov, A and Duskaev, G},
title = {Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040747},
pmid = {38674691},
issn = {2076-2607},
support = {22-16-00036//Russian Science Foundation/ ; FNWZ-2022-0010//research project/ ; },
abstract = {The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.},
}

@article {pmid38674657,
year = {2024},
author = {Zhang, M and Zhou, Y and Cui, X and Zhu, L},
title = {The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040713},
pmid = {38674657},
issn = {2076-2607},
support = {32270546//National Natural Science Foundation of China/ ; },
abstract = {Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.},
}

@article {pmid38674651,
year = {2024},
author = {Zhu, P and Hou, J and Xiong, Y and Xie, R and Wang, Y and Wang, F},
title = {Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040707},
pmid = {38674651},
issn = {2076-2607},
support = {42230401//National Natural Science Foundation of China/ ; WH510244001//Shanghai Jiao Tong University 2030 Project/ ; 2023M742235//China Postdoctoral Science Foundation/ ; },
abstract = {Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA's enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.},
}

@article {pmid38674647,
year = {2024},
author = {Wu, J and Xu, W and Xu, Y and Su, H and Hu, X and Cao, Y and Zhang, J and Wen, G},
title = {Impact of Organic Carbons Addition on the Enrichment Culture of Nitrifying Biofloc from Aquaculture Water: Process, Efficiency, and Microbial Community.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040703},
pmid = {38674647},
issn = {2076-2607},
support = {NSFC 32373135//National Natural Science Foundation of China/ ; },
abstract = {In this study, we developed a rapid and effective method for enriching the culture of nitrifying bioflocs (NBF) from aquacultural brackish water. The self-designed mixotrophic mediums with a single or mixed addition of sodium acetate, sodium citrate, and sucrose were used to investigate the enrichment process and nitrification efficiency of NBF in small-scale reactors. The results showed that NBF with an MLVSSs from 1170.4 mg L[-1] to 2588.0 mg L[-1] were successfully enriched in a period of less than 16 days. The citrate group performed the fastest enrichment time of 10 days, while the sucrose group had the highest biomass of 2588.0 ± 384.7 mg L[-1]. In situ testing showed that the highest nitrification efficiency was achieved in the citrate group, with an ammonia oxidation rate of 1.45 ± 0.34 mg N L[-1] h[-1], a net nitrification rate of 2.02 ± 0.20 mg N L[-1] h[-1], and a specific nitrification rate of 0.72 ± 0.14 mg N g[-1] h[-1]. Metagenomic sequencing revealed that Nitrosomonas (0.0~1.0%) and Nitrobacter (10.1~26.5%) were dominant genera for AOB and NOB, respectively, both of which had the highest relative abundances in the citrate group. Linear regression analysis further demonstrated significantly positive linear relations between nitrification efficiencies and nitrifying bacterial genera and gene abundance in NBF. The results of this study provide an efficient enrichment culture method of NBF for the operation of biofloc technology aquaculture systems, which will further promote its wide application in modern intensive aquaculture.},
}

@article {pmid38674632,
year = {2024},
author = {Couto, RDS and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Deng, X and Delwart, E and da Costa, AC and Leal, E},
title = {Genomoviruses in Liver Samples of Molossus molossus Bats.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040688},
pmid = {38674632},
issn = {2076-2607},
abstract = {CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.},
}

@article {pmid38673740,
year = {2024},
author = {Matys, J and Kensy, J and Gedrange, T and Zawiślak, I and Grzech-Leśniak, K and Dobrzyński, M},
title = {A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review.},
journal = {International journal of molecular sciences},
volume = {25},
number = {8},
pages = {},
doi = {10.3390/ijms25084154},
pmid = {38673740},
issn = {1422-0067},
mesh = {*Fungi/genetics ; *Aerosols ; *Bacteria/genetics/classification/isolation & purification ; *Air Microbiology ; Humans ; Health Facilities ; },
abstract = {Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information.},
}

*Fungi/genetics
*Aerosols
*Bacteria/genetics/classification/isolation & purification
*Air Microbiology
Humans
Health Facilities

@article {pmid38672848,
year = {2024},
author = {Tenea, GN and Reyes, P and Molina, D},
title = {Fungal Mycobiome of Mature Strawberry Fruits (Fragaria x ananassa Variety 'Monterey') Suggests a Potential Market Site Contamination with Harmful Yeasts.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/foods13081175},
pmid = {38672848},
issn = {2304-8158},
support = {7874/2023//Universidad Técnica del Norte/ ; },
abstract = {An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to investigate the diversity of fungi associated with mature strawberries collected from a volcanic orchard and open-air market stands. Based on the Kruskal-Wallis test, no statistically significant differences were observed in both non-phylogenetic and phylogenetic alpha diversity indices. According to beta diversity analyses, significant differences in fungal communities were found between groups (orchard vs. market). Taxonomic assignment of amplicon sequence variables (ASVs) revealed 7 phyla and 31 classes. The prevalent fungal phyla were Basidiomycota (29.59-84.58%), Ascomycota (15.33-70.40%), and Fungi-phy-Insertae-sedis (0.45-2.89%). The most predominant classes among the groups were Saccharomycetes in the market group, and Microbotryomycetes and Tremellomycetes in the orchard group. Based on the analysis of microbiome composition (ANCOM), we found that the most differentially fungal genera were Hanseniaspora, Kurtzmaniella, and Phyllozyma. Endophytic yeasts Curvibasidium cygneicollum were prevalent in both groups, while Candida railenensis was detected in fruits originating only from the market. In addition, Rhodotorula graminis (relative abundance varying from 1.7% to 21.18%) and Papiliotrema flavescens (relative abundance varying from 1.58% to 16.55%) were detected in all samples regardless of origin, while Debaryomyces prosopidis was detected in samples from the market only, their relative abundance varying with the sample (from 0.80% to 19.23%). Their role in fruit quality and safety has not been yet documented. Moreover, several clinically related yeasts, such as Meyerozyma guilliermondii and Candida parapsilosis, were detected in samples only from the market. Understanding the variety and makeup of the mycobiome in ripe fruits during the transition from the orchard to the market is crucial for fruit safety after harvest.},
}

@article {pmid38672421,
year = {2024},
author = {Zhang, L and Tang, X and Fan, C and Ren, S and Cheng, Q and Zhou, H and Liu, K and Jia, S and Zhang, Y},
title = {Dysbiosis of Gut Microbiome Aggravated Male Infertility in Captivity of Plateau Pika.},
journal = {Biomolecules},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biom14040403},
pmid = {38672421},
issn = {2218-273X},
support = {LHZX-2023-02//Sanjiangyuan National Park Collaborative Research Special Fund/ ; 31670394, U21A20186//National Natural Science Foundation of China/ ; 2021-ZJ-Y01//Qinghai innovation platform construction project by Chinese Academy of Sciences/ ; },
mesh = {Animals ; Male ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Infertility, Male/microbiology/metabolism ; *Testosterone/metabolism ; *Lagomorpha/microbiology ; Testis/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites' short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.},
}

Animals
Male
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism
*Infertility, Male/microbiology/metabolism
*Testosterone/metabolism
*Lagomorpha/microbiology
Testis/microbiology/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid38672407,
year = {2024},
author = {Schiano-Lomoriello, D and Abicca, I and Contento, L and Gabrielli, F and Alfonsi, C and Di Pietro, F and Papa, FT and Ballesteros-Sánchez, A and Sánchez-González, JM and Rocha-De-Lossada, C and Mazzotta, C and Giannaccare, G and Bonzano, C and Borroni, D},
title = {Infectious Keratitis: Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index.},
journal = {Biomolecules},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biom14040389},
pmid = {38672407},
issn = {2218-273X},
mesh = {*Keratitis/microbiology ; Humans ; *Biodiversity ; Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Microbiota/genetics ; },
abstract = {Purpose: To characterize microbial keratitis diversity utilizing species richness and Shannon Diversity Index. Methods: Corneal impression membrane was used to collect samples. All swabs were processed and analyzed by Biolab Laboratory (level V-SSN Excellence: ISO 9001:2015), Biolab Srl (Ascoli Piceno, Italy). DNA extraction, library preparation, and sequencing were performed in all samples. After sequencing, low-quality and polyclonal sequences were filtered out by the Ion software. At this point, we employed Kraken2 for microbial community analysis in keratitis samples. Nuclease-free water and all the reagents included in the experiment were used as a negative control. The primary outcome was the reduction in bacterial DNA (microbial load) at T1, expressed as a percentage of the baseline value (T0). Richness and Shannon alpha diversity metrics, along with Bray-Curtis beta diversity values, were calculated using the phyloseq package in R. Principal coordinate analysis was also conducted to interpret these metrics. Results: 19 samples were included in the study. The results exhibited a motley species richness, with the highest recorded value surpassing 800 species. Most of the samples displayed richness values ranging broadly from under 200 to around 600, indicating considerable variability in species count among the keratitis samples. Conclusions: A significant presence of both typical and atypical bacterial phyla in keratitis infections, underlining the complexity of the disease's microbial etiology.},
}

*Keratitis/microbiology
Humans
*Biodiversity
Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics
Microbiota/genetics

@article {pmid38672329,
year = {2024},
author = {Zhao, H and Mo, Q and Kulyar, MF and Guan, J and Zhang, X and Luo, X and Li, J},
title = {Metagenomic Analysis Reveals A Gut Microbiota Structure and Function Alteration between Healthy and Diarrheic Juvenile Yaks.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/ani14081181},
pmid = {38672329},
issn = {2076-2615},
support = {2022YFN0037//Sichuan Provincial Department of Science and Technology/ ; 2021-NK-A5//Qinghai Science and Technology Major Program/ ; 2022YFD1601603//National Key Research and Development Program of China/ ; },
abstract = {Diarrhea-induced mortality among juvenile yaks is highly prevalent in the pastoral areas of the Qinghai-Tibet plateau. Although numerous diseases have been linked to the gut microbial community, little is known about how diarrhea affects the gut microbiota in yaks. In this work, we investigated and compared changes in the gut microbiota of juvenile yaks with diarrhea. The results demonstrated a considerable drop in the alpha diversity of the gut microbiota in diarrheic yaks, accompanied by Eysipelatoclostridium, Parabacteroides, and Escherichia-Shigella, which significantly increased during diarrhea. Furthermore, a PICRust analysis verified the elevation of the gut-microbial metabolic pathways in diarrhea groups, including glycine, serine, and threonine metabolism, alanine, aspartate, oxidative phosphorylation, glutamate metabolism, antibiotic biosynthesis, and secondary metabolite biosynthesis. Taken together, our study showed that the harmful bacteria increased, and beneficial bacteria decreased significantly in the gut microbiota of yaks with diarrhea. Moreover, these results also indicated that the dysbiosis of the gut microbiota may be a significant driving factor of diarrhea in yaks.},
}

@article {pmid38671923,
year = {2024},
author = {Yue, Y and Yang, HJ and Zhang, T and Li, C and Kim, MJ and Kim, KN and Park, S},
title = {Porcine Brain Enzyme Hydrolysate Enhances Immune Function and Antioxidant Defense via Modulation of Gut Microbiota in a Cyclophosphamide-Induced Immunodeficiency Model.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/antiox13040476},
pmid = {38671923},
issn = {2076-3921},
support = {23-12//the "Food Functionality Evaluation program" under the Ministry of Agriculture, Food and Rural Affairs/ ; },
abstract = {This study examined how consuming porcine brain enzyme hydrolysate (PBEH) affects the immune function and composition of the gut microbiota in an immunodeficient animal model. Male Wistar rats aged 6 weeks were fed casein (control), 100 mg/kg body weight (BW), red ginseng extract (positive-control), and 6, 13, and 26 mg PBEH per kg BW (PBEH-L, PBEH-M, and PBEH-H, respectively) daily for 4 weeks. At 30 min after consuming assigned compounds, they were orally administered cyclophosphamide (CTX; 5 mg/kg BW), an immunosuppressive agent, to suppress the immune system by inhibiting the proliferation of lymphocytes. The normal-control rats were fed casein and water instead of CTX. Natural killer cell activity and splenocyte proliferation induced by 1 μg/mL lipopolysaccharide were lower in the control group than the normal-control group, and they significantly increased with PBEH consumption, particularly at high doses. The PBEH consumption increased dose-dependently in the Th1/Th2 ratio compared to the control. The lipid peroxide contents were lower in the PBEH group than in the control group. Moreover, PBEH m and PBEH-H consumption mitigated white pulp cell damage, reduced red pulp congestion, and increased spleen mast cells in the histological analysis. Intestinal microbiota composition demonstrated differences between the groups at the genus levels, with Akkermansia being more abundant in the control group than the normal-control group and the PBEH-H group showing a decrease. However, Bifidobacterium decreased in the control group but increased in the PBEH-H group. The β-diversity revealed distinct microbial communities of PBEH and positive-control groups compared to the control group (p < 0.05). The metagenome predictions revealed that PBEH-H influenced amino acid metabolism, antioxidant defense, insulin sensitivity, and longevity pathways. In conclusion, PBEH-H intake boosted immune responses and reduced lipid peroxides by modulating gut microbiota composition. These findings suggest that PBEH-H has the potential as a dietary supplement for improving immune function and gut health in individuals with immunodeficiency.},
}

@article {pmid38670851,
year = {2024},
author = {Chen, H and Zhan, M and Liu, S and Balloux, F and Wang, H},
title = {Unraveling the potential of metagenomic next-generation sequencing in infectious disease diagnosis: Challenges and prospects.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2024.04.033},
pmid = {38670851},
issn = {2095-9281},
}

@article {pmid38670644,
year = {2024},
author = {Akinsuyi, OS and Xhumari, J and Ojeda, A and Roesch, LFW},
title = {Gut permeability among Astronauts during Space missions.},
journal = {Life sciences in space research},
volume = {41},
number = {},
pages = {171-180},
doi = {10.1016/j.lssr.2024.03.003},
pmid = {38670644},
issn = {2214-5532},
mesh = {*Space Flight ; *Astronauts ; Humans ; Animals ; *Permeability ; *Gastrointestinal Microbiome ; Mice ; Transcriptome ; Gastrointestinal Tract/microbiology ; },
abstract = {The space environment poses substantial challenges to human physiology, including potential disruptions in gastrointestinal health. Gut permeability has only recently become widely acknowledged for its potential to cause adverse effects on a systemic level, rendering it a critical factor to investigate in the context of spaceflight. Here, we propose that astronauts experience the onset of leaky gut during space missions supported by transcriptomic and metagenomic analysis of human and murine samples. A genetic map contributing to intestinal permeability was constructed from a systematic review of current literature. This was referenced against our re-analysis of three independent transcriptomic datasets which revealed significant changes in gene expression patterns associated with the gut barrier. Specifically, in astronauts during flight, we observed a substantial reduction in the expression genes that are crucial for intestinal barrier function, goblet cell development, gut microbiota modulation, and immune responses. Among rodent spaceflight studies, differential expression of cytokines, chemokines, and genes which regulate mucin production and post-translational modifications suggest a similar dysfunction of intestinal permeability. Metagenomic analysis of feces from two murine studies revealed a notable reduction probiotic, short chain fatty acid-producing bacteria and an increase in the Gram-negative pathogens, including Citrobacter rodentium, Enterobacter cloacea, Klebsiella aerogenes, and Proteus hauseri which promote LPS circulation, a recipe for barrier disruption and systemic inflammatory activation. These findings emphasize the critical need to understand the underlying mechanisms and develop interventions to maintain gastrointestinal health in space.},
}

*Space Flight
*Astronauts
Humans
Animals
*Permeability
*Gastrointestinal Microbiome
Mice
Transcriptome
Gastrointestinal Tract/microbiology

@article {pmid38670293,
year = {2024},
author = {Clagnan, E and Petrini, S and Pioli, S and Piergiacomo, F and Aziz Chowdhury, A and Brusetti, L and Foladori, P},
title = {Conventional activated sludge vs. photo-sequencing batch reactor for enhanced nitrogen removal in municipal wastewater: Microalgal-bacterial consortium and pathogenic load insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130735},
doi = {10.1016/j.biortech.2024.130735},
pmid = {38670293},
issn = {1873-2976},
abstract = {Municipal wastewater treatment plants are mostly based on traditional activated sludge (AS) processes. These systems are characterised by major drawbacks: high energy consumption, large amount of excess sludge and high greenhouse gases emissions. Treatment through microalgal-bacterial consortia (MBC) is an alternative and promising solution thanks to lower energy consumption and emissions, biomass production and water sanitation. Here, microbial difference between a traditional anaerobic sludge (AS) and a consortium-based system (photo-sequencing batch reactor (PSBR)) with the same wastewater inlet were characterised through shotgun metagenomics. Stable nitrification was achieved in the PSBR ensuring ammonium removal > 95 % and significant total nitrogen removal thanks to larger flocs enhancing denitrification. The new system showed enhanced pathogen removal, a higher abundance of photosynthetic and denitrifying microorganisms with a reduced emissions potential identifying this novel PSBR as an effective alternative to AS.},
}

@article {pmid38670268,
year = {2024},
author = {Han, D and Yu, F and Zhang, D and Hu, J and Zhang, X and Xiang, D and Lou, B and Chen, Y and Zheng, S},
title = {Molecular Rapid Diagnostic Testing for Bloodstream Infections: Nanopore Targeted Sequencing with Pathogen-Specific Primers.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106166},
doi = {10.1016/j.jinf.2024.106166},
pmid = {38670268},
issn = {1532-2742},
abstract = {BACKGROUND: Nanopore sequencing, known for real-time analysis, shows promise for rapid clinical infection diagnosis but lacks effective assays for bloodstream infections (BSIs).

METHODS: We prospectively assessed the performance of a novel nanopore targeted sequencing (NTS) assay in identifying pathogens and predicting antibiotic resistance in BSIs, analyzing 387 blood samples from December 2021 to April 2023.

RESULTS: The positivity rate for NTS (69.5%, 269/387) nearly matches that of metagenomic next-generation sequencing (mNGS) (74.7%, 289/387; p=0.128) and surpasses the positivity rate of conventional blood culture (BC) (33.9%, 131/387; p<0.01). Frequent pathogens detected by NTS included Klebsiella pneumoniae (n=54), Pseudomonas aeruginosa (n=36), Escherichia coli (n=36), Enterococcus faecium(n=30), Acinetobacter baumannii(n=26), Staphylococcus aureus(n=23), and Human cytomegalovirus (n=37). Against a composite BSI diagnostic standard, NTS demonstrated a sensitivity and specificity of 84.0% (95% CI 79.5%-87.7%) and 90.1% (95% CI 81.7%-88.5%), respectively. The concordance between NTS and mNGS results (the percentage of total cases where both either detected BSI-related pathogens or were both negative) was 90.2% (359/387), whereas the consistency between NTS and BC was only 60.2% (233/387). In 80.6% (50/62) of the samples with identical pathogens identified by both NTS tests and BCs, the genotypic resistance identified by NTS correlated with culture-confirmed phenotypic resistance. Using NTS, 95% of samples can be tested and analyzed in approximately 7hours, allowing for early patient diagnosis.

CONCLUSIONS: NTS is rapid, sensitive, and efficient for detecting BSIs and drug-resistant genes, making it a potential preferred diagnostic tool for early infection identification in critically ill patients.},
}

@article {pmid38670213,
year = {2024},
author = {Sun, Y and Du, P and Li, H and Zhou, K and Shou, L and Chen, J and Meng Li, },
title = {Prokaryotic community assembly patterns and nitrogen metabolic potential in oxygen minimum zone of Yangtze Estuary water column.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119011},
doi = {10.1016/j.envres.2024.119011},
pmid = {38670213},
issn = {1096-0953},
abstract = {It is predicted that oxygen minimum zones (OMZs) in the ocean will expand as a consequence of global warming and environmental pollution. This will affect the overall microbial ecology and microbial nitrogen cycle. As one of the world's largest alluvial estuaries, the Yangtze Estuary has exhibited a seasonal OMZ since the 1980s. In this pioneering study, we have uncovered the microbial composition, the patterns of community assembly and the potential for microbial nitrogen cycling within the water column of the Yangtze Estuary, with a particular focus on OMZ. Based on the 16S rRNA gene sequencing, a specific spatial variation in the composition of prokaryotic communities was observed for each water layer, with the Proteobacteria (46.1%), Bacteroidetes (20.3%), and Cyanobacteria (10.3%) dominant. Stochastic and deterministic processes together shaped the community assembly in the water column. Further, pH was the most important environmental factor influencing prokaryotic composition in the surface water, followed by silicate, PO4[3-], and distance offshore (p<0.05). Water depth, NH4[+], and PO4[3-] were the main factors in the bottom water (p<0.05). At last, species analysis and marker gene annotation revealed candidate nitrogen cycling performers, and a rich array of nitrogen cycling potential in the bottom water of the Yangtze Estuary. The determined physiochemical parameters and potential for nitrogen respiration suggested that organic nitrogen and NO3[-] (or NO2[-]) are the preferred nitrogen sources for microorganisms in the Yangtze Estuary OMZ. These findings are expected to advance research on the ecological responses of estuarine oxygen minimum zones (OMZs) to future global climate perturbations.},
}

@article {pmid38669903,
year = {2024},
author = {Liu, H and Al-Dhabi, NA and Jiang, H and Liu, B and Qing, T and Feng, B and Ma, T and Tang, W and Zhang, P},
title = {Toward nitrogen recovery: Co-cultivation of microalgae and bacteria enhances the production of high-value nitrogen-rich cyanophycin.},
journal = {Water research},
volume = {256},
number = {},
pages = {121624},
doi = {10.1016/j.watres.2024.121624},
pmid = {38669903},
issn = {1879-2448},
abstract = {The algal-bacterial wastewater treatment process has been proven to be highly efficient in removing nutrients and recovering nitrogen (N). However, the recovery of the valuable N-rich biopolymer, cyanophycin, remains limited. This research explored the synthesis mechanism and recovery potential of cyanophycin within two algal-bacterial symbiotic reactors. The findings reveal that the synergy between algae and bacteria enhances the removal of N and phosphorus. The crude contents of cyanophycin in the algal-bacterial consortia reached 115 and 124 mg/g of mixed liquor suspended solids (MLSS), respectively, showing an increase of 11.7 %-20.4 % (p < 0.001) compared with conventional activated sludge. Among the 170 metagenome-assembled genomes (MAGs) analyzed, 50 were capable of synthesizing cyanophycin, indicating that cyanophycin producers are common in algal-bacterial systems. The compositions of cyanophycin producers in the two algal-bacterial reactors were affected by different lighting initiation time. The study identified two intracellular synthesis pathways for cyanophycin. Approximately 36 MAGs can synthesize cyanophycin de novo using ammonium and glucose, while the remaining 14 MAGs require exogenous arginine for production. Notably, several MAGs with high abundance are capable of assimilating both nitrate and ammonium into cyanophycin, demonstrating a robust N utilization capability. This research also marks the first identification of potential horizontal gene transfer of the cyanophycin synthase encoding gene (cphA) within the wastewater microbial community. This suggests that the spread of cphA could expand the population of cyanophycin producers. The study offers new insights into recycling the high-value N-rich biopolymer cyanophycin, contributing to the advancement of wastewater resource utilization.},
}

@article {pmid38669570,
year = {2024},
author = {Madi, N and Cato, ET and Abu Sayeed, M and Creasy-Marrazzo, A and Cuénod, A and Islam, K and Khabir, MIU and Bhuiyan, MTR and Begum, YA and Freeman, E and Vustepalli, A and Brinkley, L and Kamat, M and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Shapiro, BJ and Nelson, EJ},
title = {Phage predation, disease severity, and pathogen genetic diversity in cholera patients.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6693},
pages = {eadj3166},
doi = {10.1126/science.adj3166},
pmid = {38669570},
issn = {1095-9203},
mesh = {*Cholera/microbiology ; *Vibrio cholerae/genetics/virology ; *Bacteriophages/genetics/physiology ; Humans ; *Genetic Variation ; Bangladesh ; Anti-Bacterial Agents/therapeutic use ; Severity of Illness Index ; Adult ; Metagenomics ; },
abstract = {Despite an increasingly detailed picture of the molecular mechanisms of bacteriophage (phage)-bacterial interactions, we lack an understanding of how these interactions evolve and impact disease within patients. In this work, we report a year-long, nationwide study of diarrheal disease patients in Bangladesh. Among cholera patients, we quantified Vibrio cholerae (prey) and its virulent phages (predators) using metagenomics and quantitative polymerase chain reaction while accounting for antibiotic exposure using quantitative mass spectrometry. Virulent phage (ICP1) and antibiotics suppressed V. cholerae to varying degrees and were inversely associated with severe dehydration depending on resistance mechanisms. In the absence of antiphage defenses, predation was "effective," with a high predator:prey ratio that correlated with increased genetic diversity among the prey. In the presence of antiphage defenses, predation was "ineffective," with a lower predator:prey ratio that correlated with increased genetic diversity among the predators. Phage-bacteria coevolution within patients should therefore be considered in the deployment of phage-based therapies and diagnostics.},
}

*Cholera/microbiology
*Vibrio cholerae/genetics/virology
*Bacteriophages/genetics/physiology
Humans
*Genetic Variation
Bangladesh
Anti-Bacterial Agents/therapeutic use
Severity of Illness Index
Adult
Metagenomics

@article {pmid38669355,
year = {2024},
author = {Vinces, TC and de Souza, AS and Carvalho, CF and Visnardi, AB and Teixeira, RD and Llontop, EE and Bismara, BAP and Vicente, EJ and Pereira, JO and de Souza, RF and Yonamine, M and Marana, SR and Farah, CS and Guzzo, CR},
title = {Monomeric Esterase: Insights into Cooperative Behavior, Hysteresis/Allokairy.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.3c00668},
pmid = {38669355},
issn = {1520-4995},
abstract = {Herein, we present a novel esterase enzyme, Ade1, isolated from a metagenomic library of Amazonian dark earths soils, demonstrating its broad substrate promiscuity by hydrolyzing ester bonds linked to aliphatic groups. The three-dimensional structure of the enzyme was solved in the presence and absence of substrate (tributyrin), revealing its classification within the α/β-hydrolase superfamily. Despite being a monomeric enzyme, enzymatic assays reveal a cooperative behavior with a sigmoidal profile (initial velocities vs substrate concentrations). Our investigation brings to light the allokairy/hysteresis behavior of Ade1, as evidenced by a transient burst profile during the hydrolysis of substrates such as p-nitrophenyl butyrate and p-nitrophenyl octanoate. Crystal structures of Ade1, coupled with molecular dynamics simulations, unveil the existence of multiple conformational structures within a single molecular state (E̅1). Notably, substrate binding induces a loop closure that traps the substrate in the catalytic site. Upon product release, the cap domain opens simultaneously with structural changes, transitioning the enzyme to a new molecular state (E̅2). This study advances our understanding of hysteresis/allokairy mechanisms, a temporal regulation that appears more pervasive than previously acknowledged and extends its presence to metabolic enzymes. These findings also hold potential implications for addressing human diseases associated with metabolic dysregulation.},
}

@article {pmid38669328,
year = {2024},
author = {Dong, X and Zhang, T and Wu, W and Peng, Y and Liu, X and Han, Y and Chen, X and Gao, Z and Xia, J and Shao, Z and Greening, C},
title = {A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps.},
journal = {Science advances},
volume = {10},
number = {17},
pages = {eadl2281},
doi = {10.1126/sciadv.adl2281},
pmid = {38669328},
issn = {2375-2548},
mesh = {*Geologic Sediments/microbiology ; *Microbiota ; *Metagenome ; Bacteria/metabolism/genetics ; Metabolome ; Ecosystem ; Secondary Metabolism ; Archaea/metabolism/genetics ; Multigene Family ; Cold Temperature ; Metabolomics/methods ; Phylogeny ; Metagenomics/methods ; },
abstract = {In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.},
}

*Geologic Sediments/microbiology
*Microbiota
*Metagenome
Bacteria/metabolism/genetics
Metabolome
Ecosystem
Secondary Metabolism
Archaea/metabolism/genetics
Multigene Family
Cold Temperature
Metabolomics/methods
Phylogeny
Metagenomics/methods

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

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

@article {pmid38668594,
year = {2024},
author = {Bishop, SL and Solonenka, JT and Giebelhaus, RT and Bakker, DTR and Li, ITS and Murch, SJ},
title = {Microbial Diversity Impacts Non-Protein Amino Acid Production in Cyanobacterial Bloom Cultures Collected from Lake Winnipeg.},
journal = {Toxins},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/toxins16040169},
pmid = {38668594},
issn = {2072-6651},
support = {Unknown//Natural Sciences and Engineering Research Council/ ; Unknown//Canadian Foundation for Innovation/ ; },
mesh = {*Lakes/microbiology ; *Cyanobacteria/metabolism/genetics/isolation & purification ; Manitoba ; Harmful Algal Bloom ; Amino Acids/analysis/metabolism ; Tandem Mass Spectrometry ; Biodiversity ; Microbiota ; Cyanobacteria Toxins ; },
abstract = {Lake Winnipeg in Manitoba, Canada is heavily impacted by harmful algal blooms that contain non-protein amino acids (NPAAs) produced by cyanobacteria: N-(2-aminoethyl)glycine (AEG), β-aminomethyl-L-alanine (BAMA), β-N-methylamino-L-alanine (BMAA), and 2,4-diaminobutyric acid (DAB). Our objective was to investigate the impact of microbial diversity on NPAA production by cyanobacteria using semi-purified crude cyanobacterial cultures established from field samples collected by the Lake Winnipeg Research Consortium between 2016 and 2021. NPAAs were detected and quantified by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) using validated analytical methods, while Shannon and Simpson alpha diversity scores were determined from 16S rRNA metagenomic sequences. Alpha diversity in isolate cultures was significantly decreased compared to crude cyanobacterial cultures (p < 0.001), indicating successful semi-purification. BMAA and AEG concentrations were higher in crude compared to isolate cultures (p < 0.0001), and AEG concentrations were correlated to the alpha diversity in cultures (r = 0.554; p < 0.0001). BAMA concentrations were increased in isolate cultures (p < 0.05), while DAB concentrations were similar in crude and isolate cultures. These results demonstrate that microbial community complexity impacts NPAA production by cyanobacteria and related organisms.},
}

*Lakes/microbiology
*Cyanobacteria/metabolism/genetics/isolation & purification
Manitoba
Harmful Algal Bloom
Amino Acids/analysis/metabolism
Tandem Mass Spectrometry
Biodiversity
Microbiota
Cyanobacteria Toxins

@article {pmid38668472,
year = {2024},
author = {Corredor, D and Duchicela, J and Flores, FJ and Maya, M and Guerron, E},
title = {Review of Explosive Contamination and Bioremediation: Insights from Microbial and Bio-Omic Approaches.},
journal = {Toxics},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/toxics12040249},
pmid = {38668472},
issn = {2305-6304},
abstract = {Soil pollution by TNT(2,4,6-trinitrotoluene), RDX(hexahydro-1,3,5-trinitro-1,3,5-triazacyclohexane), and HMX(octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), resulting from the use of explosives, poses significant challenges, leading to adverse effects such as toxicity and alteration of microbial communities. Consequently, there is a growing need for effective bioremediation strategies to mitigate this damage. This review focuses on Microbial and Bio-omics perspectives within the realm of soil pollution caused by explosive compounds. A comprehensive analysis was conducted, reviewing 79 articles meeting bibliometric criteria from the Web of Science and Scopus databases from 2013 to 2023. Additionally, relevant patents were scrutinized to establish a comprehensive research database. The synthesis of these findings serves as a critical resource, enhancing our understanding of challenges such as toxicity, soil alterations, and microbial stress, as well as exploring bio-omics techniques like metagenomics, transcriptomics, and proteomics in the context of environmental remediation. The review underscores the importance of exploring various remediation approaches, including mycorrhiza remediation, phytoremediation, bioaugmentation, and biostimulation. Moreover, an examination of patented technologies reveals refined and efficient processes that integrate microorganisms and environmental engineering. Notably, China and the United States are pioneers in this field, based on previous successful bioremediation endeavors. This review underscores research's vital role in soil pollution via innovative, sustainable bioremediation for explosives.},
}

@article {pmid38668317,
year = {2024},
author = {Shen, W and Zhao, M and Xu, W and Shi, X and Ren, F and Tu, P and Gao, N and Shan, J and Gao, B},
title = {Sex-Specific Effects of Polystyrene Microplastic and Lead(II) Co-Exposure on the Gut Microbiome and Fecal Metabolome in C57BL/6 Mice.},
journal = {Metabolites},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/metabo14040189},
pmid = {38668317},
issn = {2218-1989},
support = {42107459//National Natural Science Foundation of China/ ; },
abstract = {The wide spread of microplastics has fueled growing public health concern globally. Due to their porous structure and large surface area, microplastics can serve as carriers for other environmental pollutants, including heavy metals. Although the toxic effects of microplastics or heavy metals have been reported previously, investigations into the sex-differential health effects of combined exposure to microplastics and heavy metals are lacking. In the present study, the effects of polystyrene microplastics and lead(II) co-exposure on the gut microbiome, intestinal permeability, and fecal metabolome were examined in both male and female mice. Combined exposure of polystyrene microplastics and lead(II) increased intestinal permeability in both male and female mice. Sex-specific responses to the co-exposure were found in gut bacteria, fungi, microbial metabolic pathways, microbial genes encoding antibiotic resistance and virulence factors, as well as fecal metabolic profiles. In particular, Shannon and Simpson indices of gut bacteria were reduced by the co-exposure only in female mice. A total of 34 and 13 fecal metabolites were altered in the co-exposure group in female and male mice, respectively, among which only three metabolites were shared by both sexes. These sex-specific responses to the co-exposure need to be taken into consideration when investigating the combined toxic effects of microplastics and heavy metals on the gut microbiota.},
}

@article {pmid38668230,
year = {2024},
author = {Quek, ZBR and Ng, SH},
title = {Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/pathogens13040275},
pmid = {38668230},
issn = {2076-0817},
support = {NA//Ministry of Defence/ ; },
abstract = {High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.},
}

@article {pmid38666991,
year = {2024},
author = {Itzhari, D and Shuai, W and Hartmann, EM and Ronen, Z},
title = {Heterogeneous Antibiotic Resistance Gene Removal Impedes Evaluation of Constructed Wetlands for Effective Greywater Treatment.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/antibiotics13040315},
pmid = {38666991},
issn = {2079-6382},
support = {1237//Marcus Zuckerberg Institute for Water Research- Northwestern Awards/ ; },
abstract = {Microorganisms carrying antimicrobial resistance genes are often found in greywater. As the reuse of greywater becomes increasingly needed, it is imperative to determine how greywater treatment impacts antimicrobial resistance genes (ARGs). Using qPCR and SmartChip™ qPCR, we characterized ARG patterns in greywater microbial communities before, during, and after treatment by a recirculating vertical flow constructed wetland. In parallel, we examined the impact of greywater-treated irrigation on soil, including the occurrence of emerging micropollutants and the taxonomic and ARG compositions of microbial communities. Most ARGs in raw greywater are removed efficiently during the winter season, while some ARGs in the effluents increase in summer. SmartChip™ qPCR revealed the presence of ARGs, such as tetracycline and beta-lactam resistance genes, in both raw and treated greywater, but most abundantly in the filter bed. It also showed that aminoglycoside and vancomycin gene abundances significantly increased after treatment. In the irrigated soil, the type of water (potable or treated greywater) had no specific impact on the total bacterial abundance (16S rRNA gene). No overlapping ARGs were found between treated greywater and greywater-irrigated soil. This study indicates ARG abundance and richness increased after treatment, possibly due to the concentration effects of the filter beds.},
}

@article {pmid38666987,
year = {2024},
author = {Kardos, G and Laczkó, L and Kaszab, E and Timmer, B and Szarka, K and Prépost, E and Bányai, K},
title = {Phylogeny of Transferable Oxazolidinone Resistance Genes and Homologs.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/antibiotics13040311},
pmid = {38666987},
issn = {2079-6382},
support = {GINOP-2.3.4-15-2020-00008//GINOP/ ; RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; TKP2021-EGA-01//National Research, Development and Innovation Office/ ; SA-27/2021//Eötvös Loránd Research Network/ ; ÚNKP-20-4-I-DE-277//National Research, Development and Innovation Office/ ; },
abstract = {Oxazolidinone resistance, especially transmissible resistance, is a major public health concern, and the origin of this resistance mechanism is not yet resolved. This study aims to delve into the phylogenetic origin of the transmissible oxazolidinone resistance mechanisms conferring cross-resistance to other drugs of human and veterinary importance. The amino acid sequences of the five cfr ribosomal methylases and optrA and poxtA were used as queries in searches against 219,549 bacterial proteomes in the NCBI RefSeq database. Hits with >40% amino acid identity and >80% query coverage were aligned, and phylogenetic trees were reconstructed. All five cfr genes yielded highly similar trees, with rlmN housekeeping ribosomal methylases located basal to the sister groups of S-adenosyl-methionine-dependent methyltransferases from various Deltaproteobacteria and Actinomycetia, including antibiotic-producing Streptomyces species, and the monophyletic group of cfr genes. The basal branches of the latter contained paenibacilli and other soil bacteria; they then could be split into the clades [cfr(C):cfr(E)] and [[cfr:cfr(B)]:cfr(D)], always with different Bacillaceae in their stems. Lachnospiraceae were encountered in the basal branches of both optrA and poxtA trees. The ultimate origin of the cfr genes is the rlmN housekeeping ribosomal methylases, which evolved into a suicide-avoiding methylase in antibiotic producers; a soil organism (Lachnospiraceae, Paenibacilli) probably acted as a transfer organism into pathogenic bacteria. In the case of optrA, the porcine pathogenic Streptococcus suis was present in all branches, while the proteins closest to poxtA originated from Clostridia.},
}

@article {pmid38666967,
year = {2024},
author = {Konechnyi, Y and Rumynska, T and Yushyn, I and Holota, S and Turkina, V and Ryviuk Rydel, M and Sękowska, A and Salyha, Y and Korniychuk, O and Lesyk, R},
title = {A New 4-Thiazolidinone Derivative (Les-6490) as a Gut Microbiota Modulator: Antimicrobial and Prebiotic Perspectives.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/antibiotics13040291},
pmid = {38666967},
issn = {2079-6382},
support = {0121U100690, 0120U102460, 0123U100153//Ministry of Health of Ukraine/ ; 2020.02/0035//National Research Foundation of Ukraine/ ; },
abstract = {A novel 4-thiazolidinone derivative Les-6490 (pyrazol-4-thiazolidinone hybrid) was designed, synthesized, and characterized by spectral data. The compound was screened for its antimicrobial activity against some pathogenic bacteria and fungi and showed activity against Staphylococcus and Saccharomyces cerevisiae (the Minimum Inhibitory Concentration (MIC) 820 μM). The compound was studied in the rat adjuvant arthritis model (Freund's Adjuvant) in vivo. Parietal and fecal microbial composition using 16S rRNA metagenome sequences was checked. We employed a range of analytical techniques, including Taxonomic Profiling (Taxa Analysis), Diversity Metrics (Alpha and Beta Diversity Analysis), Multivariate Statistical Methods (Principal Coordinates Analysis, Principal Component Analysis, Non-Metric Multidimensional Scaling), Clustering Analysis (Unweighted Pair-group Method with Arithmetic Mean), and Comparative Statistical Approaches (Community Differences Analysis, Between Group Variation Analysis, Metastat Analysis). The compound significantly impacted an increasing level of anti-inflammatory microorganisms (Blautia, Faecalibacterium prausnitzii, Succivibrionaceae, and Coriobacteriales) relative recovery of fecal microbiota composition. Anti-Treponemal activity in vivo was also noted. The tested compound Les-6490 has potential prebiotic activity with an indirect anti-inflammatory effect.},
}

@article {pmid38666955,
year = {2024},
author = {Bilski, K and Żeber-Lubecka, N and Kulecka, M and Dąbrowska, M and Bałabas, A and Ostrowski, J and Dobruch, A and Dobruch, J},
title = {Microbiome Sex-Related Diversity in Non-Muscle-Invasive Urothelial Bladder Cancer.},
journal = {Current issues in molecular biology},
volume = {46},
number = {4},
pages = {3595-3609},
doi = {10.3390/cimb46040225},
pmid = {38666955},
issn = {1467-3045},
support = {2019/33/B/NZ5/02447//National Science Center/ ; },
abstract = {Sex-specific discrepancies in bladder cancer (BCa) are reported, and new studies imply that microbiome may partially explain the diversity. We aim to provide characterization of the bladder microbiome in both sexes diagnosed with non-muscle-invasive BCa with specific insight into cancer grade. In our study, 16S rRNA next-generation sequencing was performed on midstream urine, bladder tumor sample, and healthy-appearing bladder mucosa. Bacterial DNA was isolated using QIAamp Viral RNA Mini Kit. Metagenomic analysis was performed using hypervariable fragments of the 16S rRNA gene on Ion Torrent Personal Genome Machine platform. Of 41 sample triplets, 2153 taxa were discovered: 1739 in tumor samples, 1801 in healthy-appearing bladder mucosa and 1370 in midstream urine. Women were found to have smaller taxa richness in Chao1 index than men (p = 0.03). In comparison to low-grade tumors, patients with high-grade lesions had lower bacterial diversity and richness in urine. Significant differences between sexes in relative abundance of communities at family level were only observed in high-grade tumors.},
}

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

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

@article {pmid38666708,
year = {2024},
author = {Li, H and Wu, J and Mai, X and Zeng, W and Cai, S and Huang, X and Zhou, C and Li, J and Jiang, Q and Lai, C and Xie, C},
title = {Novel Patterns in High-Resolution Computed Tomography in Whipple Pneumonia.},
journal = {Emerging infectious diseases},
volume = {30},
number = {5},
pages = {1042-1045},
doi = {10.3201/eid3005.231130},
pmid = {38666708},
issn = {1080-6059},
mesh = {Humans ; Male ; Middle Aged ; *Tomography, X-Ray Computed ; *Whipple Disease/diagnosis/drug therapy/diagnostic imaging ; Pneumonia, Bacterial/diagnostic imaging/microbiology/diagnosis ; Aged ; Tropheryma/genetics/isolation & purification ; Female ; Anti-Bacterial Agents/therapeutic use ; Lung/diagnostic imaging/pathology ; China ; High-Throughput Nucleotide Sequencing ; },
abstract = {With the use of metagenomic next-generation sequencing, patients diagnosed with Whipple pneumonia are being increasingly correctly diagnosed. We report a series of 3 cases in China that showed a novel pattern of movable infiltrates and upper lung micronodules. After treatment, the 3 patients recovered, and lung infiltrates resolved.},
}

Humans
Male
Middle Aged
*Tomography, X-Ray Computed
*Whipple Disease/diagnosis/drug therapy/diagnostic imaging
Pneumonia, Bacterial/diagnostic imaging/microbiology/diagnosis
Aged
Tropheryma/genetics/isolation & purification
Female
Anti-Bacterial Agents/therapeutic use
Lung/diagnostic imaging/pathology
China
High-Throughput Nucleotide Sequencing

@article {pmid38666081,
year = {2024},
author = {Omar, KM and Kitundu, GL and Jimoh, AO and Namikelwa, DN and Lisso, FM and Babajide, AA and Olufemi, SE and Awe, OI},
title = {Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17181},
doi = {10.7717/peerj.17181},
pmid = {38666081},
issn = {2167-8359},
mesh = {Animals ; Cattle ; *Metagenomics ; Kenya/epidemiology ; Uganda/epidemiology ; Tanzania ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genes, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.},
}

Animals
Cattle
*Metagenomics
Kenya/epidemiology
Uganda/epidemiology
Tanzania
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology/therapeutic use
Genes, Bacterial/genetics

@article {pmid38665997,
year = {2024},
author = {Zhou, X and Sun, H and Ren, J and Yan, G and Yang, L and Zhang, H and Lu, H and Li, X and Makino, T and Yin, F and Li, J and Wang, X},
title = {Mineral crude drug mirabilite (Mangxiao) inhibits the occurrence of colorectal cancer by regulating the Lactobacillus-bile acid-intestinal farnesoid X receptor axis based on multiomics integration analysis.},
journal = {MedComm},
volume = {5},
number = {5},
pages = {e556},
doi = {10.1002/mco2.556},
pmid = {38665997},
issn = {2688-2663},
abstract = {Mineral crude drug has revolutionized the treatment landscape in precision oncology niche that leads to the improvement in therapeutic efficiency on various tumor subtypes. Mangxiao (MX), a mineral crude drug in traditional Chinese medicine, has been used for treating gastrointestinal diseases for thousands of years. However, the action mechanisms are still ambiguous. Here, we attempt to explore inhibitory roles and associated pharmacological mechanisms of MX upon colorectal cancer (CRC) in APC[Min/+] male mice by integrating metabolomics, 16S rDNA sequencing analyses, and metagenomic-based microbiota analysis. We found that MX can significantly inhibit the occurrence of CRC through the regulation of the dysregulated gut microbe metabolism. Furthermore, the correlation analysis of metabolomes and 16S rDNA revealed that MX could restore the disorders of gut microbes by specifically enriching the abundance of Lactobacilli to improve bile acid metabolism, which further activated the farnesoid X receptor (FXR) in CRC mice, then the improvement of gut dysbiosis could inhibit the development of CRC. Collectively, our effort confirmed MX has the capacity to intervene the development of CRC and further discovered that it targets Lactobacillus-bile acid-intestinal FXR axis, which can be regarded as a candidate medicine for future drug discovery and development against CRC.},
}

@article {pmid38665771,
year = {2024},
author = {Ottesen, A and Kocurek, B and Reed, E and Commichaux, S and Mammel, M and Ramachandran, P and McDermott, P and Flannery, BM and Strain, E},
title = {Paired metagenomic and chemical evaluation of aflatoxin-contaminated dog kibble.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1374839},
doi = {10.3389/fvets.2024.1374839},
pmid = {38665771},
issn = {2297-1769},
abstract = {INTRODUCTION: Identification of chemical toxins from complex or highly processed foods can present 'needle in the haystack' challenges for chemists. Metagenomic data can be used to guide chemical toxicity evaluations by providing DNA-based description of the wholistic composition (eukaryotic, bacterial, protozoal, viral, and antimicrobial resistance) of foods suspected to harbor toxins, allergens, or pathogens. This type of information can focus chemistry-based diagnostics, improve hazard characterization and risk assessment, and address data gaps. Additionally, there is increasing recognition that simultaneously co-occurring mycotoxins, either from single or multiple species, can impact dietary toxicity exposure. Metagenomic data provides a way to address data gaps related to co-occurrence of multiple fungal species.

METHODS: Paired metagenomic and chemical data were used to evaluate aflatoxin-contaminated kibble with known levels of specific mycotoxins. Kibble was ground to a fine powder for both chemical and molecular analyses. Chemical analyses were performed with Liquid Chromatography Mass Spectrometry (LCMS) and according to the AOAC Official method 2005.08: Aflatoxins in Corn, Raw Peanuts, and Peanut Butter using Liquid Chromatography with Post-Column Photochemical Derivatization. Metagenomes were created from DNA extracted from ground kibble and sequenced on an Illumina NextSeq 2000 with an average sequence depth of 180 million reads per replicate.

RESULTS AND DISCUSSION: Metagenomic data demonstrated that the abundance of DNA from putative aflatoxigenic Aspergillus spp. correlated with the levels of aflatoxin quantified by LCMS. Metagenomic data also identified an expansive range of co-occurring fungal taxa which may produce additional mycotoxins. DNA data paired with chemical data provides a novel modality to address current data gaps surrounding dietary mycotoxin exposure, toxigenic fungal taxonomy, and mycotoxins of emerging concern.},
}

@article {pmid38665607,
year = {2024},
author = {Shearer, J and Shah, S and Shen-Tu, G and Schlicht, K and Laudes, M and Mu, C},
title = {Microbial Features Linked to Medication Strategies in Cardiometabolic Disease Management.},
journal = {ACS pharmacology & translational science},
volume = {7},
number = {4},
pages = {991-1001},
doi = {10.1021/acsptsci.3c00261},
pmid = {38665607},
issn = {2575-9108},
abstract = {Human gut microbiota are recognized as critical players in both metabolic disease and drug metabolism. However, medication-microbiota interactions in cardiometabolic diseases are not well understood. To gain a comprehensive understanding of how medication intake impacts the gut microbiota, we investigated the association of microbial structure with the use of single or multiple medications in a cohort of 134 middle-aged adults diagnosed with cardiometabolic disease, recruited from Alberta's Tomorrow Project. Predominant cardiometabolic prescription medication classes (12 total) were included in our analysis. Multivariate Association with Linear Model (MaAsLin2) was employed and results were corrected for age, BMI, sex, and diet to evaluate the relationship between microbial features and single- or multimedication use. Highly individualized microbiota profiles were observed across participants, and increasing medication use was negatively correlated with α-diversity. A total of 46 associations were identified between microbial composition and single medications, exemplified by the depletion of Akkermansia muciniphila by β-blockers and statins, and the enrichment of Escherichia/Shigella and depletion of Bacteroides xylanisolvens by metformin. Metagenomics prediction further indicated alterations in microbial functions associated with single medications such as the depletion of enzymes involved in energy metabolism encoded by Eggerthella lenta due to β-blocker use. Specific dual medication combinations also had profound impacts, including the depletion of Romboutsia and Butyriciocccus by statin plus metformin. Together, these results show reductions in bacterial diversity as well as species and microbial functional potential associated with both single- and multimedication use in cardiometabolic disease.},
}

@article {pmid38665155,
year = {2024},
author = {Babalola, OO and Adedayo, AA and Akinola, SA},
title = {High-throughput metagenomic assessment of Cango Cave microbiome-A South African limestone cave.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110381},
doi = {10.1016/j.dib.2024.110381},
pmid = {38665155},
issn = {2352-3409},
abstract = {Microorganisms inhabiting caves exhibit medical or biotechnological promise, most of which have been attributed to factors such as antimicrobial activity or the induction of mineral precipitation. This dataset explored the shotgun metagenomic sequencing of the Cango cave microbial community in Oudtshoorn, South Africa. The aimed to elucidate both the structure and function of the microbial community linked to the cave. DNA sequencing was conducted using the Illumina NovaSeq platform, a next-generation sequencing. The data comprises 4,738,604 sequences, with a cumulative size of 1,180,744,252 base pairs and a GC content of 52%. Data derived from the metagenome sequences can be accessed through the bioproject number PRJNA982691 on NCBI. Using an online metagenome server, MG-RAST, the subsystem database revealed that bacteria displayed the highest taxonomical representation, constituting about 98.66%. Archaea accounted for 0.05%, Eukaryotes at 1.20%, viruses were 0.07%, while unclassified sequences had a representation of 0.02%. The most abundant phyla were Proteobacteria (81.74%), Bacteroidetes (10.57%), Actinobacteria (4.16%), Firmicutes (SK‒1.03%), Acidobacteria (0.20), and Planctomycetes (SK‒0.16%). Functional annotation using subsystem analysis revealed that clustering based on subsystems had 13.44%, while amino acids and derivatives comprised 11.41%. Carbohydrates sequences constituted 9.55%, along with other advantageous functional traits essential for growth promotion and plant management.},
}

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

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

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

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

@article {pmid38664753,
year = {2024},
author = {Song, L and Langmead, B},
title = {Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {106},
pmid = {38664753},
issn = {1474-760X},
support = {P20GM130454/GM/NIGMS NIH HHS/United States ; R35GM139602/GM/NIGMS NIH HHS/United States ; 3P20GM130454-05WS/GM/NIGMS NIH HHS/United States ; R01HG011392/HG/NHGRI NIH HHS/United States ; },
mesh = {*Data Compression/methods ; *Metagenomics/methods ; Software ; Genome, Microbial ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; },
abstract = {Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. In Centrifuger, the Burrows-Wheeler transformed genome sequences are losslessly compressed using a novel scheme called run-block compression. Run-block compression achieves sublinear space complexity and is effective at compressing diverse microbial databases like RefSeq while supporting fast rank queries. Combining this compression method with other strategies for compacting the Ferragina-Manzini (FM) index, Centrifuger reduces the memory footprint by half compared to other FM-index-based approaches. Furthermore, the lossless compression and the unconstrained match length help Centrifuger achieve greater accuracy than competing methods at lower taxonomic levels.},
}

*Data Compression/methods
*Metagenomics/methods
Software
Genome, Microbial
Genome, Bacterial
Sequence Analysis, DNA/methods

@article {pmid38664747,
year = {2024},
author = {Li, Y and Liu, H and Lv, Q and Long, J},
title = {Diagnosis model of early Pneumocystis jirovecii pneumonia based on convolutional neural network: a comparison with traditional PCR diagnostic method.},
journal = {BMC pulmonary medicine},
volume = {24},
number = {1},
pages = {205},
pmid = {38664747},
issn = {1471-2466},
support = {202206010093//Guangzhou Science and Technology Plan Project, China./ ; },
mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis ; *Neural Networks, Computer ; *Tomography, X-Ray Computed ; *Pneumocystis carinii/isolation & purification/genetics ; *Polymerase Chain Reaction/methods ; Male ; Middle Aged ; Female ; Early Diagnosis ; Adult ; Aged ; },
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is an interstitial pneumonia caused by pneumocystis jirovecii (PJ). The diagnosis of PJP primarily relies on the detection of the pathogen from lower respiratory tract specimens. However, it faces challenges such as difficulty in obtaining specimens and low detection rates. In the clinical diagnosis process, it is necessary to combine clinical symptoms, serological test results, chest Computed tomography (CT) images, molecular biology techniques, and metagenomics next-generation sequencing (mNGS) for comprehensive analysis.

PURPOSE: This study aims to overcome the limitations of traditional PJP diagnosis methods and develop a non-invasive, efficient, and accurate diagnostic approach for PJP. By using this method, patients can receive early diagnosis and treatment, effectively improving their prognosis.

METHODS: We constructed an intelligent diagnostic model for PJP based on the different Convolutional Neural Networks. Firstly, we used the Convolutional Neural Network to extract CT image features from patients. Then, we fused the CT image features with clinical information features using a feature fusion function. Finally, the fused features were input into the classification network to obtain the patient's diagnosis result.

RESULTS: In this study, for the diagnosis of PJP, the accuracy of the traditional PCR diagnostic method is 77.58%, while the mean accuracy of the optimal diagnostic model based on convolutional neural networks is 88.90%.

CONCLUSION: The accuracy of the diagnostic method proposed in this paper is 11.32% higher than that of the traditional PCR diagnostic method. The method proposed in this paper is an efficient, accurate, and non-invasive early diagnosis approach for PJP.},
}

Humans
*Pneumonia, Pneumocystis/diagnosis
*Neural Networks, Computer
*Tomography, X-Ray Computed
*Pneumocystis carinii/isolation & purification/genetics
*Polymerase Chain Reaction/methods
Male
Middle Aged
Female
Early Diagnosis
Adult
Aged

@article {pmid38665202,
year = {2023},
author = {Hesketh-Best, PJ and Bosco-Santos, A and Garcia, SL and O'Beirne, MD and Werne, JP and Gilhooly, WP and Silveira, CB},
title = {Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms.},
journal = {Communications earth & environment},
volume = {4},
number = {1},
pages = {126},
doi = {10.1038/s43247-023-00796-4},
pmid = {38665202},
issn = {2662-4435},
abstract = {Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA, encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past.},
}

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

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

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

@article {pmid38664402,
year = {2024},
author = {Zheng, Y and Cao, X and Zhou, Y and Ma, S and Wang, Y and Li, Z and Zhao, D and Yang, Y and Zhang, H and Meng, C and Xie, Z and Sui, X and Xu, K and Li, Y and Zhang, CS},
title = {Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3520},
pmid = {38664402},
issn = {2041-1723},
support = {32101289//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32171948//National Natural Science Foundation of China (National Science Foundation of China)/ ; ZR2021QD026//Natural Science Foundation of Shandong Province (Shandong Provincial Natural Science Foundation)/ ; },
mesh = {*Pseudomonas/genetics/metabolism ; *Glycine max/microbiology/metabolism/genetics ; *Plant Roots/microbiology/metabolism ; *Rhizosphere ; Microbiota/drug effects ; Purines/metabolism/pharmacology ; Salt Stress/genetics ; Chemotaxis/genetics ; Salt Tolerance/genetics ; Soil Microbiology ; Xanthine/metabolism ; Bacterial Proteins/metabolism/genetics ; },
abstract = {The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.},
}

*Pseudomonas/genetics/metabolism
*Glycine max/microbiology/metabolism/genetics
*Plant Roots/microbiology/metabolism
*Rhizosphere
Microbiota/drug effects
Purines/metabolism/pharmacology
Salt Stress/genetics
Chemotaxis/genetics
Salt Tolerance/genetics
Soil Microbiology
Xanthine/metabolism
Bacterial Proteins/metabolism/genetics

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

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

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

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

@article {pmid38663298,
year = {2024},
author = {Rout, AK and Dixit, S and Tripathy, PS and Rout, SS and Parida, SN and Parida, PK and Sarkar, DJ and Kumar Das, B and Singh, AK and Behera, BK},
title = {Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134377},
doi = {10.1016/j.jhazmat.2024.134377},
pmid = {38663298},
issn = {1873-3336},
abstract = {The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.},
}

@article {pmid38664337,
year = {2024},
author = {Ullah Khan, N and Sadiq, A and Khan, J and Basharat, N and Hassan, ZU and Ali, I and Shah, TA and Bourhia, M and Bin Jardan, YA and Wondmie, GF},
title = {Molecular characterization of plasma virome of hepatocellular carcinoma (HCC) patients.},
journal = {AMB Express},
volume = {14},
number = {1},
pages = {46},
pmid = {38664337},
issn = {2191-0855},
abstract = {Hepatocellular carcinoma (HCC) stands as the most common cancer type, arising from various causes, and responsible for a substantial number of cancer-related fatalities. Recent advancements in viral metagenomics have empowered scientists to delve into the intricate diversity of the virosphere, viral evolution, interactions between viruses and their hosts, and the identification of viral causes behind disease outbreaks, the development of specific symptoms, and their potential role in altering the host's physiology. The present study had the objective of "Molecular Characterization of HBV, HCV, anelloviruses, CMV, SENV-D, SENV-H, HEV, and HPV viruses among individuals suffering from HCC." A total of 381 HCC patients contributed 10 cc of blood each for this study. The research encompassed the assessment of tumor markers, followed by molecular characterization of HBV, HCV, Anelloviruses (TTV, TTMV, and TTMDV), SENV-H and SENV-D viruses, HEV, CMV, and HPV, as well as histopathological examinations. The outcomes of this study revealed that majority of the HCC patients 72.4% (276/381) were male as compared to females. HCV infection, at 76.4% (291 out of 381), exhibited a significant association (p < 0.05) with HCC. Most patients displayed singular lesions in the liver, with Child Pugh Score Type B being the predominant finding in 45.2% of cases. Plasma virome analysis indicated the prevalence of TTMDV (75%), followed by TTMV (70%) and TTV (42.1%) among anelloviruses in HCC patients. Similarly, SENV-H (52%) was followed by SENV-D (20%), with co-infections at 15%. The presence of CMV and HEV among the HCC patients was recorded 5% each however 3.5% of the patients showed the presence of HPV. In conclusion, this study underscores that HCC patients serve as reservoirs for various pathogenic and non-pathogenic viruses, potentially contributing to the development, progression, and severity of the disease.},
}

@article {pmid38664270,
year = {2024},
author = {Cadena, S and Cerqueda-García, D and Uribe-Flores, MM and Ramírez, SI},
title = {Metagenomic profiling of halites from the Atacama Desert: an extreme environment with natural perchlorate does not promote high diversity of perchlorate reducing microorganisms.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {2},
pages = {25},
pmid = {38664270},
issn = {1433-4909},
support = {377887//Consejo Nacional de Humanidades Ciencias y Tecnologías/ ; 570049-2022-2023//Consejo Nacional de Humanidades Ciencias y Tecnologías/ ; 88//Consejo de Ciencia y Tecnología del Estado de Morelos/ ; },
mesh = {*Perchlorates/metabolism ; *Oxidation-Reduction ; *Desert Climate ; *Extreme Environments ; Metagenome ; Microbiota ; },
abstract = {We surveyed the presence of perchlorate-reducing microorganisms in available metagenomic data of halite environments from the Atacama Desert, an extreme environment characterized by high perchlorate concentrations, intense ultraviolet radiation, saline and oxidizing soils, and severe desiccation. While the presence of perchlorate might suggest a broad community of perchlorate reducers or a high abundance of a dominant taxa, our search reveals a scarce presence. In fact, we identified only one halophilic species, Salinibacter sp003022435, carrying the pcrA and pcrC genes, represented in low abundance. Moreover, we also discovered some napA genes and organisms carrying the nitrate reductase nasB gene, which hints at the possibility of cryptic perchlorate reduction occurring in these ecosystems. Our findings contribute with the knowledge of perchlorate reduction metabolism potentially occurring in halites from Atacama Desert and point towards promising future research into the perchlorate-reducing mechanism in Salinibacter, a common halophilic bacterium found in hypersaline ecosystems, whose metabolic potential remains largely unknown.},
}

*Perchlorates/metabolism
*Oxidation-Reduction
*Desert Climate
*Extreme Environments
Metagenome
Microbiota

@article {pmid38664214,
year = {2024},
author = {Feng, JC and Gao, MX and Chen, SL and Zhang, W and Luo, WY},
title = {[A case of treatment for severe hip trauma].},
journal = {Zhongguo gu shang = China journal of orthopaedics and traumatology},
volume = {37},
number = {4},
pages = {411-413},
doi = {10.12200/j.issn.1003-0034.20220780},
pmid = {38664214},
issn = {1003-0034},
mesh = {Humans ; Male ; *Hip Injuries/therapy/surgery ; Adult ; Middle Aged ; },
}

Humans
Male
*Hip Injuries/therapy/surgery
Adult
Middle Aged

@article {pmid38663623,
year = {2024},
author = {Liang, X and Zhu, Y and Liu, H and Xie, Z and Li, G and Li, D and Liang, Y and Peng, C},
title = {Nitrogen-fixing cyanobacteria enhance microbial carbon utilization by modulating the microbial community composition in paddy soils of the Mollisols region.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172609},
doi = {10.1016/j.scitotenv.2024.172609},
pmid = {38663623},
issn = {1879-1026},
abstract = {Nitrogen-fixing cyanobacteria (NFC) are photosynthetic prokaryotic microorganisms capable of nitrogen fixation. They can be used as biofertilizers in paddy fields, thereby improving the rice tillering capacity and yield. To reveal the microbiological mechanisms by which nitrogen-fixing cyanobacteria alter soil carbon storage, we conducted a field experiment using NFC as a partial substitute for nitrogen fertilizer in paddy fields in the Sanjiang Plain of Northeast China's Mollisols region. Using metagenomic sequencing technology and Biolog Ecoplate™ carbon matrix metabolism measurements, we explored the changes in the soil microbial community structure and carbon utilization in paddy fields. The results indicated that the replacement of nitrogen fertilizer with NFC predisposed the soil microbial community to host a great number of copiotrophic bacterial taxa, and Proteobacteria and Actinobacteria were closely associated with the metabolism of soil carbon sources. Moreover, through co-occurrence network analysis, we found that copiotrophic bacteria clustered in modules that were positively correlated with the metabolic level of carbon sources. The addition of NFC promoted the growth of copiotrophic bacteria, which increased the carbon utilization level of soil microorganisms, improved the diversity of the microbial communities, and had a potential impact on the soil carbon stock. The findings of this study are helpful for assessing the impact of NFC on the ecological function of soil microbial communities in paddy fields in the black soil area of Northeast China, which is highly important for promoting sustainable agricultural development and providing scientific reference for promoting the use of algal-derived nitrogen fertilizers.},
}

@article {pmid38662518,
year = {2024},
author = {Lages da Silva, DH and Marques da Silva, RL and Rios, DL and Glória de Souza, DD and Aburjaile, F and de Freitas Neto, OC and Camargos Lara, LJ and Araújo, MD and Ecco, R},
title = {Intestinal microbiota diversity from broilers with runting and stunting syndrome performed by metagenomics.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/03079457.2024.2348509},
pmid = {38662518},
issn = {1465-3338},
abstract = {Runting and stunting syndrome (RSS) is an enteric viral disease in commercial poultry that directly affects gut health; however, its influence on gut microbiota remains unknown. This study aimed to investigate the compositional changes in the bacterial community of the ileum of 7-day-old broiler chicks naturally affected and not affected by RSS, using next-generation sequencing (NGS) technology. Twenty-one samples were obtained from the ileal contents and mucosa of 11 chicks with RSS and 10 healthy chicks, raised in a dark house system located on a farm in the state of Minas Gerais, Brazil. The results revealed overall changes in the gut microbiota of the chicks with RSS, including a decrease in microbial richness and diversity. In particular, there was a decrease in Lactobacillus and an increase in Candidatus Arthromitus and Clostridium sensu stricto 1. These results indicate a relationship between viral infection and the gut microbial composition, which can cause gut dysbiosis and may influence inflammation in this organ.RESEARCH HIGHLIGHTSRSS causes dysbiosis of the gut microbiota of the ilea of chicks.A difference was found in gut microbiota between chicks with and without RSS.Candidatus Arthromitus was predominant in chicks with RSS.Clostridium sensu stricto 1 was strictly associated with chicks with RSS.},
}

@article {pmid38662307,
year = {2024},
author = {Wang, Z and Zhou, H and Cheng, Y and An, L and Yan, D and Chao, H and Wu, J},
title = {Novel small multidrug resistance protein Tmt endows the Escherichia coli with triphenylmethane dyes bioremediation capability.},
journal = {Biotechnology letters},
volume = {},
number = {},
pages = {},
pmid = {38662307},
issn = {1573-6776},
support = {31800111//National Natural Science Foundation of China/ ; },
abstract = {Dye contamination in printing and dyeing wastewater has long been a major concern due to its serious impact on both the environment and human health. In the quest for bioremediation of these hazardous dyes, biological resources such as biodegradation bacteria and enzymes have been investigated in severely polluted environments. In this context, the triphenylmethane transporter gene (tmt) was identified in six distinct clones from a metagenomic library of the printing and dyeing wastewater treatment system. Escherichia coli expressing tmt revealed 98.1% decolorization efficiency of triphenylmethane dye malachite green within 24 h under shaking culture condition. The tolerance to malachite green was improved over eightfold in the Tmt strain compared of the none-Tmt expressed strain. Similarly, the tolerance of Tmt strain to other triphenylmethane dyes like crystal violet and brilliant green, was improved by at least fourfold. Site-directed mutations, including A75G, A75S and V100G, were found to reinforce the tolerance of malachite green, and double mutations of these even further improve the tolerance. Therefore, the tmt has been demonstrated to be a specific efflux pump for triphenylmethane dyes, particularly the malachite green. By actively pumping out toxic triphenylmethane dyes, it significantly extends the cells tolerance in a triphenylmethane dye-rich environment, which may provide a promising strategy for bioremediation of triphenylmethane dye pollutants in the environments.},
}

@article {pmid38662153,
year = {2024},
author = {Choudhary, G and Kumari, S and Anu, K and Devi, S},
title = {Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38662153},
issn = {1678-4405},
abstract = {Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.},
}

@article {pmid38661581,
year = {2024},
author = {Suarez, SA and Martiny, AC},
title = {Intraspecific variation in antibiotic resistance potential within E. coli.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0316223},
doi = {10.1128/spectrum.03162-23},
pmid = {38661581},
issn = {2165-0497},
abstract = {Intraspecific genomic diversity brings the potential for an unreported and diverse reservoir of cryptic antibiotic resistance genes in pathogens, as cryptic resistance can occur without major mutations and horizontal transmission. Here, we predicted the differences in the types of antibiotics and genes that induce cryptic and latent resistance between micro-diverse Escherichia coli strains. For example, we hypothesize that known resistance genes will be the culprit of latent resistance within clinical strains. We used a modified functional metagenomics method to induce expression in eight E. coli strains. We found a total of 66 individual genes conferring phenotypic resistance to 11 out of 16 antibiotics. A total of 14 known antibiotic resistance genes comprised 21% of total identified genes, whereas the majority (52 genes) were unclassified cryptic resistance genes. Between the eight strains, 1.2% of core orthologous genes were positive (conferred resistance in at least one strain). Sixty-four percent of positive orthologous genes conferred resistance to only one strain, demonstrating high intraspecific variability of latent resistance genes. Cryptic resistance genes comprised most resistance genes among laboratory and clinical strains as well as natural, semisynthetic, and synthetic antibiotics. Known antibiotic resistance genes primarily conferred resistance to multiple antibiotics from varying origins and within multiple strains. Hence, it is uncommon for E. coli to develop cross-cryptic resistance to antibiotics from multiple origins or within multiple strains. We have uncovered prospective and previously unknown resistance genes as well as antibiotics that have the potential to trigger latent antibiotic resistance in E. coli strains from varying origins.IMPORTANCEIntraspecific genomic diversity may be a driving force in the emergence of adaptive antibiotic resistance. Adaptive antibiotic resistance enables sensitive bacterial cells to acquire temporary antibiotic resistance, creating an optimal window for the development of permanent mutational resistance. In this study, we investigate cryptic resistance, an adaptive resistance mechanism, and unveil novel (cryptic) antibiotic resistance genes that confer resistance when amplified within eight E. coli strains derived from clinical and laboratory origins. We identify the potential of cryptic resistance genes to confer cross-resistance to antibiotics from varying origins and within multiple strains. We discern antibiotic characteristics that promote latent resistance in multiple strains, considering intraspecific diversity. This study may help detect novel resistance genes and functional genes that could become responsible for cryptic resistance among diverse strains and antibiotics, thus also identifying potential novel antibiotic targets and mechanisms.},
}

@article {pmid38661445,
year = {2024},
author = {Sánchez-Terrón, G and Martínez, R and Morcuende, D and Caballero, V and Estévez, M},
title = {Pomegranate supplementation alleviates dyslipidemia and the onset of non-alcoholic fatty liver disease in Wistar rats by shifting microbiota and producing urolithin-like microbial metabolites.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo00688g},
pmid = {38661445},
issn = {2042-650X},
abstract = {Non-alcoholic fatty liver disease (NAFLD), obesity and related chronic diseases are major non-communicable diseases with high mortality rates worldwide. While dietary sugars are known to be responsible for insulin resistance and metabolic syndrome (MetS), the underlying pathophysiological effects of sustained fructose consumption require further elucidation. We hypothesize that certain bioactive compounds (i.e. punicalagin and ellagic acid) from dietary pomegranate could counteract the harmful effects of sustained fructose consumption in terms of obesity and liver damage. The present study aimed to elucidate both the molecular mechanisms involved in the pathophysiology associated with fructose intake and the effect of a punicalagin-rich commercial pomegranate dietary supplement (P) used as a nutritional strategy to alleviate fructose-induced metabolic impairments. Thus, nineteen Wistar rats fed on a basal commercial feed were supplemented with either 30% (w/v) fructose in drinking water (F; n = 7) or 30% (w/v) fructose solution plus 0.2% (w/v) P (F + P; n = 6) for 10 weeks. The results were compared to those from a control group fed on the basal diet and provided with drinking water (C; n = 6). Body weight and energy intake were registered weekly. P supplementation decreased fat depots, counteracted the dyslipidemia caused by F and improved markers of liver injury including steatosis. The study of the microbiota by metagenomics and urine by untargeted MS-based metabolomics revealed microbial metabolites from P that may be responsible for these health benefits.},
}

@article {pmid38661414,
year = {2024},
author = {Alexander, CC and Gaudier-Diaz, MM and Kleinschmit, AJ and Dihle, PJ and Salger, SA and Vega, N and Robertson, SD},
title = {A case study to engage students in the research design and ethics of high-throughput metagenomics.},
journal = {Journal of microbiology & biology education},
volume = {25},
number = {1},
pages = {e0007423},
doi = {10.1128/jmbe.00074-23},
pmid = {38661414},
issn = {1935-7877},
abstract = {Case studies present students with an opportunity to learn and apply course content through problem solving and critical thinking. Supported by the High-throughput Discovery Science & Inquiry-based Case Studies for Today's Students (HITS) Research Coordination Network, our interdisciplinary team designed, implemented, and assessed two case study modules entitled "You Are What You Eat." Collectively, the case study modules present students with an opportunity to engage in experimental research design and the ethical considerations regarding microbiome research and society. In this manuscript, we provide instructors with tools for adopting or adapting the research design and/or the ethics modules. To date, the case has been implemented using two modalities (remote and in-person) in three courses (Microbiology, Physiology, and Neuroscience), engaging over 200 undergraduate students. Our assessment data demonstrate gains in content knowledge and students' perception of learning following case study implementation. Furthermore, when reflecting on our experiences and student feedback, we identified ways in which the case study could be modified for different settings. In this way, we hope that the "You Are What You Eat" case study modules can be implemented widely by instructors to promote problem solving and critical thinking in the traditional classroom or laboratory setting when discussing next-generation sequencing and/or metagenomics research.},
}

@article {pmid38661357,
year = {2023},
author = {Chen, XX and Zeng, MX and Cai, D and Zhou, HH and Wang, YJ and Liu, Z},
title = {Correlation between APOE4 gene and gut microbiota in Alzheimer's disease.},
journal = {Beneficial microbes},
volume = {14},
number = {4},
pages = {349-360},
doi = {10.1163/18762891-20220116},
pmid = {38661357},
issn = {1876-2891},
mesh = {*Alzheimer Disease/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome ; *Apolipoprotein E4/genetics ; Aged ; Male ; Female ; China ; *Bacteria/genetics/classification/isolation & purification ; Dysbiosis/microbiology ; United States ; Middle Aged ; Aged, 80 and over ; Feces/microbiology ; Case-Control Studies ; },
abstract = {Gut microbiota (GM) dysbiosis has been increasingly associated with Alzheimer's disease (AD). However, the association between APOE4, the most common genetic risk factor for sporadic AD, and GM in AD remains unclear. In this study, we conducted a comparative analysis of the GM of participants from China and the USA, with and without APOE4 genes and with or without AD (67 AD cases, 67 control cases). Our results revealed that the GM alpha diversity was not different between groups (AD_APOE4, Control_APOE4, AD_non-APOE4, and Control_non-APOE4) (419.031 ± 143.631 vs 391.091 ± 126.081, 351.086 ± 169.174 and 386.089 ± 177.200, respectively. P > 0.05). Interestingly, individuals in the AD_APOE4 group had different bacterial compositions and bacterial biomarkers. The Kruskal-Wallis rank sum test indicated that the abundances of many bacterial species in the AD_APOE4 patients differed from those in control individuals, including decreases in unclassified_g__Escherichia-Shigella (1.763 ± 6.73, 4.429 ± 11.13, 8.245 ± 16.55, and 5.69 ± 13.91 in four groups, respectively; P < 0.05), and unclassified_g_Clostridium_sensu_stricto_1 (0.1519 ± 0.348, 2.502 ± 5.913, 0.5146 ± 0.9487, 1.063 ± 3.428 in four groups, respectively; P < 0.05), and increases in gut_metagenome_g_Faecalibacterium (2.885 ± 4.47, 2.174 ± 3.957, 0.5765 ± 1.784, 1.582 ± 2.92 in four groups, respectively. P < 0.01) and unclassified_g_Bacteroides (3.875 ± 3.738, 2.47 ± 2.748, 2.046 ± 3.674, 3.206 ± 3.446 in four groups, respectively; P < 0.05). In the KEGG pathway level 2 analysis, we identified three significant differences in relative abundances of predicted functions between AD_APOE4 and AD_non-APOE4_carrier groups: neurodegenerative diseases (0.0007 ± 0.0005 vs 0.0009 ± 0.0004; P < 0.01), metabolism (0.0240 ± 0.0003 vs 0.0250 ± 0.0003; P < 0.05), and biosynthesis of other secondary metabolites (0.0094 ± 0.0002 vs 0.0090 ± 0.0002; P < 0.05). Receiver operating characteristic curves further demonstrated an area under the curve (AUC) of 0.74 for the discrimination of AD_APOE4_carrier and AD_non-APOE4_carrier individuals.},
}

*Alzheimer Disease/microbiology/genetics
Humans
*Gastrointestinal Microbiome
*Apolipoprotein E4/genetics
Aged
Male
Female
China
*Bacteria/genetics/classification/isolation & purification
Dysbiosis/microbiology
United States
Middle Aged
Aged, 80 and over
Feces/microbiology
Case-Control Studies

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

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

@article {pmid38660910,
year = {2024},
author = {Mao, WY and Lan, JE and Gan, MY and Zhang, XJ and Yu, H and Hu, LY and Zhang, R and Cao, Y and Xiao, ML},
title = {[Moxifloxacin treatment for Mycoplasma hominis meningitis in an extremely preterm infant].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {26},
number = {4},
pages = {432-436},
pmid = {38660910},
issn = {1008-8830},
mesh = {Humans ; *Mycoplasma hominis/isolation & purification ; Infant, Newborn ; Male ; *Infant, Extremely Premature ; *Moxifloxacin/therapeutic use/administration & dosage ; Meningitis, Bacterial/drug therapy/microbiology/diagnosis ; Mycoplasma Infections/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; },
abstract = {The patient, a male newborn, was admitted to the hospital 2 hours after birth due to prematurity (gestational age 27[+5] weeks) and respiratory distress occurring 2 hours postnatally. After admission, the infant developed fever and elevated C-reactive protein levels. On the fourth day after birth, metagenomic next-generation sequencing of cerebrospinal fluid indicated a positive result for Mycoplasma hominis (9 898 reads). On the eighth day, a retest of cerebrospinal fluid metagenomics confirmed Mycoplasma hominis (56 806 reads). The diagnosis of purulent meningitis caused by Mycoplasma hominis was established, and the antibiotic treatment was switched to moxifloxacin [5 mg/(kg·day)] administered intravenously for a total of 4 weeks. After treatment, the patient's cerebrospinal fluid tests returned to normal, and he was discharged as cured on the 76th day after birth. This article focuses on the diagnosis and treatment of neonatal Mycoplasma hominis purulent meningitis, introducing the multidisciplinary diagnosis and treatment of the condition in extremely preterm infants.},
}

Humans
*Mycoplasma hominis/isolation & purification
Infant, Newborn
Male
*Infant, Extremely Premature
*Moxifloxacin/therapeutic use/administration & dosage
Meningitis, Bacterial/drug therapy/microbiology/diagnosis
Mycoplasma Infections/drug therapy/diagnosis
Anti-Bacterial Agents/therapeutic use/administration & dosage

@article {pmid38660245,
year = {2024},
author = {Qian, X and Chen, Z and Ji, XM and Ji, YL and Wang, J and Liu, YC and Zhou, XC and Li, QL and Li, CY and Zhang, AQ},
title = {Qingfei mixture modulates the immune responses in lung cancer through modulating mTOR signaling and gut microbiota-derived short-chain fatty acids.},
journal = {Heliyon},
volume = {10},
number = {8},
pages = {e29404},
pmid = {38660245},
issn = {2405-8440},
abstract = {Lung cancer ranks among the primary contributors to cancer-related fatalities on a global scale. Multiple research investigations have demonstrated that there exists a dysbiosis within the intestinal bacteria and short-chain fatty acids (SCFAs) is linked with immune responses in lung cancer. Qingfei mixture (QFM) has been widely used in treating lung cancer, yet the active ingredients and roles of the QFM on immune responses by targeting gut microbiota remain to be elucidated. The chemical constituents of QFM were qualitatively examined by UPLC/Q-TOF-MS. Additionally, we evaluated the therapeutic impact of the organic substance QFM on lung cancer, aiming to elucidate its mechanisms for improving the tumor-immune microenvironment. Herein, we constructed a Lewis lung carcinoma (LLC)-bearing mice model with QFM treatment to observe tumor growth and immune cell changes. Then, the feces were collected and a combinatory study using metagenomes, non-targeted metabonomics, and targeted metabonomics of SCFAs was performed. In vitro experiments have been conducted to estimate the roles of acetate and sodium propionate in CD8[+] T cells. Furthermore, we treated tumor-bearing mice with QFM, QFM + MHY1485 (an mTOR activator), and QFM + an antibiotic mixture (ABX) to explore the potential therapeutic benefit of regulation of the tumor microenvironment. A total of 96 compounds were obtained from QFM by UPLC/Q-TOF-MS. Besides, the findings demonstrated that QFM exhibited significant efficacy against lung cancer, manifesting in reduced tumor growth and improved immune responses. In investigating its mechanisms, we integrated gut microbiota sequencing and fecal metabolomics, revealing that QFM effectively restored disruptions in gut microbiota and SCFAs in mice with lung cancer. QFM, acetate, or sodium propionate contributed to the up-regulation of IFN-γ, Gzms-B, perforin, IL-17, IL-6, IL-12, TNF-α expressions and decreased HDAC and IL-10 levels in vitro and in vivo. Moreover, MHY1485 and ABX weakened the effects of QFM on immunomodulation. Collectively, these results suggest that QFM may facilitate immune responses in the LLC-bearing mice via regulating the gut microbiota-derived SCFAs at least partially through targeting the mTOR signaling pathway.},
}

@article {pmid38660073,
year = {2024},
author = {Yang, XL and Zhang, JY and Ren, JM},
title = {Successful treatment of Purpureocillium lilacinum pulmonary infection with isavuconazole: A case report.},
journal = {World journal of clinical cases},
volume = {12},
number = {10},
pages = {1772-1777},
pmid = {38660073},
issn = {2307-8960},
abstract = {BACKGROUND: Purpureocillium lilacinum (P. lilacinum) is a saprophytic fungus widespread in soil and vegetation. As a causative agent, it is very rarely detected in humans, most commonly in the skin.

CASE SUMMARY: In this article, we reported the case of a 72-year-old patient with chronic lymphocytic leukemia who was admitted with cough and fever. Computed tomography revealed an infection in the right lower lobe. Bronchoalveolar lavage fluid culture and metagenomic next-generation sequencing were ultimately confirmed to have a pulmonary infection with P. lilacinum. She was eventually discharged with good outcomes after treatment with isavuconazole.

CONCLUSION: Pulmonary infection with P. lilacinum was exceedingly rare. While currently there are no definitive therapeutic agents, there are reports of high resistance to amphotericin B and fluconazole and good sensitivity to second-generation triazoles. The present report is the first known use of isavuconazole for pulmonary P. lilacinum infection. It provides new evidence for the characterization and treatment of clinical P. lilacinum lung infections.},
}

@article {pmid38659981,
year = {2024},
author = {Gand, M and Navickaite, I and Bartsch, LJ and Grützke, J and Overballe-Petersen, S and Rasmussen, A and Otani, S and Michelacci, V and Matamoros, BR and González-Zorn, B and Brouwer, MSM and Di Marcantonio, L and Bloemen, B and Vanneste, K and Roosens, NHCJ and AbuOun, M and De Keersmaecker, SCJ},
title = {Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1336532},
pmid = {38659981},
issn = {1664-302X},
abstract = {Metagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount of data obtained requires performant bioinformatics tools and databases, with intuitive and straightforward interpretation. In this study, based on long-read metagenomics data of chicken fecal samples with a spike-in mock community, we proposed confidence levels for taxonomic identification and AMR gene detection, with interpretation guidelines, to help with the analysis of the output data generated by KMA, a popular k-mer read alignment tool. Additionally, we demonstrated that the completeness and diversity of the genomes present in the reference databases are key parameters for accurate and easy interpretation of the sequencing data. Finally, we explored whether KMA, in a two-step procedure, can be used to link the detected AMR genes to their bacterial host chromosome, both detected within the same long-reads. The confidence levels were successfully tested on 28 metagenomics datasets which were obtained with sequencing of real and spiked samples from fecal (chicken, pig, and buffalo) or food (minced beef and food enzyme products) origin. The methodology proposed in this study will facilitate the analysis of metagenomics sequencing datasets for KMA users. Ultimately, this will contribute to improvements in the rapid diagnosis and surveillance of pathogens and AMR genes in food-producing environments, as prioritized by the EU.},
}

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

@article {pmid38659737,
year = {2024},
author = {Jiang, D and Soo, N and Tan, CY and Dankwa, S and Wang, HY and Theriot, BS and Ardeshir, A and Siddiqui, NY and Van Rompay, KKA and De Paris, K and Permar, SR and Goswami, R and Surana, NK},
title = {Commensal bacteria inhibit viral infections via a tryptophan metabolite.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.21.589969},
pmid = {38659737},
abstract = {There is growing appreciation that commensal bacteria impact the outcome of viral infections, though the specific bacteria and their underlying mechanisms remain poorly understood. Studying a simian-human immunodeficiency virus (SHIV)-challenged cohort of pediatric nonhuman primates, we bioinformatically associated Lactobacillus gasseri and the bacterial family Lachnospiraceae with enhanced resistance to infection. We experimentally validated these findings by demonstrating two different Lachnospiraceae isolates, Clostridium immunis and Ruminococcus gnavus, inhibited HIV replication in vitro and ex vivo. Given the link between tryptophan catabolism and HIV disease severity, we found that an isogenic mutant of C. immunis that lacks the aromatic amino acid aminotransferase (ArAT) gene, which is key to metabolizing tryptophan into 3-indolelactic acid (ILA), no longer inhibits HIV infection. Intriguingly, we confirmed that a second commensal bacterium also inhibited HIV in an ArAT-dependent manner, thus establishing the generalizability of this finding. In addition, we found that purified ILA inhibited HIV infection by agonizing the aryl hydrocarbon receptor (AhR). Given that the AhR has been implicated in the control of multiple viral infections, we demonstrated that C. immunis also inhibited human cytomegalovirus (HCMV) infection in an ArAT-dependent manner. Importantly, metagenomic analysis of individuals at-risk for HIV revealed that those who ultimately acquired HIV had a lower fecal abundance of the bacterial ArAT gene compared to individuals who did not, which indicates our findings translate to humans. Taken together, our results provide mechanistic insights into how commensal bacteria decrease susceptibility to viral infections. Moreover, we have defined a microbiota-driven antiviral pathway that offers the potential for novel therapeutic strategies targeting a broad spectrum of viral pathogens.},
}

@article {pmid38659344,
year = {2024},
author = {Wang, L and Zhu, Y and Zhao, C and Zhao, M and Li, Z and Xu, W and Mu, W},
title = {Engineering Escherichia coli for Highly Efficient Biosynthesis of Lacto-N-difucohexaose II through De Novo GDP-l-fucose Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c01264},
pmid = {38659344},
issn = {1520-5118},
abstract = {Lacto-N-difucohexaose II (LNDFH II) is a typical fucosylated human milk oligosaccharide and can be enzymatically produced from lacto-N-tetraose (LNT) by a specific α1,3/4-fucosyltransferase from Helicobacter pylori DMS 6709, referred to as FucT14. Previously, we constructed an engineered Escherichia coli BL21(DE3) with a single plasmid for highly efficient biosynthesis of LNT. In this study, two additional plasmids harboring the de novo GDP-L-fucose pathway module and FucT14, respectively, were further introduced to construct the strain for successful biosynthesis of LNDFH II. FucT14 was actively expressed, and the engineered strain produced LNDFH II as the major product, lacto-N-fucopentaose (LNFP) V as the minor product, and a trace amount of LNFP II and 3-fucosyllactose as very minor products. Additional expression of the α1,3-fucosyltransferase FutM1 from a Bacteroidaceae bacterium from the gut metagenome could obviously enhance the LNDFH II biosynthesis. After optimization of induction conditions, the maximum titer reached 3.011 g/L by shake-flask cultivation. During the fed-batch cultivation, LNDFH II was highly efficiently produced with the highest titer of 18.062 g/L and the productivity yield of 0.301 g/L·h.},
}

@article {pmid38659188,
year = {2024},
author = {Pérez-Castillo, ÍM and Sabag-Daigle, A and López-Chicharro, J and Mihic, N and Rueda, R and Bouzamondo, H},
title = {The athlete gut microbiota: state of the art and practical guidance.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-30},
doi = {10.1163/18762891-bja00007},
pmid = {38659188},
issn = {1876-2891},
abstract = {The gut microbiota has been proposed to grant the athlete a metabolic advantage that might be key when optimising performance. While a taxonomic core set of microorganisms characterising the athlete's gut microbiota has not been delineated, some compositional features might be associated with improved metabolic efficiency, which appears to be driven by the production of bacterial metabolites, such as short-chain fatty acids. Not only long-term exercise but also dietary patterns associated with high-level sports practice contribute to this microbial environment, yet isolating the impact of individual dietary components is challenging. The present review synthetises the available evidence on the compositional aspects of the athlete's gut microbiota, discusses mechanisms involved in the bidirectional association between exercise and the gut environment, and evaluates the role of athletes' diet in this interplay. Additionally, a practical approach to indicators commonly reported in metagenomic and metabolomic analyses is provided to explore how these insights can translate to support dietary protocols.},
}

@article {pmid38659008,
year = {2024},
author = {Santos, JD and Sobral, D and Pinheiro, M and Isidro, J and Bogaardt, C and Pinto, M and Eusébio, R and Santos, A and Mamede, R and Horton, DL and Gomes, JP and , and Borges, V},
title = {INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {61},
pmid = {38659008},
issn = {1756-994X},
support = {101102733//EU4Health Programme (DURABLE)/ ; 773830//European Union's Horizon 2020 Research and Innovation program/ ; EU4H-2022-DGA-MS-IBA-1//EU4H programme (GENEO)/ ; },
mesh = {*Metagenomics/methods ; Humans ; *SARS-CoV-2/genetics/classification ; *Genome, Viral ; *Software ; *COVID-19/virology ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Internet ; Genomics/methods ; },
abstract = {BACKGROUND: Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification.

RESULTS: The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis.

CONCLUSIONS: The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).},
}

*Metagenomics/methods
Humans
*SARS-CoV-2/genetics/classification
*Genome, Viral
*Software
*COVID-19/virology
*Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
Internet
Genomics/methods

@article {pmid38658858,
year = {2024},
author = {Liu, C and Liu, F and Nie, D and Xiao, Y and Wu, W and Jia, Y and Jin, L and Qiao, N and Cai, K and Ru, S and Liu, X and Song, Y and Xu, J and Cao, L and Gui, S},
title = {Gut microbiota composition and metabolic characteristics in patients with Craniopharyngioma.},
journal = {BMC cancer},
volume = {24},
number = {1},
pages = {521},
pmid = {38658858},
issn = {1471-2407},
mesh = {Humans ; *Craniopharyngioma/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *Pituitary Neoplasms/metabolism/microbiology ; *Feces/microbiology ; Middle Aged ; Case-Control Studies ; Young Adult ; Adolescent ; Metabolomics/methods ; Metagenomics/methods ; Metabolome ; },
abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiota is associated with various intracranial neoplastic diseases. It has been observed that alterations in the gut microbiota are present in gliomas, meningiomas, and pituitary neuroendocrine tumors (Pit-NETs). However, the correlation between gut microbiota and craniopharyngioma (CP), a rare embryonic malformation tumor in the sellar region, has not been previously mentioned. Consequently, this study aimed to investigate the gut microbiota composition and metabolic patterns in CP patients, with the goal of identifying potential therapeutic approaches.

METHODS: We enrolled 15 medication-free and non-operated patients with CP and 15 healthy controls (HCs), conducting sequential metagenomic and metabolomic analyses on fecal samples to investigate changes in the gut microbiota of CP patients.

RESULTS: The composition of gut microbiota in patients with CP compared to HCs show significant discrepancies at both the genus and species levels. The CP group exhibits greater species diversity. And the metabolic patterns between the two groups vary markedly.

CONCLUSIONS: The gut microbiota composition and metabolic patterns in patients with CP differ significantly from the healthy population, presenting potential new therapeutic opportunities.},
}

Humans
*Craniopharyngioma/metabolism
*Gastrointestinal Microbiome
Male
Female
Adult
*Pituitary Neoplasms/metabolism/microbiology
*Feces/microbiology
Middle Aged
Case-Control Studies
Young Adult
Adolescent
Metabolomics/methods
Metagenomics/methods
Metabolome

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

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

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

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

@article {pmid38658176,
year = {2024},
author = {Ramachandran, P and Grose, C},
title = {Serious neurological adverse events in immunocompetent children and adolescents caused by viral reactivation in the years following varicella vaccination.},
journal = {Reviews in medical virology},
volume = {34},
number = {3},
pages = {e2538},
doi = {10.1002/rmv.2538},
pmid = {38658176},
issn = {1099-1654},
support = {AI153817//National Institutes of Health Bethesda/ ; },
mesh = {Humans ; *Chickenpox Vaccine/adverse effects/administration & dosage/immunology ; Child ; Adolescent ; Virus Activation/drug effects ; Vaccination/adverse effects ; Child, Preschool ; Herpesvirus 3, Human/immunology ; Acyclovir/therapeutic use/adverse effects ; Antiviral Agents/therapeutic use/adverse effects ; Meningitis, Viral/virology/etiology ; Chickenpox/prevention & control/virology ; Male ; Nervous System Diseases/virology/etiology ; Female ; },
abstract = {Serious adverse events following vaccination include medical complications that require hospitalisation. The live varicella vaccine that was approved by the Food and Drug Administration in the United States in 1995 has an excellent safety record. Since the vaccine is a live virus, adverse events are more common in immunocompromised children who are vaccinated inadvertently. This review includes only serious adverse events in children considered to be immunocompetent. The serious adverse event called varicella vaccine meningitis was first reported in a hospitalised immunocompetent child in 2008. When we carried out a literature search, we found 15 cases of immunocompetent children and adolescents with varicella vaccine meningitis; the median age was 11 years. Eight of the children had received two varicella vaccinations. Most of the children also had a concomitant herpes zoster rash, although three did not. The children lived in the United States, Greece, Germany, Switzerland, and Japan. During our literature search, we found five additional cases of serious neurological events in immunocompetent children; these included 4 cases of progressive herpes zoster and one case of acute retinitis. Pulses of enteral corticosteroids as well as a lack of herpes simplex virus antibody may be risk factors for reactivation in immunocompetent children. All 20 children with adverse events were treated with acyclovir and recovered; 19 were hospitalised and one child was managed as an outpatient. Even though the number of neurological adverse events remains exceedingly low following varicella vaccination, we recommend documentation of those caused by the vaccine virus.},
}

Humans
*Chickenpox Vaccine/adverse effects/administration & dosage/immunology
Child
Adolescent
Virus Activation/drug effects
Vaccination/adverse effects
Child, Preschool
Herpesvirus 3, Human/immunology
Acyclovir/therapeutic use/adverse effects
Antiviral Agents/therapeutic use/adverse effects
Meningitis, Viral/virology/etiology
Chickenpox/prevention & control/virology
Male
Nervous System Diseases/virology/etiology
Female

@article {pmid38657817,
year = {2024},
author = {Gong, W and Guo, L and Huang, C and Xie, B and Jiang, M and Zhao, Y and Zhang, H and Wu, Y and Liang, H},
title = {A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172601},
doi = {10.1016/j.scitotenv.2024.172601},
pmid = {38657817},
issn = {1879-1026},
abstract = {Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.},
}

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

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

@article {pmid38658654,
year = {2024},
author = {Han, G and Huang, T and Liu, X and Liu, R},
title = {Bacteriophage EPP-1, a potential antibiotic alternative for controlling edwardsiellosis caused by Edwardsiella piscicida while mitigating drug-resistant gene dissemination.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9399},
pmid = {38658654},
issn = {2045-2322},
support = {42377120//the National Natural Science Foundation of China/ ; },
abstract = {Edwardsiella piscicida causes significant economic losses to the aquaculture industry worldwide. Phage-based biocontrol methods are experiencing a renaissance because of the spread of drug-resistant genes and bacteria resulting from the heavy use of antibiotics. Here, we showed that the novel Edwardsiella phage EPP-1 could achieve comparable efficacy to florfenicol using a zebrafish model of Edwardsiella piscicida infection and could reduce the content of the floR resistance gene in zebrafish excreta. Specifically, phage EPP-1 inhibited bacterial growth in vitro and significantly improved the zebrafish survival rate in vivo (P = 0.0035), achieving an efficacy comparable to that of florfenicol (P = 0.2304). Notably, integrating the results of 16S rRNA sequencing, metagenomic sequencing, and qPCR, although the effects of phage EPP-1 converged with those of florfenicol in terms of the community composition and potential function of the zebrafish gut microbiota, it reduced the floR gene content in zebrafish excreta and aquaculture water. Overall, our study highlights the feasibility and safety of phage therapy for edwardsiellosis control, which has profound implications for the development of antibiotic alternatives to address the antibiotic crisis.},
}

@article {pmid38658559,
year = {2024},
author = {Chen, KH and Feng, J and Bodelier, PLE and Yang, Z and Huang, Q and Delgado-Baquerizo, M and Cai, P and Tan, W and Liu, YR},
title = {Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3471},
pmid = {38658559},
issn = {2041-1723},
support = {32071595//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371731//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and [13]CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, [13]CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating [13]C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of [13]C-metagenome-assembled genomes and [13]C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.},
}

@article {pmid38658525,
year = {2024},
author = {Arthofer, P and Panhölzl, F and Delafont, V and Hay, A and Reipert, S and Cyran, N and Wienkoop, S and Willemsen, A and Sifaoui, I and Arberas-Jiménez, I and Schulz, F and Lorenzo-Morales, J and Horn, M},
title = {A giant virus infecting the amoeboflagellate Naegleria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3307},
pmid = {38658525},
issn = {2041-1723},
support = {P37198-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 891572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 101039843//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.},
}

@article {pmid38657818,
year = {2024},
author = {Stewart, DI and Vasconcelos, EJR and Burke, IT and Baker, A},
title = {Metagenomes from microbial populations beneath a chromium waste tip give insight into the mechanism of Cr (VI) reduction.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172507},
doi = {10.1016/j.scitotenv.2024.172507},
pmid = {38657818},
issn = {1879-1026},
abstract = {Dumped Chromium Ore Processing Residue (COPR) at legacy sites poses a threat to health through leaching of toxic Cr(VI) into groundwater. Previous work implicates microbial activity in reducing Cr(VI) to less mobile and toxic Cr(III), but the mechanism has not been explored. To address this question a combined metagenomic and geochemical study was undertaken. Soil samples from below the COPR waste were used to establish anaerobic microcosms which were challenged with Cr(VI), with or without acetate as an electron donor, and incubated for 70 days. Cr was rapidly reduced in both systems, which also reduced nitrate, nitrite then sulfate, but this sequence was accelerated in the acetate amended microcosms. 16S rRNA gene sequencing revealed that the original soil sample was diverse but both microcosm systems became less diverse by the end of the experiment. A high proportion of 16S rRNA gene reads and metagenome-assembled genomes (MAGs) with high completeness could not be taxonomically classified, highlighting the distinctiveness of these alkaline Cr impacted systems. Examination of the coding capacity revealed widespread capability for metal tolerance and Fe uptake and storage, and both populations possessed metabolic capability to degrade a wide range of organic molecules. The relative abundance of genes for fatty acid degradation was 4× higher in the unamended compared to the acetate amended system, whereas the capacity for dissimilatory sulfate metabolism was 3× higher in the acetate amended system. We demonstrate that naturally occurring in situ bacterial populations have the metabolic capability to couple acetate oxidation to sequential reduction of electron acceptors which can reduce Cr(VI) to less mobile and toxic Cr(III), and that microbially produced sulfide may be important in reductive precipitation of chromate. This capability could be harnessed to create a Cr(VI) trap-zone beneath COPR tips without the need to disturb the waste.},
}

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

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

@article {pmid38656275,
year = {2024},
author = {Divilov, K},
title = {Whole-genome assembly of a novel invertebrate herpesvirus from the gastropod Babylonia areolata.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001237},
pmid = {38656275},
issn = {2057-5858},
mesh = {Animals ; *Genome, Viral ; *Gastropoda/virology ; *Phylogeny ; *Herpesviridae/genetics/classification ; Whole Genome Sequencing/methods ; Genomics/methods ; Synteny ; },
abstract = {Molluscan herpesviruses cause disease in species of major importance to aquaculture and are the only known herpesviruses to infect invertebrates, which lack an adaptive immune system. Understanding the evolution of malacoherpesviruses in relation to their hosts will likely require comparative genomic studies on multiple phylogenetic scales. Currently, only two malacoherpesvirus species have genomes that have been fully assembled, which limits the ability to perform comparative genomic studies on this family of viruses. In the present study, we fully assemble a herpesvirus from Illumina and Nanopore sequence data that were previously used to assemble the genome of the gastropod Babylonia areolata. We tentatively assign this novel herpesvirus to the genus Aurivirus within the family Malacoherpesviridae based on a phylogenetic analysis of DNA polymerase. While structurally similar to other malacoherpesvirus genomes, a synteny analysis of the novel herpesvirus with another Aurivirus species indicates that genomic rearrangements might be an important process in the evolution of this genus. We anticipate that future complete assemblies of malacoherpesviruses will be a valuable resource in comparative herpesvirus research.},
}

Animals
*Genome, Viral
*Gastropoda/virology
*Phylogeny
*Herpesviridae/genetics/classification
Whole Genome Sequencing/methods
Genomics/methods
Synteny

@article {pmid38655538,
year = {2024},
author = {Tay, HW and Tay, KS},
title = {Future directions for early detection of fracture related infections.},
journal = {Journal of orthopaedics},
volume = {55},
number = {},
pages = {64-68},
pmid = {38655538},
issn = {0972-978X},
abstract = {INTRODUCTION: Fracture related infection (FRI) refers to pathogens infecting a fracture site and hence impeding fracture healing. It is a significant complication that carries substantial disease burden and socio-economic costs, but has had limited scientific development. Hence, this paper will review the existing strategies for early detection of FRI, in the form of serum markers, molecular diagnostics and imaging modalities, and further discuss potential future directions for improved detection of FRI.

The Anti-infection Global Expert Committee (AIGEC) developed a consensus definition for FRI in 2017, which includes confirmatory and suggestive criteria for diagnosis of FRI. Existing strategies for diagnosis include clinical, laboratory, histopathological, microbiological and radiological investigations.

With increasing recognition of FRI, early detection is crucial for early treatment to be enforced. We have identified potential areas for future development in diagnostics for early detection of FRI, which are discussed in this manuscript. They include inflammatory cytokines, serum calcium levels, platelet count, improved management of histopathological and microbiological specimens, metagenomics, wound biomarkers, gut microbiota analysis, and novel imaging technologies.},
}

@article {pmid38655084,
year = {2024},
author = {Orf, GS and Ahouidi, AD and Mata, M and Diedhiou, C and Mboup, A and Padane, A and Manga, NM and Dela-Del Lawson, AT and Averhoff, F and Berg, MG and Cloherty, GA and Mboup, S},
title = {Next-generation sequencing survey of acute febrile illness in Senegal (2020-2022).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1362714},
pmid = {38655084},
issn = {1664-302X},
abstract = {INTRODUCTION: Acute febrile illnesses (AFI) in developing tropical and sub-tropical nations are challenging to diagnose due to the numerous causes and non-specific symptoms. The proliferation of rapid diagnostic testing and successful control campaigns against malaria have revealed that non-Plasmodium pathogens still contribute significantly to AFI burden. Thus, a more complete understanding of local trends and potential causes is important for selecting the correct treatment course, which in turn will reduce morbidity and mortality. Next-generation sequencing (NGS) in a laboratory setting can be used to identify known and novel pathogens in individuals with AFI.

METHODS: In this study, plasma was collected from 228 febrile patients tested negative for malaria at clinics across Senegal from 2020-2022. Total nucleic acids were extracted and converted to metagenomic NGS libraries. To identify viral pathogens, especially those present at low concentration, an aliquot of each library was processed with a viral enrichment panel and sequenced. Corresponding metagenomic libraries were also sequenced to identify non-viral pathogens.

RESULTS AND DISCUSSION: Sequencing reads for pathogens with a possible link to febrile illness were identified in 51/228 specimens, including (but not limited to): Borrelia crocidurae (N = 7), West Nile virus (N = 3), Rickettsia felis (N = 2), Bartonella quintana (N = 1), human herpesvirus 8 (N = 1), and Saffold virus (N = 1). Reads corresponding to Plasmodium falciparum were detected in 19 specimens, though their presence in the cohort was likely due to user error of rapid diagnostic testing or incorrect specimen segregation at the clinics. Mosquito-borne pathogens were typically detected just after the conclusion of the rainy season, while tick-borne pathogens were mostly detected before the rainy season. The three West Nile virus strains were phylogenetically characterized and shown to be related to both European and North American clades. Surveys such as this will increase the understanding of the potential causes of non-malarial AFI, which may help inform diagnostic and treatment options for clinicians who provide care to patients in Senegal.},
}

@article {pmid38655082,
year = {2024},
author = {Thøgersen, MS and Zervas, A and Stougaard, P and Ellegaard-Jensen, L},
title = {Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1358787},
pmid = {38655082},
issn = {1664-302X},
abstract = {The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.},
}

@article {pmid38654702,
year = {2024},
author = {Hewel, C and Schmidt, H and Runkel, S and Kohnen, W and Schweiger-Seemann, S and Michel, A and Bikar, SE and Lieb, B and Plachter, B and Hankeln, T and Linke, M and Gerber, S},
title = {Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case.},
journal = {Journal of medical virology},
volume = {96},
number = {5},
pages = {e29610},
doi = {10.1002/jmv.29610},
pmid = {38654702},
issn = {1096-9071},
mesh = {Humans ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Mpox (monkeypox)/epidemiology/virology ; *Monkeypox virus/genetics/isolation & purification ; *Whole Genome Sequencing/methods ; Nanopores ; DNA, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. In addition to that, only Nanopore data allowed us to resolve the entire monkeypox virus genome, with respect to two structural variants belonging to the genes OPG015 and OPG208. These SVs in important host range genes seem stable throughout the outbreak and are frequently misassembled and/or misannotated due to the prevalence of short read sequencing or short read first assembly. Ideally, standalone standard Illumina sequencing should not be used for Monkeypox WGS and de novo assembly, since it will obfuscate the structure of the genome, which has an impact on the quality and completeness of the genomes deposited in public databases and thus possibly on the ability to evaluate the complete genetic reason for the host range change of monkeypox in the current pandemic.},
}

Humans
*Genome, Viral/genetics
*Metagenomics/methods
*Nanopore Sequencing/methods
*Mpox (monkeypox)/epidemiology/virology
*Monkeypox virus/genetics/isolation & purification
*Whole Genome Sequencing/methods
Nanopores
DNA, Viral/genetics
High-Throughput Nucleotide Sequencing/methods

@article {pmid38653968,
year = {2024},
author = {Serra Moncadas, L and Hofer, C and Bulzu, PA and Pernthaler, J and Andrei, AS},
title = {Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3421},
pmid = {38653968},
issn = {2041-1723},
support = {PZ00P3_193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Fresh Water/microbiology ; *Phylogeny ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Evolution, Molecular ; Genome Size ; Proteome/genetics/metabolism ; },
abstract = {The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.},
}

*Genome, Bacterial
*Bacteria/genetics/classification
*Fresh Water/microbiology
*Phylogeny
*Adaptation, Physiological/genetics
Metagenomics/methods
Evolution, Molecular
Genome Size
Proteome/genetics/metabolism

@article {pmid38653418,
year = {2024},
author = {Yu, T and Liu, Z and Hu, B and Zhu, L},
title = {Field-based investigation reveals selective enrichment of companion microbes in vegetables leading to specific accumulation of antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172636},
doi = {10.1016/j.scitotenv.2024.172636},
pmid = {38653418},
issn = {1879-1026},
abstract = {Vegetables capture antibiotic resistance genes (ARGs) from the soil and then pass them on to consumers through the delivery chain and food chain, and are therefore the key node that may increase the risk of human exposure to ARGs. This study investigates the patterns and driving forces behind the transmission of ARGs from soil to vegetables by the commonly planted cash crops in the coastal region of southern China, i.e. broccoli, pumpkin, and broad bean, to investigate. The study used metagenomic data to reveal the microbial and ARGs profiles of various vegetables and the soil they are grown. The results indicate significant differences in the accumulation of ARGs among different vegetables harvested in the same area at the same time frame, and the ARGs accumulation ability of the three vegetables was in the order of broccoli, broad bean, and pumpkin. In addition, broccoli collected the highest number of ARGs in types (n = 14), while pumpkin (n = 13) does not obtain trimethoprim resistance genes and broad beans (n = 10) do not obtain chloramphenicol, fosmidomycin, quinolone, rifamycin, or trimethoprim resistance genes. Host tracking analysis shows a strong positive correlation (|rho| > 0.8, p < 0.05) between enriched ARGs and plant companion microbes. Enrichment analysis of metabolic pathways of companion microbes shows that vegetables exhibit a discernible enrichment of companion microbes, with significant differences among vegetables. This phenomenon is primarily due to the screening of carbohydrate metabolism capabilities among companion microbes and leads varied patterns of ARGs that spread from the soil to vegetables. This offers a novel insight into the intervention of foodborne transmission of ARGs.},
}

@article {pmid38653417,
year = {2024},
author = {Haobo, G and Zhaofeng, C and Zhiyong, L and Qipeng, D and Mingdeng, X and Tong, Z and Zhenchi, L and Zijuan, Z and Yunjiang, Y},
title = {Enhanced humification of full-scale apple wood and cow manure by promoting lignocellulose degradation via biomass pretreatments.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172646},
doi = {10.1016/j.scitotenv.2024.172646},
pmid = {38653417},
issn = {1879-1026},
abstract = {Agroforestry waste and cow manure pollute the environment, of which, agroforestry waste is difficult to degrade. Compost is an effective way to dispose agroforestry waste; however, the low degradation efficiency of lignocellulose in agroforestry waste affects the process of composting humification. This study investigated lignocellulose degradation and composting humification in full-size apple wood and cow manure composting processes by applying different pretreatments (acidic, alkaline, and high-temperature) to apple wood. Simultaneously, physicochemical characterization and metagenome sequencing were combined to analyze the function of carbohydrate-active enzymes database (CAZy). Therefore, microbial communities and functions were linked during the composting process and the lignocellulose degradation mechanism was elaborated. The results showed that the addition of apple wood increased the compost humus (HS) yield, and pretreatment of apple wood enhanced the lignocellulose degradation during composting processes. In addition, pretreatment improved the physicochemical properties, such as temperature, pH, electric conductivity (EC), ammonium nitrogen (NH4[+]), and nitrate nitrogen (NO3[-]) in the compost, of which, acid treated apple wood compost (AcAWC) achieved the highest temperature of 58.4 °C, effectively promoting nitrification with NO3[-] ultimately reaching 0.127 g/kg. In all composts, microbial networks constructed a high proportion of positively correlated connections, and microorganisms promoted the composting process through cooperation. The proportions of glycosyltransferase (GT) and glycoside hydrolase (GH) promoted the separation and degradation of lignocellulose during composting to form HS. Notably, the adverse effects of the alkali-treated apple wood compost on bacteria were greater. AcAWC showed significant correlations between bacterial and fungal communities and both lignin and hemicellulose, and had more biomarkers associated with lignocellulose degradation and humification. The lignin degradation rate was 24.57 % and the HS yield increased by 27.49 %. Therefore, AcAWC has been confirmed to enhance lignocellulose degradation and promote compost humification by altering the properties of the apple wood and establishing a richer microbial community.},
}

@article {pmid38652444,
year = {2024},
author = {Li, D and Wang, H and Chen, N and Jiang, H and Chen, N},
title = {Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38652444},
issn = {1678-4405},
support = {WXBSH2021001//Postdoctoral Science Foundation of West Anhui University/ ; WGKQ2021021//The High-level Talent Project of West Anhui University/ ; GXYQ2020127//the Provincial Level Nature Science Foundation of Anhui Education Department/ ; 2022AH010090//Anhui Scientific Research and Innovation Team of Quality Evaluation and Improvement of Traditional Chinese Medicine/ ; KJ2021A0924//Natural Science Research Project of Anhui Provincial Colleges and Universities/ ; },
abstract = {To investigate the impact of Poa alpigena Lindm on rhizosphere and bulk soil microorganisms in Haixin Mountain, Qinghai Lake, this study employed metagenomics technology to analyze the microbial communities of the samples. Results showed that 65 phyla, 139 classes, 278 orders, 596 families, 2376 genera, and 5545 species of soil microorganisms were identified from rhizosphere and bulk soil samples. Additionally, a microbial gene library specific to Poa alpigena Lindm was established for Qinghai Lake. Through α-diversity analysis, the richness and diversity of bulk microorganisms both significantly had a higher value than that in rhizosphere soil. The indicator microorganisms of rhizosphere and bulk soil at class level were Actinobacteria and Alphaproteobacteria, respectively. KEGG pathway analysis indicated that Carotenoid biosynthesis, Starch and sucrose metabolism, Bacterial chemotaxis, MAPK signaling pathway, Terpenoid backbone biosynthesis, and vancomycin resistance were the key differential metabolic pathways of rhizosphere soil microorganisms; in contrast, in bulk soil, the key differential metabolic were Benzoate degradation, Glycolysis gluconeogenesis, Aminobenzoate degradation, ABC transporters, Glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, Degradation of aromatic compounds, Methane metabolism, Pyruvate metabolism and Microbial metabolism diverse environments. Our results indicated that Poa alpigena Lindm rhizosphere soil possessed selectivity for microorganisms in Qinghai Lake Haixin Mountain, and the rhizosphere soil also provided a suitable survival environment for microorganisms.},
}

@article {pmid38651930,
year = {2024},
author = {Reygner, J and Delannoy, J and Barba-Goudiaby, M-T and Gasc, C and Levast, B and Gaschet, E and Ferraris, L and Paul, S and Kapel, N and Waligora-Dupriet, A-J and Barbut, F and Thomas, M and Schwintner, C and Laperrousaz, B and Corvaïa, N},
title = {Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0001624},
doi = {10.1128/aem.00016-24},
pmid = {38651930},
issn = {1098-5336},
abstract = {Growing evidence demonstrates the key role of the gut microbiota in human health and disease. The recent success of microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on its potential in conditions associated with gut dysbiosis, such as acute graft-versus-host disease, intestinal bowel diseases, neurodegenerative diseases, or even cancer. However, the difficulty in defining a "good" donor as well as the intrinsic variability of donor-derived products' taxonomic composition limits the translatability and reproducibility of these studies. Thus, the pooling of donors' feces has been proposed to homogenize product composition and achieve higher taxonomic richness and diversity. In this study, we compared the metagenomic profile of pooled products to corresponding single donor-derived products. We demonstrated that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria known to produce anti-inflammatory short chain fatty acids compared to single donor-derived products. We then evaluated pooled products' efficacy compared to corresponding single donor-derived products in Salmonella and C. difficile infectious mouse models. We were able to demonstrate that pooled products decreased pathogenicity by inducing a structural change in the intestinal microbiota composition. Single donor-derived product efficacy was variable, with some products failing to control disease progression. We further performed in vitro growth inhibition assays of two extremely drug-resistant bacteria, Enterococcus faecium vanA and Klebsiella pneumoniae oxa48, supporting the use of pooled microbiotherapies. Altogether, these results demonstrate that the heterogeneity of donor-derived products is corrected by pooled fecal microbiotherapies in several infectious preclinical models.IMPORTANCEGrowing evidence demonstrates the key role of the gut microbiota in human health and disease. Recent Food and Drug Administration approval of fecal microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on their potential to treat pathological conditions associated with gut dysbiosis. In this study, we combined metagenomic analysis with in vitro and in vivo studies to compare the efficacy of pooled microbiotherapy products to corresponding single donor-derived products. We demonstrate that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria compared to single donor-derived products. We further reveal that pooled products decreased Salmonella and Clostridioides difficile pathogenicity in mice, while single donor-derived product efficacy was variable, with some products failing to control disease progression. Altogether, these findings support the development of pooled microbiotherapies to overcome donor-dependent treatment efficacy.},
}

@article {pmid38651915,
year = {2024},
author = {Jia, C and Wu, C and Li, Y and Wang, S and Liu, J and Liu, J and Su, H and Tian, X and Li, J},
title = {Metagenome-assembled genomes from enrichment cultures grown on xenobiotic solvents.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0010724},
doi = {10.1128/mra.00107-24},
pmid = {38651915},
issn = {2576-098X},
abstract = {Microbes play a significant role in the cleanup of xenobiotic contaminants. Based on metagenomes derived from long-term enrichment cultures grown on xenobiotic solvents, we report 166 metagenome-assembled genomes, of which 137 are predicted to be more than 90% complete. These genomes broaden the representation of xenobiotic degraders.},
}

@article {pmid38651910,
year = {2024},
author = {Rodríguez-Ramos, J and Nicora, CD and Purvine, SO and Borton, MA and McGivern, BB and Hoyt, DW and Lipton, MS and Wrighton, KC},
title = {Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0003324},
doi = {10.1128/mra.00033-24},
pmid = {38651910},
issn = {2576-098X},
abstract = {Rivers are critical ecosystems that impact global biogeochemical cycles. Nonetheless, a mechanistic understanding of river microbial metabolisms and their influences on geochemistry is lacking. Here, we announce metaproteomes of river sediments that are paired with metagenomes and metabolites, enabling an understanding of the microbial underpinnings of river respiration.},
}

@article {pmid38651859,
year = {2024},
author = {Cai, X and Yi, P and Chen, X and Wu, J and Lan, G and Li, S and Luo, S and Huang, F and Huang, J and Shen, P},
title = {Intake of compound probiotics accelerates the construction of immune function and gut microbiome in Holstein calves.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0190923},
doi = {10.1128/spectrum.01909-23},
pmid = {38651859},
issn = {2165-0497},
abstract = {UNLABELLED: Acquired immunity is an important way to construct the intestinal immune barrier in mammals, which is almost dependent on suckling. To develop a new strategy for accelerating the construction of gut microbiome, newborn Holstein calves were continuously fed with 40 mL of compound probiotics (containing Lactobacillus plantarum T-14, Enterococcus faecium T-11, Saccharomyces cerevisiae T-209, and Bacillus licheniformis T-231) per day for 60 days. Through diarrhea rate monitoring, immune index testing, antioxidant capacity detection, and metagenome sequencing, the changes in diarrhea incidence, average daily gain, immune index, and gut microbiome of newborn calves within 60 days were investigated. Results indicated that feeding the compound probiotics reduced the average diarrhea rate of calves by 42.90%, increased the average daily gain by 43.40%, raised the antioxidant indexes of catalase, superoxide dismutase, total antioxidant capacity, and Glutathione peroxidase by 22.81%, 6.49%, 8.33%, and 13.67%, respectively, and increased the immune indexes of IgA, IgG, and IgM by 10.44%, 4.85%, and 6.12%, respectively. Moreover, metagenome sequencing data showed that feeding the compound probiotics increased the abundance of beneficial strains (e.g., Lactococcus lactis and Bacillus massionigeriensis) and decreased the abundance of some harmful strains (e.g., Escherichia sp. MOD1-EC5189 and Mycobacterium brisbane) in the gut microbiome of calves, thus contributing to accelerating the construction of healthy gut microbiome in newborn Holstein calves.

IMPORTANCE: The unstable gut microbiome and incomplete intestinal function of newborn calves are important factors for the high incidence of early diarrhea. This study presents an effective strategy to improve the overall immunity and gut microbiome in calves and provides new insights into the application of compound probiotics in mammals.},
}