@article {pmid39039015,
year = {2024},
author = {Vanharanta, M and Santoro, M and Villena-Alemany, C and Piiparinen, J and Piwosz, K and Grossart, HP and Labrenz, M and Spilling, K},
title = {Microbial remineralization processes during post-spring-bloom with excess phosphate available in the northern Baltic Sea.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae103},
pmid = {39039015},
issn = {1574-6941},
abstract = {The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the south-west Finnish archipelago, we examined nitrogen, phosphorus and carbon acquiring extracellular enzyme activities in three size fractions (<0.2 µm, 0.2-3 µm, and >3 µm), bacterial abundance, production, community composition and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters towards the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.},
}

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

@article {pmid39030520,
year = {2024},
author = {Joo, M and Nam, S},
title = {Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {268},
pmid = {39030520},
issn = {1471-2180},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Adolescent ; *RNA, Ribosomal, 16S/genetics ; *Obesity/microbiology/immunology ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; *Phylogeny ; Inflammatory Bowel Diseases/microbiology/immunology ; Crohn Disease/microbiology/immunology ; Colitis, Ulcerative/microbiology/immunology ; Dysbiosis/microbiology ; Prevotella/genetics/classification/isolation & purification ; Faecalibacterium prausnitzii/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents.

METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs.

RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence.

CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.},
}

Humans
*Gastrointestinal Microbiome/genetics
Adolescent
*RNA, Ribosomal, 16S/genetics
*Obesity/microbiology/immunology
Female
Male
*Bacteria/classification/genetics/isolation & purification
*Phylogeny
Inflammatory Bowel Diseases/microbiology/immunology
Crohn Disease/microbiology/immunology
Colitis, Ulcerative/microbiology/immunology
Dysbiosis/microbiology
Prevotella/genetics/classification/isolation & purification
Faecalibacterium prausnitzii/genetics
Feces/microbiology

@article {pmid38916294,
year = {2024},
author = {Chadwick, GL and Dury, GA and Nayak, DD},
title = {Physiological and transcriptomic response to methyl-coenzyme M reductase limitation in Methanosarcina acetivorans.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0222023},
pmid = {38916294},
issn = {1098-5336},
support = {//Searle Scholars Program (SSP)/ ; Beckman Young Investigator Award//Arnold and Mabel Beckman Foundation (AMBF)/ ; Simons Early Career Investigator in Marine Microbial Ecology and Evolution//Simons Foundation (SF)/ ; Packard Fellowship in Science and Engineering//David and Lucile Packard Foundation (PF)/ ; Chan-Zuckerberg Biohub - San Francisco Investigator//Chan Zuckerberg Initiative (CZI)/ ; 5T32GM06698-14//HHS | National Institutes of Health (NIH)/ ; //Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley (MIBRS)/ ; },
mesh = {*Methanosarcina/genetics/enzymology/metabolism ; *Oxidoreductases/metabolism/genetics ; *Transcriptome ; Methane/metabolism ; Archaeal Proteins/genetics/metabolism ; Gene Expression Regulation, Archaeal ; Operon ; },
abstract = {UNLABELLED: Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis, the microbial metabolism responsible for nearly all biological methane emissions to the atmosphere. Decades of biochemical and structural research studies have generated detailed insights into MCR function in vitro, yet very little is known about the interplay between MCR and methanogen physiology. For instance, while it is routinely stated that MCR catalyzes the rate-limiting step of methanogenesis, this has not been categorically tested. In this study, to gain a more direct understanding of MCR's control on the growth of Methanosarcina acetivorans, we generate a strain with an inducible mcr operon on the chromosome, allowing for careful control of MCR expression. We show that MCR is not growth rate-limiting in substrate-replete batch cultures. However, through careful titration of MCR expression, growth-limiting state(s) can be obtained. Transcriptomic analysis of M. acetivorans experiencing MCR limitation reveals a global response with hundreds of differentially expressed genes across diverse functional categories. Notably, MCR limitation leads to strong induction of methylsulfide methyltransferases, likely due to insufficient recycling of metabolic intermediates. In addition, the mcr operon is not transcriptionally regulated, i.e., it is constitutively expressed, suggesting that the overabundance of MCR might be beneficial when cells experience nutrient limitation or stressful conditions. Altogether, we show that there is a wide range of cellular MCR concentrations that can sustain optimal growth, suggesting that other factors such as anabolic reactions might be rate-limiting for methanogenic growth.

IMPORTANCE: Methane is a potent greenhouse gas that has contributed to ca. 25% of global warming in the post-industrial era. Atmospheric methane is primarily of biogenic origin, mostly produced by microorganisms called methanogens. Methyl-coenzyme M reductase (MCR) catalyzes methane formatio in methanogens. Even though MCR comprises ca. 10% of the cellular proteome, it is hypothesized to be growth-limiting during methanogenesis. In this study, we show that Methanosarcina acetivorans cells grown in substrate-replicate batch cultures produce more MCR than its cellular demand for optimal growth. The tools outlined in this study can be used to refine metabolic models of methanogenesis and assay lesions in MCR in a higher-throughput manner than isolation and biochemical characterization of pure protein.},
}

*Methanosarcina/genetics/enzymology/metabolism
*Oxidoreductases/metabolism/genetics
*Transcriptome
Methane/metabolism
Archaeal Proteins/genetics/metabolism
Gene Expression Regulation, Archaeal
Operon

@article {pmid39030408,
year = {2024},
author = {Gilbert, JA and Hartmann, EM},
title = {The indoors microbiome and human health.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39030408},
issn = {1740-1534},
abstract = {Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.},
}

@article {pmid39029405,
year = {2024},
author = {Kozaeva, E and Eida, AA and Gunady, EF and Dangl, JL and Conway, JM and Brophy, JA},
title = {Roots of synthetic ecology: microbes that foster plant resilience in the changing climate.},
journal = {Current opinion in biotechnology},
volume = {88},
number = {},
pages = {103172},
doi = {10.1016/j.copbio.2024.103172},
pmid = {39029405},
issn = {1879-0429},
abstract = {Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.},
}

@article {pmid39025292,
year = {2024},
author = {Guo, X and Zhao, W and Yin, D and Mei, Z and Wang, F and Tiedje, J and Ling, S and Hu, S and Xu, T},
title = {Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124566},
doi = {10.1016/j.envpol.2024.124566},
pmid = {39025292},
issn = {1873-6424},
abstract = {Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.},
}

@article {pmid39021442,
year = {2024},
author = {Bowers, RM and Gonzalez-Pena, V and Wardhani, K and Goudeau, D and Blow, MJ and Udwary, D and Klein, D and Vill, AC and Brito, IL and Woyke, T and Malmstrom, RR and Gawad, C},
title = {scMicrobe PTA: near complete genomes from single bacterial cells.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae085},
pmid = {39021442},
issn = {2730-6151},
abstract = {Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.},
}

@article {pmid39021414,
year = {2024},
author = {Marin, C and Migura-García, L and Rodríguez, JC and Ventero, MP and Pérez-Gracia, MT and Vega, S and Tort-Miró, C and Marco-Fuertes, A and Lorenzo-Rebenaque, L and Montoro-Dasi, L},
title = {Swine farm environmental microbiome: exploring microbial ecology and functionality across farms with high and low sanitary status.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1401561},
pmid = {39021414},
issn = {2297-1769},
abstract = {INTRODUCTION: Stringent regulations in pig farming, such as antibiotic control and the ban on certain additives and disinfectants, complicate disease control efforts. Despite the evolution of microbial communities inside the house environment, they maintain stability over the years, exhibiting characteristics specific to each type of production and, in some cases, unique to a particular company or farm production type. In addition, some infectious diseases are recurrent in specific farms, while other farms never present these diseases, suggesting a connection between the presence of these microorganisms in animals or their environment. Therefore, the aim of this study was to characterise environmental microbiomes of farms with high and low sanitary status, establishing the relationships between both, health status, environmental microbial ecology and its functionality.

METHODS: For this purpose, 6 pig farms were environmentally sampled. Farms were affiliated with a production company that handle the majority of the pigs slaughtered in Spain. This study investigated the relationship among high health and low health status farms using high throughput 16S rRNA gene sequencing. In addition, to identify ecologically relevant functions and potential pathogens based on the 16S rRNA gene sequences obtained, functional Annotation with PROkaryotic TAXa (FAPROTAX) was performed.

RESULTS AND DISCUSSION: This study reveals notable differences in microbial communities between farms with persistent health issues and those with good health outcomes, suggesting a need for protocols tailored to address specific challenges. The variation in microbial populations among farms underscores the need for specific and eco-friendly cleaning and disinfection protocols. These measures are key to enhancing the sustainability of livestock farming, ensuring safer products and boosting competitive edge in the market.},
}

@article {pmid39019971,
year = {2024},
author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N},
title = {Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16555},
pmid = {39019971},
issn = {2045-2322},
mesh = {*Charcoal/chemistry ; *Fertilizers ; *Crops, Agricultural/growth & development ; *Minerals/chemistry ; Nitrogen/chemistry ; Brassica/growth & development ; Soil/chemistry ; Nutrients ; Agriculture/methods ; Magnesium/chemistry ; },
abstract = {Mechanized biochar field application remains challenging due to biochar's poor flowability and bulk density. Granulation of biochar with fertilizer provides a product ready for application with well-established machinery. However, it's unknown whether granulated biochar-based fertilizers (gBBF) are as effective as co-application of non-granulated biochar with fertilizer. Here, we compared a gBBF with a mineral compound fertilizer (control), and with a non-granulated biochar that was co-applied at a rate of 1.1 t ha[-1] with the fertilizer in a white cabbage greenhouse pot trial. Half the pots received heavy rain simulation treatments to investigate nutrient leaching. Crop yields were not significantly increased by biochar without leaching compared to the control. With leaching, cabbage yield increased with gBBF and biochar-co-application by 14% (p > 0.05) and 34% (p < 0.05), respectively. Nitrogen leaching was reduced by 26-35% with both biochar amendments. Biochar significantly reduced potassium, magnesium, and sulfur leaching. Most nitrogen associated with gBBF was released during the trial and the granulated biochar regained its microporosity. Enriching fertilizers with biochar by granulation or co-application can improve crop yields and decrease nutrient leaching. While the gBBF yielded less biomass compared to biochar co-application, improved mechanized field application after granulation could facilitate the implementation of biochar application in agriculture.},
}

*Charcoal/chemistry
*Fertilizers
*Crops, Agricultural/growth & development
*Minerals/chemistry
Nitrogen/chemistry
Brassica/growth & development
Soil/chemistry
Nutrients
Agriculture/methods
Magnesium/chemistry

@article {pmid39018765,
year = {2024},
author = {Bittleston, LS},
title = {Connecting microbial community assembly and function.},
journal = {Current opinion in microbiology},
volume = {80},
number = {},
pages = {102512},
doi = {10.1016/j.mib.2024.102512},
pmid = {39018765},
issn = {1879-0364},
abstract = {Microbial ecology is moving away from purely descriptive analyses to experiments that can determine the underlying mechanisms driving changes in community assembly and function. More species-rich microbial communities generally have higher functional capabilities depending on if there is positive selection of certain species or complementarity among different species. When building synthetic communities or laboratory enrichment cultures, there are specific choices that can increase the number of species able to coexist. Higher resource complexity or the addition of physical niches are two of the many factors leading to greater biodiversity and associated increases in functional capabilities. We can use principles from community ecology and knowledge of microbial physiology to generate improved microbiomes for use in medicine, agriculture, or environmental management.},
}

@article {pmid39017940,
year = {2024},
author = {Kim, YS and Yun, HS and Lee, JH and Lee, KL and Choi, JS and Won, DH and Kim, YJ and Kim, HS and Yoon, HS},
title = {Comparison of Metabarcoding and Microscopy Methodologies to Analyze Diatom Communities in Five Estuaries Along the Southern Coast of the Korean Peninsula.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {95},
pmid = {39017940},
issn = {1432-184X},
support = {2016R1A6A1A05011910//National Research Foundation of Korea/ ; 2016R1A6A1A05011910//National Research Foundation of Korea/ ; 2021R1I1A205551711//National Research Foundation of Korea/ ; },
mesh = {*Diatoms/classification/growth & development ; *DNA Barcoding, Taxonomic ; *Microscopy/methods ; *Estuaries ; Republic of Korea ; Biodiversity ; Phylogeny ; Ecosystem ; },
abstract = {The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined.},
}

*Diatoms/classification/growth & development
*DNA Barcoding, Taxonomic
*Microscopy/methods
*Estuaries
Republic of Korea
Biodiversity
Phylogeny
Ecosystem

@article {pmid39012154,
year = {2024},
author = {Salazar-Jaramillo, L and de la Cuesta-Zuluaga, J and Chica, LA and Cadavid, M and Ley, RE and Reyes, A and Escobar, JS},
title = {Gut microbiome diversity within Clostridia is negatively associated with human obesity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0062724},
doi = {10.1128/msystems.00627-24},
pmid = {39012154},
issn = {2379-5077},
abstract = {UNLABELLED: Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.

IMPORTANCE: The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.},
}

@article {pmid39012115,
year = {2024},
author = {Luyt, NA and de Witt, RN and Divol, B and Patterton, HG and Setati, ME and Taillandier, P and Bauer, FF},
title = {Physical cell-cell contact elicits specific transcriptomic responses in wine yeast species.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057223},
doi = {10.1128/spectrum.00572-23},
pmid = {39012115},
issn = {2165-0497},
abstract = {Fermenting grape juice provides a habitat for a well-mapped and evolutionarily relevant microbial ecosystem consisting of many natural or inoculated strains of yeasts and bacteria. The molecular nature of many of the ecological interactions within this ecosystem remains poorly understood, with the partial exception of interactions of a metabolic nature such as competition for nutrients and production of toxic metabolites/peptides. Data suggest that physical contact between species plays a significant role in the phenotypic outcome of interspecies interactions. However, the molecular nature of the mechanisms regulating these phenotypes remains unknown. Here, we present a transcriptomic analysis of physical versus metabolic contact between two wine relevant yeast species, Saccharomyces cerevisiae and Lachancea thermotolerans. The data show that these species respond to the physical presence of the other species. In S. cerevisiae, physical contact results in the upregulation of genes involved in maintaining cell wall integrity, cell wall structural components, and genes involved in the production of H2S. In L. thermotolerans, HSP stress response genes were the most significantly upregulated gene family. Both yeasts downregulated genes belonging to the FLO family, some of which play prominent roles in cellular adhesion. qPCR analysis indicates that the expression of some of these genes is regulated in a species-specific manner, suggesting that yeasts adjust gene expression to specific biotic challenges or interspecies interactions. These findings provide fundamental insights into yeast interactions and evolutionary adaptations of these species to the wine ecosystem.IMPORTANCEWithin the wine ecosystem, yeasts are the most relevant contributors to alcoholic fermentation and wine organoleptic characteristics. While some studies have described yeast-yeast interactions during alcoholic fermentation, such interactions remain ill-defined, and little is understood regarding the molecular mechanisms behind many of the phenotypes observed when two or more species are co-cultured. In particular, no study has investigated transcriptional regulation in response to physical interspecies cell-cell contact, as opposed to the generally better understood/characterized metabolic interactions. These data are of direct relevance to our understanding of microbial ecological interactions in general while also creating opportunities to improve ecosystem-based biotechnological applications such as wine fermentation. Furthermore, the presence of competitor species has rarely been considered an evolutionary biotic selection pressure. In this context, the data reveal novel gene functions. This, and further such analysis, is likely to significantly enlarge the genome annotation space.},
}

@article {pmid39011025,
year = {2024},
author = {Alam, M and Pandit, B and Moin, A and Iqbal, UN},
title = {Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture.},
journal = {Indian journal of microbiology},
volume = {64},
number = {2},
pages = {343-366},
pmid = {39011025},
issn = {0046-8991},
abstract = {Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.},
}

@article {pmid39010847,
year = {2024},
author = {Qing, J and Zhang, L and Li, C and Li, Y},
title = {Mendelian randomization analysis revealed that albuminuria is the key factor affecting socioeconomic status in CKD patients.},
journal = {Renal failure},
volume = {46},
number = {2},
pages = {2367705},
doi = {10.1080/0886022X.2024.2367705},
pmid = {39010847},
issn = {1525-6049},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Albuminuria ; *Renal Insufficiency, Chronic/complications ; *Social Class ; *Glomerular Filtration Rate ; },
abstract = {Previous studies indicate a strong correlation between the incidence of chronic kidney disease (CKD) and lower economic status. However, these studies often struggle to delineate a clear cause-effect relationship, leaving healthcare providers uncertain about how to manage kidney disease in a way that improves patients' financial outcomes. Our study aimed to explore and establish a causal relationship between CKD and socioeconomic status, identifying critical influencing factors. We utilized summary meta-analysis data from the CKDGen Consortium and UK Biobank. Genetic variants identified from these sources served as instrumental variables (IVs) to estimate the association between CKD and socioeconomic status. The presence or absence of CKD, estimated glomerular filtration rate (eGFR), and albuminuria were used as exposures, while income and regional deprivation were analyzed as outcomes. We employed the R packages 'TwoSampleMR' and 'Mendelianrandomization' to conduct both univariable and multivariable Mendelian randomization (MR) analyses, assessing for potential pleiotropy and heterogeneity. Our univariable MR analysis revealed a significant causal relationship between high levels of albuminuria and lower income (OR = 0.84, 95% CI: 0.73-0.96, p = 0.013), with no significant pleiotropy detected. In the multivariable MR analysis, both CKD (OR = 0.867, 95% CI: 0.786-0.957, p = 0.0045) and eGFR (OR = 0.065, 95% CI: 0.010-0.437, p = 0.0049) exhibited significant effects on income. This study underscores that higher albuminuria levels in CKD patients are associated with decreased income and emphasizes the importance of effective management and treatment of albuminuria in CKD patients to mitigate both social and personal economic burdens.},
}

Humans
*Mendelian Randomization Analysis
*Albuminuria
*Renal Insufficiency, Chronic/complications
*Social Class
*Glomerular Filtration Rate

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

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

@article {pmid39008061,
year = {2024},
author = {Helmy, KG and Abu-Hussien, SH},
title = {Root Rot Management in Common Bean (Phaseolus vulgaris L.) Through Integrated Biocontrol Strategies using Metabolites from Trichoderma harzianum, Serratia marcescens, and Vermicompost Tea.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {94},
pmid = {39008061},
issn = {1432-184X},
mesh = {*Phaseolus/microbiology ; *Plant Diseases/microbiology/prevention & control ; *Serratia marcescens/physiology/metabolism ; *Rhizoctonia/physiology ; *Plant Roots/microbiology ; Biological Control Agents/pharmacology ; Pest Control, Biological ; Antibiosis ; Hypocreales/physiology/metabolism ; Egypt ; Composting ; Soil Microbiology ; },
abstract = {Common bean (Phaseolus vulgaris L.) is an essential food staple and source of income for small-holder farmers across Africa. However, yields are greatly threatened by fungal diseases like root rot induced by Rhizoctonia solani. This study aimed to evaluate an integrated approach utilizing vermicompost tea (VCT) and antagonistic microbes for effective and sustainable management of R. solani root rot in common beans. Fourteen fungal strains were first isolated from infected common bean plants collected across three Egyptian governorates, with R. solani being the most virulent isolate with 50% dominance. Subsequently, the antagonistic potential of vermicompost tea (VCT), Serratia sp., and Trichoderma sp. was assessed against this destructive pathogen. Combinations of 10% VCT and the biocontrol agent isolates displayed potent inhibition of R. solani growth in vitro, prompting in planta testing. Under greenhouse conditions, integrated applications of 5 or 10% VCT with Serratia marcescens, Trichoderma harzianum, or effective microorganisms (EM1) afforded up to 95% protection against pre- and post-emergence damping-off induced by R. solani in common bean cv. Giza 6. Similarly, under field conditions, combining VCT with EM1 (VCT + EM1) or Trichoderma harzianum (VCT + Trichoderma harzianum) substantially suppressed disease severity by 65.6% and 64.34%, respectively, relative to untreated plants. These treatments also elicited defense enzyme activity and distinctly improved growth parameters including 136.68% and 132.49% increases in pod weight per plant over control plants. GC-MS profiling of Trichoderma harzianum, Serratia marcescens, and vermicompost tea (VCT) extracts revealed unique compounds dominated by cyclic pregnane, fatty acid methyl esters, linoleic acid derivatives, and free fatty acids like oleic, palmitic, and stearic acids with confirmed biocontrol and plant growth-promoting activities. The results verify VCT-mediated delivery of synergistic microbial consortia as a sustainable platform for integrated management of debilitating soil-borne diseases, enhancing productivity and incomes for smallholder bean farmers through regeneration of soil health. Further large-scale validation can pave the adoption of this climate-resilient approach for securing food and nutrition security.},
}

*Phaseolus/microbiology
*Plant Diseases/microbiology/prevention & control
*Serratia marcescens/physiology/metabolism
*Rhizoctonia/physiology
*Plant Roots/microbiology
Biological Control Agents/pharmacology
Pest Control, Biological
Antibiosis
Hypocreales/physiology/metabolism
Egypt
Composting
Soil Microbiology

@article {pmid38982749,
year = {2024},
author = {Schrecengost, A and Rotterová, J and Poláková, K and Čepička, I and Beinart, RA},
title = {Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae125},
pmid = {38982749},
issn = {1751-7370},
support = {//Simons Foundation Early Career Investigator in Marine Microbial Ecology and Evolution Award/ ; 1330406//United States National Science Foundation EPSCoR Track II Cooperative Agreement Award/ ; 23-06004S//Czech Science Foundation/ ; OIA-1655221//National Science Foundation EPSCoR/ ; //Viničná Microscopy Core Facility/ ; LM2023050//MEYS CR/ ; 1919588//National Science Foundation Major Research Instrumentation/ ; },
mesh = {*Symbiosis ; *Ciliophora/classification/genetics/physiology ; *Phylogeny ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 18S/genetics ; DNA, Archaeal/genetics/chemistry ; Sequence Analysis, DNA ; Seawater/microbiology/parasitology ; },
abstract = {Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the ubiquity of these symbioses in anoxic habitats, patterns of symbiont specificity and fidelity are not well known. We surveyed two unrelated, commonly found groups of anaerobic ciliates, the Plagiopylea and Metopida, isolated from anoxic marine sediments. We sequenced host 18S rRNA and symbiont 16S rRNA marker genes as well as the symbiont internal transcribed spacer region from our cultured ciliates to identify hosts and their associated methanogenic symbionts. We found that marine ciliates from both of these co-occurring, divergent groups harbor closely related yet distinct intracellular archaea within the Methanocorpusculum genus. The symbionts appear to be stable at the host species level, but at higher taxonomic levels, there is evidence that symbiont replacements have occurred. Gaining insight into this unique association will deepen our understanding of the complex transmission modes of marine microbial symbionts, and the mutualistic microbial interactions occurring across domains of life.},
}

*Symbiosis
*Ciliophora/classification/genetics/physiology
*Phylogeny
Anaerobiosis
*RNA, Ribosomal, 16S/genetics
*Geologic Sediments/microbiology
RNA, Ribosomal, 18S/genetics
DNA, Archaeal/genetics/chemistry
Sequence Analysis, DNA
Seawater/microbiology/parasitology

@article {pmid39007602,
year = {2024},
author = {Jensen, N and Maldonado-Gomez, M and Krishnakumar, N and Weng, C-Y and Castillo, J and Razi, D and Kalanetra, K and German, JB and Lebrilla, CB and Mills, DA and Taft, DH},
title = {Dietary fiber monosaccharide content alters gut microbiome composition and fermentation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0096424},
doi = {10.1128/aem.00964-24},
pmid = {39007602},
issn = {1098-5336},
abstract = {UNLABELLED: Members of the mammalian gut microbiota metabolize diverse complex carbohydrates that are not digested by the host, which are collectively labeled "dietary fiber." While the enzymes and transporters that each strain uses to establish a nutrient niche in the gut are often exquisitely specific, the relationship between carbohydrate structure and microbial ecology is imperfectly understood. The present study takes advantage of recent advances in complex carbohydrate structure determination to test the effects of fiber monosaccharide composition on microbial fermentation. Fifty-five fibers with varied monosaccharide composition were fermented by a pooled feline fecal inoculum in a modified MiniBioReactor array system over a period of 72 hours. The content of the monosaccharides glucose and xylose was significantly associated with the reduction of pH during fermentation, which was also predictable from the concentrations of the short-chain fatty acids lactic acid, propionic acid, and the signaling molecule indole-3-acetic acid. Microbiome diversity and composition were also predictable from monosaccharide content and SCFA concentration. In particular, the concentrations of lactic acid and propionic acid correlated with final alpha diversity and were significantly associated with the relative abundance of several of the genera, including Lactobacillus and Dubosiella. Our results suggest that monosaccharide composition offers a generalizable method to compare any dietary fiber of interest and uncover links between diet, gut microbiota, and metabolite production.

IMPORTANCE: The survival of a microbial species in the gut depends on the availability of the nutrients necessary for that species to survive. Carbohydrates in the form of non-host digestible fiber are of particular importance, and the set of genes possessed by each species for carbohydrate consumption can vary considerably. Here, differences in the monosaccharides that are the building blocks of fiber are considered for their impact on both the survival of different species of microbes and on the levels of microbial fermentation products produced. This work demonstrates that foods with similar monosaccharide content will have consistent effects on the survival of microbial species and on the production of microbial fermentation products.},
}

@article {pmid39003240,
year = {2024},
author = {Vass, M and Székely, A and Carlsson-Graner, U and Wikner, J and Andersson, A},
title = {Microeukaryote community coalescence strengthens community stability and elevates diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae100},
pmid = {39003240},
issn = {1574-6941},
abstract = {Mixing of entire microbial communities represents a frequent, yet understudied phenomenon. Here, we mimicked estuarine condition in a microcosm experiment by mixing a freshwater river community with a brackish sea community and assessed the effects of both environmental and community coalescences induced by varying mixing processes on microeukaryotic communities. Signs of shifted community composition of coalesced communities towards the sea parent community suggest asymmetrical community coalescence outcome, which, in addition, was generally less impacted by environmental coalescence. Community stability, inferred from community cohesion, differed among river and sea parent communities and increased following coalescence treatments. Generally, community coalescence increased alpha diversity and promoted competition from the introduction (or emergence) of additional (or rare) species. These competitive interactions in turn had community stabilizing effect as evidenced by the increased proportion of negative cohesion. The fate of microeukaryotes was influenced by mixing ratios and frequencies (i.e., one-time versus repeated coalescence). Namely, diatoms were negatively impacted by coalescence, while fungi, ciliates, and cercozoans were promoted to varying extents, depending on the mixing ratios of the parent communities. Our study suggests that the predictability of coalescence outcomes was greater when the sea parent community dominated the final community, and this predictability was further enhanced when communities collided repeatedly.},
}

@article {pmid39003046,
year = {2025},
author = {Lamprea Pineda, PA and Demeestere, K and Alvarado-Alvarado, AA and Devlieghere, F and Boon, N and Van Langenhove, H and Walgraeve, C},
title = {Degradation of gaseous hydrocarbons in aerated stirred bioreactors inoculated with Rhodococcus erythropolis: Effect of the carbon source and SIFT-MS method development.},
journal = {Journal of environmental sciences (China)},
volume = {147},
number = {},
pages = {268-281},
doi = {10.1016/j.jes.2023.10.020},
pmid = {39003046},
issn = {1001-0742},
mesh = {*Rhodococcus/metabolism ; *Bioreactors/microbiology ; *Biodegradation, Environmental ; *Hydrocarbons/metabolism ; Carbon/metabolism ; Air Pollutants/metabolism/analysis ; Mass Spectrometry ; Toluene/metabolism ; Xylenes/metabolism ; Butanes/metabolism ; Benzene Derivatives ; Pentanes ; },
abstract = {The study of microbial hydrocarbons removal is of great importance for the development of future bioremediation strategies. In this study, we evaluated the removal of a gaseous mixture containing toluene, m-xylene, ethylbenzene, cyclohexane, butane, pentane, hexane and heptane in aerated stirred bioreactors inoculated with Rhodococcus erythropolis and operated under non-sterile conditions. For the real-time measurement of hydrocarbons, a novel systematic approach was implemented using Selected-Ion Flow Tube Mass Spectrometry (SIFT-MS). The effect of the carbon source (∼9.5 ppmv) on (i) the bioreactors' performance (BR1: dosed with only cyclohexane as a single hydrocarbon versus BR2: dosed with a mixture of the 8 hydrocarbons) and (ii) the evolution of microbial communities over time were investigated. The results showed that cyclohexane reached a maximum removal efficiency (RE) of 53% ± 4% in BR1. In BR2, almost complete removal of toluene, m-xylene and ethylbenzene, being the most water-soluble and easy-to-degrade carbon sources, was observed. REs below 32% were obtained for the remaining compounds. By exposing the microbial consortium to only the five most recalcitrant hydrocarbons, REs between 45% ± 5% and 98% ± 1% were reached. In addition, we observed that airborne microorganisms populated the bioreactors and that the type of carbon source influenced the microbial communities developed. The abundance of species belonging to the genus Rhodococcus was below 10% in all bioreactors at the end of the experiments. This work provides fundamental insights to understand the complex behavior of gaseous hydrocarbon mixtures in bioreactors, along with a systematic approach for the development of SIFT-MS methods.},
}

*Rhodococcus/metabolism
*Bioreactors/microbiology
*Biodegradation, Environmental
*Hydrocarbons/metabolism
Carbon/metabolism
Air Pollutants/metabolism/analysis
Mass Spectrometry
Toluene/metabolism
Xylenes/metabolism
Butanes/metabolism
Benzene Derivatives
Pentanes

@article {pmid39002491,
year = {2024},
author = {Meroz, N and Livny, T and Friedman, J},
title = {Quantifying microbial interactions: concepts, caveats, and applications.},
journal = {Current opinion in microbiology},
volume = {80},
number = {},
pages = {102511},
doi = {10.1016/j.mib.2024.102511},
pmid = {39002491},
issn = {1879-0364},
abstract = {Microbial communities are fundamental to every ecosystem on Earth and hold great potential for biotechnological applications. However, their complex nature hampers our ability to study and understand them. A common strategy to tackle this complexity is to abstract the community into a network of interactions between its members - a phenomenological description that captures the overall effects of various chemical and physical mechanisms that underpin these relationships. This approach has proven useful for numerous applications in microbial ecology, including predicting community dynamics and stability and understanding community assembly and evolution. However, care is required in quantifying and interpreting interactions. Here, we clarify the concept of an interaction and discuss when interaction measurements are useful despite their context-dependent nature. Furthermore, we categorize different approaches for quantifying interactions, highlighting the research objectives each approach is best suited for.},
}

@article {pmid39001714,
year = {2024},
author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ},
title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae129},
pmid = {39001714},
issn = {1751-7370},
abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.},
}

@article {pmid38995161,
year = {2024},
author = {Seixas, MH and Munroe, JS and Eggleston, EM},
title = {Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA.},
journal = {MicrobiologyOpen},
volume = {13},
number = {4},
pages = {e1426},
pmid = {38995161},
issn = {2045-8827},
support = {//Middlebury College/ ; },
mesh = {Utah ; *Bacteria/classification/genetics/isolation & purification ; *Caves/microbiology ; *Ice ; Soil Microbiology ; Biodiversity ; Microscopy, Electron, Scanning ; Seasons ; Water Microbiology ; },
abstract = {The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.},
}

Utah
*Bacteria/classification/genetics/isolation & purification
*Caves/microbiology
*Ice
Soil Microbiology
Biodiversity
Microscopy, Electron, Scanning
Seasons
Water Microbiology

@article {pmid38995046,
year = {2024},
author = {Gibson, C and Jauffur, S and Guo, B and Frigon, D},
title = {Activated sludge microbial community assembly: the role of influent microbial community immigration.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0059824},
doi = {10.1128/aem.00598-24},
pmid = {38995046},
issn = {1098-5336},
abstract = {Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs.IMPORTANCEIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. This study developed a reproducible protocol to investigate the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls, allowing intrinsic definitions of core and immigrant populations to be established. The method developed herein will allow sequential manipulative experiments to be performed to test specific hypothesis and optimize wastewater treatment processes to meet new treatment goals.},
}

@article {pmid38993674,
year = {2024},
author = {Huang, C and Liu, D and Yang, S and Huang, Y and Wei, X and Zhang, P and Lin, J and Xu, B and Liu, Y and Guo, D and Li, Y and Li, J and Zhang, H},
title = {Effect of time-restricted eating regimen on weight loss is mediated by gut microbiome.},
journal = {iScience},
volume = {27},
number = {7},
pages = {110202},
pmid = {38993674},
issn = {2589-0042},
abstract = {Time-restricted eating (TRE) is a promising obesity management strategy, but weight-loss efficacy varies among participants, and the underlying mechanism is unclear. The study aimed to investigate the role of gut microbiota in weight-loss response during long-term TRE intervention. We analyzed data from 51 obese adults in a 12-month TRE program, categorizing them into distinct weight loss groups (DG) and moderate weight loss groups (MG) based on their TRE responses. Shotgun metagenomic sequencing analysis revealed a significant increase in species closely associated with weight loss effectiveness and metabolic parameter changes in the DG group. Pathways related to fatty acid biosynthesis, glycogen biosynthesis, and nucleotide metabolism were reduced in the DG group and enhanced in the MG group. Next, we identified nine specific species at baseline that contributed better responses to TRE intervention and significant weight loss. Collectively, gut microbiota contributes to responsiveness heterogeneity in TRE and can predict weight-loss effectiveness.},
}

@article {pmid38992757,
year = {2024},
author = {Zeng, X and Liu, Y and Wang, Q and Ma, H and Li, X and Wang, Q and Yang, Q},
title = {Tanning wastewater restructured nitrogen-transforming bacteria communities and promoted N2O emissions in receiving river riparian sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119580},
doi = {10.1016/j.envres.2024.119580},
pmid = {38992757},
issn = {1096-0953},
abstract = {Physicochemical and toxicological characterization of leather tanning wastewater has been widely documented. However, few reports have examined the response of denitrification N2 and N2O emissions in riparian sediments of tannery wastewater-receiving rivers. In this study, [15]N-nitrate labeling was used to reveal the effects of tanning wastewater on denitrification N2 and N2O emission in a wastewater-receiving river (the old Mang River, OMR). OMR riparian sediments were highly polluted with total organic carbon (93.39 mg/kg), total nitrogen (5.00 g/kg) and heavy metals; specifically, Cr, Zn, Cd, and Pb were found at concentrations 47.3, 5.8, 1.6, 4.3, and 2.8 times that in a nearby parallel river without tanning wastewater input (the new Mang River, NMR), respectively. The denitrification N2 emission rates (0.0015 nmol N · g[-1] · h[-1]) of OMR riparian sediments were significantly reduced by 2.5 times compared with those from the NMR (p < 0.05), but the N2O emission rates (0.31 nmol N · g[-1] · h[-1]) were significantly increased (4.1 times, p < 0.05). Although the dominant nitrogen-transforming bacteria phylum was Proteobacteria in the riparian sediments of both rivers, 11 nitrogen-transforming bacteria genera in the OMR were found to be significantly enriched; five of these were related to pollutant degradation based on linear discriminant analysis (LDA > 3). The average activity of the electron transport system in the OMR was 6.3 times lower than that of the NMR (p < 0.05). Among pollution factors, heavy metal complex pollution was the dominant factor driving variations in N2O emissions, microbial community structure, and electron transport system activity. These results provide a new understanding and reference for the treatment of tanning wastewater-receiving rivers.},
}

@article {pmid38987492,
year = {2024},
author = {Ng, MS and Soon, N and Afiq-Rosli, L and Kunning, I and Mana, RR and Chang, Y and Wainwright, BJ},
title = {Highly Diverse Symbiodiniaceae Types Hosted by Corals in a Global Hotspot of Marine Biodiversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {92},
pmid = {38987492},
issn = {1432-184X},
mesh = {*Anthozoa/microbiology ; Animals ; *Biodiversity ; *Dinoflagellida/genetics/classification/physiology ; *Symbiosis ; *Coral Reefs ; Papua New Guinea ; Phylogeny ; High-Throughput Nucleotide Sequencing ; },
abstract = {Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world's coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies.},
}

*Anthozoa/microbiology
Animals
*Biodiversity
*Dinoflagellida/genetics/classification/physiology
*Symbiosis
*Coral Reefs
Papua New Guinea
Phylogeny
High-Throughput Nucleotide Sequencing

@article {pmid38987022,
year = {2024},
author = {Litchman, E and Villéger, S and Zinger, L and Auguet, JC and Thuiller, W and Munoz, F and Kraft, NJB and Philippot, L and Violle, C},
title = {Refocusing the microbial rare biosphere concept through a functional lens.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2024.06.005},
pmid = {38987022},
issn = {1872-8383},
abstract = {The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.},
}

@article {pmid38985714,
year = {2024},
author = {Ugwuanyi, IR and Steele, A and Glamoclija, M},
title = {Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2023.0130},
pmid = {38985714},
issn = {1557-8070},
abstract = {Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.},
}

@article {pmid38983631,
year = {2024},
author = {Hawes, I and García-Maldonado, JQ and Falcón, LI},
title = {Editorial: Exploring microbial mat communities in extreme environments.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1440619},
doi = {10.3389/fmicb.2024.1440619},
pmid = {38983631},
issn = {1664-302X},
}

@article {pmid38982970,
year = {2024},
author = {Jiang, J and Xiang, X and Zhou, Q and Zhou, L and Bi, X and Khanal, SK and Wang, Z and Chen, G and Guo, G},
title = {Optimization of a Novel Engineered Ecosystem Integrating Carbon, Nitrogen, Phosphorus, and Sulfur Biotransformation for Saline Wastewater Treatment Using an Interpretable Machine Learning Approach.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c03160},
pmid = {38982970},
issn = {1520-5851},
abstract = {The denitrifying sulfur (S) conversion-associated enhanced biological phosphorus removal (DS-EBPR) process for treating saline wastewater is characterized by its unique microbial ecology that integrates carbon (C), nitrogen (N), phosphorus (P), and S biotransformation. However, operational instability arises due to the numerous parameters and intricates bacterial interactions. This study introduces a two-stage interpretable machine learning approach to predict S conversion-driven P removal efficiency and optimize DS-EBPR process. Stage one utilized the XGBoost regression model, achieving an R[2] value of 0.948 for predicting sulfate reduction (SR) intensity from anaerobic parameters with feature engineering. Stage two involved the CatBoost classification and regression model integrating anoxic parameters with the predicted SR values for predicting P removal, reaching an accuracy of 94% and an R[2] value of 0.93, respectively. This study identified key environmental factors, including SR intensity (20-45 mg S/L), influent P concentration (<9.0 mg P/L), mixed liquor volatile suspended solids (MLVSS)/mixed liquor suspended solids (MLSS) ratio (0.55-0.72), influent C/S ratio (0.5-1.0), anoxic reaction time (5-6 h), and MLSS concentration (>6.50 g/L). A user-friendly graphic interface was developed to facilitate easier optimization and control. This approach streamlines the determination of optimal conditions for enhancing P removal in the DS-EBPR process.},
}

@article {pmid38982962,
year = {2024},
author = {Sbibih, Y and Saddari, A and Alla, I and Abdesselami, O and Ben Moussa, C and Ezrari, S and Benaissa, E and Ben Lahlou, Y and Elouennass, M and Maleb, A},
title = {Microbial ecology of protective isolation room: Air and Surfaces.},
journal = {La Tunisie medicale},
volume = {102},
number = {7},
pages = {394-398},
doi = {10.62438/tunismed.v102i7.4807},
pmid = {38982962},
issn = {2724-7031},
mesh = {Humans ; *Air Microbiology ; *Cross Infection/prevention & control/epidemiology/microbiology ; Prospective Studies ; Patients' Rooms/organization & administration/statistics & numerical data ; Patient Isolation/methods ; Hospitals, University ; Immunocompromised Host ; Tunisia/epidemiology ; },
abstract = {INTRODUCTION: Healthcare-associated infections pose a significant public health burden, leading to morbidity, mortality, prolonged hospital stays, and substantial social and economic costs. Immunocompromised patients are at a heightened risk of nosocomial infections.

AIM: This prospective study conducted at Mohammed VI University Hospital of Oujda aimed to assess the microbial ecology of surfaces and air in an immunosuppressed patient room compared to a double hospitalization room.

METHODS: Microbiological air purity tests were conducted employing both the sedimentation method and the collision method with the assistance of Microflow Alpha. The sedimentation method used Mueller Hinton with 5% human blood, facilitating the free fall of contaminated dust particles. The collection program employed was set for 10 minutes per 1 m3. For surface sampling, swabs were taken from a 25 cm2 surface. The swabs were immediately forwarded to the Microbiology Laboratory. We carried out both macroscopic and microscopic identification of colonies, followed by definitive biochemical identification using the BD phoenixTM system. Antibiotic susceptibility was assessed through agar diffusion on Muller Hinton medium coupled with the determination of the minimum inhibitory concentration.

RESULTS: The results revealed a decreased bacterial count within the protective isolation room, in contrast to the standard hospital room. We noted the predominance of coagulase-negative Staphylococcus spp and Bacillus spp. Staphylococcus aureus and Aspergillus spp, common pathogens in healthcare-associated infections, were notably absent in the protective isolation room. The findings underline the pivotal role of hospital environments in the transmission of healthcare-associated infections.

CONCLUSION: The protective isolation room demonstrated effective control of microbial contamination, with fewer and less resistant germs. The study highlighted the significance of air treatment systems in preventing the spread of opportunistic infections. Our study underscored the critical role of microbiological cleanliness in preventing nosocomial infections.},
}

Humans
*Air Microbiology
*Cross Infection/prevention & control/epidemiology/microbiology
Prospective Studies
Patients' Rooms/organization & administration/statistics & numerical data
Patient Isolation/methods
Hospitals, University
Immunocompromised Host
Tunisia/epidemiology

@article {pmid38980056,
year = {2024},
author = {Henson, MW and Thrash, JC},
title = {Microbial ecology of northern Gulf of Mexico estuarine waters.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0131823},
doi = {10.1128/msystems.01318-23},
pmid = {38980056},
issn = {2379-5077},
abstract = {Estuarine and coastal ecosystems are of high economic and ecological importance, owing to their diverse communities and the disproportionate role they play in carbon cycling, particularly in carbon sequestration. Organisms inhabiting these environments must overcome strong natural fluctuations in salinity, nutrients, and turbidity, as well as numerous climate change-induced disturbances such as land loss, sea level rise, and, in some locations, increasingly severe tropical cyclones that threaten to disrupt future ecosystem health. The northern Gulf of Mexico (nGoM) along the Louisiana coast contains dozens of estuaries, including the Mississippi-Atchafalaya River outflow, which dramatically influence the region due to their vast upstream watershed. Nevertheless, the microbiology of these estuaries and surrounding coastal environments has received little attention. To improve our understanding of microbial ecology in the understudied coastal nGoM, we conducted a 16S rRNA gene amplicon survey at eight sites and multiple time points along the Louisiana coast and one inland swamp spanning freshwater to high brackish salinities, totaling 47 duplicated Sterivex (0.2-2.7 µm) and prefilter (>2.7 µm) samples. We cataloged over 13,000 Amplicon Sequence ariants (ASVs) from common freshwater and marine clades such as SAR11 (Alphaproteobacteria), Synechococcus (Cyanobacteria), and acI and Candidatus Actinomarina (Actinobacteria). We observed correlations with freshwater or marine habitats in many organisms and characterized a group of taxa with specialized distributions across brackish water sites, supporting the hypothesis of an endogenous brackish-water community. Additionally, we observed brackish-water associations for several aquatic clades typically considered marine or freshwater taxa, such as SAR11 subclade II, SAR324, and the acI Actinobacteria. The data presented here expand the geographic coverage of microbial ecology in estuarine communities, help delineate the native and transitory members of these environments, and provide critical aquatic microbiological baseline data for coastal and estuarine sites in the nGoM.IMPORTANCEEstuarine and coastal waters are diverse ecosystems influenced by tidal fluxes, interconnected wetlands, and river outflows, which are of high economic and ecological importance. Microorganisms play a pivotal role in estuaries as "first responders" and ecosystem architects, yet despite their ecological importance, they remain underrepresented in microbial studies compared to open ocean environments. This leads to substantial knowledge gaps that are important for understanding global biogeochemical cycling and making decisions about conservation and management strategies in these environments. Our study makes key contributions to the microbial ecology of estuarine and coastal habitats in the northern Gulf of Mexico. Our microbial community data support the concept of a globally distributed, core brackish microbiome and emphasize previously underrecognized brackish-water taxa. Given the projected worsening of land loss, oil spills, and natural disasters in this region, our results will serve as important baseline data for researchers investigating the microbial communities found across estuaries.},
}

@article {pmid38980052,
year = {2024},
author = {Flinkstrom, Z and Bryson, S and Candry, P and Winkler, M-KH},
title = {Metagenomic clustering links specific metabolic functions to globally relevant ecosystems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057324},
doi = {10.1128/msystems.00573-24},
pmid = {38980052},
issn = {2379-5077},
abstract = {UNLABELLED: Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome's functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute's Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data.

IMPORTANCE: Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome's metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.},
}

@article {pmid38979877,
year = {2024},
author = {Overgaard, CK and Jamy, M and Radutoiu, S and Burki, F and Dueholm, MKD},
title = {Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13991},
doi = {10.1111/1755-0998.13991},
pmid = {38979877},
issn = {1755-0998},
support = {9041-00236B//Danmarks Frie Forskningsfond/ ; 2021-04055//Vetenskapsrådet/ ; 101044505/ERC_/European Research Council/International ; },
abstract = {The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.},
}

@article {pmid38974332,
year = {2024},
author = {Johnston, JT and Quoc, BN and Abrahamson, B and Candry, P and Ramon, C and Cash, KJ and Saccomano, SC and Samo, TJ and Ye, C and Weber, PK and Winkler, MH and Mayali, X},
title = {Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae086},
pmid = {38974332},
issn = {2730-6151},
abstract = {Microbial degradation of organic carbon in sediments is impacted by the availability of oxygen and substrates for growth. To better understand how particle size and redox zonation impact microbial organic carbon incorporation, techniques that maintain spatial information are necessary to quantify elemental cycling at the microscale. In this study, we produced hydrogel microspheres of various diameters (100, 250, and 500 μm) and inoculated them with an aerobic heterotrophic bacterium isolated from a freshwater wetland (Flavobacterium sp.), and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with [13]C-labeled substrates to quantify organic carbon incorporation into biomass via nanoSIMS. Additionally, luminescent nanosensors enabled spatially explicit measurements of oxygen concentrations inside the microspheres. The experimental data were then incorporated into a reactive-transport model to project long-term steady-state conditions. Smaller (100 μm) particles exhibited the highest microbial cell-specific growth per volume, but also showed higher absolute activity near the surface compared to the larger particles (250 and 500 μm). The experimental results and computational models demonstrate that organic carbon availability was not high enough to allow steep oxygen gradients and as a result, all particle sizes remained well-oxygenated. Our study provides a foundational framework for future studies investigating spatially dependent microbial activity in aggregates using isotopically labeled substrates to quantify growth.},
}

@article {pmid38973247,
year = {2024},
author = {Akay, C and Ulrich, N and Rocha, U and Ding, C and Adrian, L},
title = {Sequential Anaerobic-Aerobic Treatment Enhances Sulfamethoxazole Removal: From Batch Cultures to Observations in a Large-Scale Wastewater Treatment Plant.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c00368},
pmid = {38973247},
issn = {1520-5851},
abstract = {Sulfamethoxazole (SMX) passes through conventional wastewater treatment plants (WWTPs) mainly unaltered. Under anoxic conditions sulfate-reducing bacteria can transform SMX but the fate of the transformation products (TPs) and their prevalence in WWTPs remain unknown. Here, we report the anaerobic formation and aerobic degradation of SMX TPs. SMX biotransformation was observed in nitrate- and sulfate-reducing enrichment cultures. We identified 10 SMX TPs predominantly showing alterations in the heterocyclic and N[4]-arylamine moieties. Abiotic oxic incubation of sulfate-reducing culture filtrates led to further degradation of the major anaerobic SMX TPs. Upon reinoculation under oxic conditions, all anaerobically formed TPs, including the secondary TPs, were degraded. In samples collected at different stages of a full-scale municipal WWTP, anaerobically formed SMX TPs were detected at high concentrations in the primary clarifier and digested sludge units, where anoxic conditions were prevalent. Contrarily, their concentrations were lower in oxic zones like the biological treatment and final effluent. Our results suggest that anaerobically formed TPs were eliminated in the aerobic treatment stages, consistent with our observations in batch biotransformation experiments. More generally, our findings highlight the significance of varying redox states determining the fate of SMX and its TPs in engineered environments.},
}

@article {pmid38971962,
year = {2024},
author = {Zhang, W and Zhang, F and Wu, Y and Liu, J and Fahad, S and Li, Z and Zhao, S and Qiu, Z and Zhu 朱, M墨},
title = {Powdery Mildew of Xanthium strumarium Caused by Podosphaera xanthii in central China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-05-24-1062-PDN},
pmid = {38971962},
issn = {0191-2917},
abstract = {Xanthium strumarium, known as cocklebur, is an annual herb and has been used in traditional Chinese medicine. In October 2020, powdery mildew-like disease signs and symptoms were observed on X. strumarium grown in a crop field, Xinxiang city, Henan Province, China (35.36076° N, 113.93467° E). The specimen (PX-XS2023) was stored in Xinxiang Key Laboratory of Plant Stress Biology. White colonies in irregular or coalesced circular shaped-lesions were abundant on both ad- and abaxial surfaces of leaves and covered up to 99 % of the leaf area. Some of the infected leaves were senesced. More than 70 % of plants (n = 130) exhibited these signs and symptoms. Conidiophores were straight or slightly curved, 55 to 160 × 11 to 13 μm composed of foot-cells, shorter cells and conidia. Conidia were ellipsoid to oval, 29 to 40 × 14 to 20 μm (n = 50), with a length/width ration of 2.0 to 2.5, containing fibrosin bodies. Dark brown to black chasmothecia were found on infected leaves. The appendages were mycelium-shaped and at the base of scattered or gregarious chasmothecia (n = 50, 70 to 120 μm in diameter). Asci were 55 to 80 × 50 to 65 μm (n=30). These morphological characteristics were consistent with those of Podosphaera xanthii (Braun and Cook 2012). The internal transcribed spacer (ITS) region and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) region of the fungus (PX-XS2023) were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were respectively deposited into GenBank (Accession No. MW300956 and PP236083). BLASTn analysis indicated that the sequences were respectively 99.82 % (564/565) and 100% (272/272) identical to P. xanthii (MT260063 and ON075658). The phylogenetic analysis indicated that the strain PX-XS2023 and P. xanthii were clustered into a same branch. Therefore, the causal agent of powdery mildew on X. strumarium was P. xanthii. To conduct pathogenicity assays, mature leaves of five healthy X. strumarium (height in 50 centimeters) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants (Zhu et al. 2020). Five untreated plants served as controls. The controls and inoculated plants were separately maintained in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). Eight days post-inoculation, signs of powdery mildew were detectable on inoculated plants, however, the controls were asymptomatic. Thus, the fungal pathogen was morphologically and molecularly identified and confirmed as P. xanthii. This powdery mildew caused by P. xanthii was previously reported on X. strumarium in Korea, Russia and India (Farr and Rossman, 2021). In addition, P. xanthii was recorded on X. strumarium in Xinjiang Province, China (Tai 1979). However, this is the first report of P. xanthii on X. strumarium in central China, where is around 3000 km away from Xinjiang Province with geographically differences. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce medical value of X. strumarium. Therefore, the identification and confirmation of P. xanthii infecting X. strumarium enhance the knowledge on the hosts of this pathogen in China and will provide fundamental information for disease control in the future.},
}

@article {pmid38969462,
year = {2024},
author = {Chen, Y and Zhou, H and Gao, H and Su, Z and Li, X and Qi, P and Li, T and Hu, C and Li, Z and Bi, Z and Xing, X and Yang, J and Chen, C and Ma, K and Chen, J},
title = {Comprehensive comparison of water quality risk and microbial ecology between new and old cast iron pipe distribution systems.},
journal = {Journal of environmental sciences (China)},
volume = {146},
number = {},
pages = {55-66},
doi = {10.1016/j.jes.2023.05.020},
pmid = {38969462},
issn = {1001-0742},
mesh = {*Iron ; *Water Quality ; *Biofilms ; Corrosion ; *Water Supply ; Water Microbiology ; Drinking Water/microbiology/chemistry ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Water Pollutants, Chemical/analysis ; Trihalomethanes/analysis ; },
abstract = {The effects of cast iron pipe corrosion on water quality risk and microbial ecology in drinking water distribution systems (DWDSs) were investigated. It was found that trihalomethane (THMs) concentration and antibiotic resistance genes (ARGs) increased sharply in the old DWDSs. Under the same residual chlorine concentration conditions, the adenosine triphosphate concentration in the effluent of old DWDSs (Eff-old) was significantly higher than that in the effluent of new DWDSs. Moreover, stronger bioflocculation ability and weaker hydrophobicity coexisted in the extracellular polymeric substances of Eff-old, meanwhile, iron particles could be well inserted into the structure of the biofilms to enhance the mechanical strength and stability of the biofilms, hence enhancing the formation of THMs. Old DWDSs significantly influenced the microbial community of bulk water and triggered stronger microbial antioxidant systems response, resulting in higher ARGs abundance. Corroded cast iron pipes induced a unique interaction system of biofilms, chlorine, and corrosion products. Therefore, as the age of cast iron pipes increases, the fluctuation of water quality and microbial ecology should be paid more attention to maintain the safety of tap water.},
}

*Iron
*Water Quality
*Biofilms
Corrosion
*Water Supply
Water Microbiology
Drinking Water/microbiology/chemistry
Drug Resistance, Microbial/genetics
Environmental Monitoring
Water Pollutants, Chemical/analysis
Trihalomethanes/analysis

@article {pmid38969457,
year = {2024},
author = {Chen, SC and Musat, F and Richnow, HH and Krüger, M},
title = {Microbial diversity and oil biodegradation potential of northern Barents Sea sediments.},
journal = {Journal of environmental sciences (China)},
volume = {146},
number = {},
pages = {283-297},
doi = {10.1016/j.jes.2023.12.010},
pmid = {38969457},
issn = {1001-0742},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Biodegradation, Environmental ; Arctic Regions ; *Microbiota ; Petroleum/metabolism ; Bacteria/classification/metabolism/genetics ; Archaea/metabolism/classification/genetics ; Water Pollutants, Chemical/analysis/metabolism ; Biodiversity ; },
abstract = {The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.},
}

*Geologic Sediments/microbiology/chemistry
*Biodegradation, Environmental
Arctic Regions
*Microbiota
Petroleum/metabolism
Bacteria/classification/metabolism/genetics
Archaea/metabolism/classification/genetics
Water Pollutants, Chemical/analysis/metabolism
Biodiversity

@article {pmid38969451,
year = {2024},
author = {Ma, B and Zheng, L and Xie, B and Ma, L and Jia, M and Xie, C and Hu, C and Ulbricht, M and Wei, Y},
title = {Sustainable wastewater treatment and reuse in space.},
journal = {Journal of environmental sciences (China)},
volume = {146},
number = {},
pages = {237-240},
doi = {10.1016/j.jes.2023.08.023},
pmid = {38969451},
issn = {1001-0742},
mesh = {*Wastewater ; *Waste Disposal, Fluid/methods ; *Water Purification/methods ; Space Flight ; },
abstract = {Exploring the vast extraterrestrial space is an inevitable trend with continuous human development. Water treatment and reuse are crucial in the limited and closed space that is available in spaceships or long-term use space bases that will be established in the foreseeable future. Dedicated water treatment technologies have experienced iterative development for more than 60 years since the first manned spaceflight was successfully launched. Herein, we briefly review the related wastewater characteristics and the history of water treatment in space stations, and we focus on future challenges and perspectives, aiming at providing insights for optimizing wastewater treatment technologies and closing the water cycle in future.},
}

*Wastewater
*Waste Disposal, Fluid/methods
*Water Purification/methods
Space Flight

@article {pmid38968348,
year = {2024},
author = {Miettinen, TP and Gomez, AL and Wu, Y and Wu, W and Usherwood, TR and Hwang, Y and Roller, BRK and Polz, MF and Manalis, SR},
title = {Cell size, density, and nutrient dependency of unicellular algal gravitational sinking velocities.},
journal = {Science advances},
volume = {10},
number = {27},
pages = {eadn8356},
pmid = {38968348},
issn = {2375-2548},
mesh = {*Cell Size ; *Nutrients/metabolism ; Gravitation ; Phytoplankton/physiology/metabolism ; Photosynthesis ; Microalgae/metabolism ; },
abstract = {Eukaryotic phytoplankton, also known as algae, form the basis of marine food webs and drive marine carbon sequestration. Algae must regulate their motility and gravitational sinking to balance access to light at the surface and nutrients in deeper layers. However, the regulation of gravitational sinking remains largely unknown, especially in motile species. Here, we quantify gravitational sinking velocities according to Stokes' law in diverse clades of unicellular marine microalgae to reveal the cell size, density, and nutrient dependency of sinking velocities. We identify a motile algal species, Tetraselmis sp., that sinks faster when starved due to a photosynthesis-driven accumulation of carbohydrates and a loss of intracellular water, both of which increase cell density. Moreover, the regulation of cell sinking velocities is connected to proliferation and can respond to multiple nutrients. Overall, our work elucidates how cell size and density respond to environmental conditions to drive the vertical migration of motile algae.},
}

*Cell Size
*Nutrients/metabolism
Gravitation
Phytoplankton/physiology/metabolism
Photosynthesis
Microalgae/metabolism

@article {pmid38965531,
year = {2024},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {148},
pmid = {38965531},
issn = {1741-7007},
support = {Intramural Research Program//U.S. National Library of Medicine/ ; },
mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; },
abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.

RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.

CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.},
}

*Gene Transfer, Horizontal
*Microbiota/genetics
Biodiversity
Symbiosis/genetics
Models, Theoretical
Models, Biological

@article {pmid38964855,
year = {2024},
author = {Zhao, F and Wang, B and Cui, Q and Wu, Y},
title = {Genetically modified indigenous Pseudomonas aeruginosa drove bacterial community to change positively toward microbial enhanced oil recovery applications.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae168},
pmid = {38964855},
issn = {1365-2672},
abstract = {AIMS: Microbial enhanced oil recovery (MEOR) is cost-effective and eco-friendly for oil exploitation. Genetically modified biosurfactants-producing high-yield strains are promising for ex-situ MEOR. However, can they survive and produce biosurfactants in petroleum reservoirs for in-situ MEOR? What is their effect on the native bacterial community?

METHODS AND RESULTS: A genetically modified indigenous biosurfactants-producing strain Pseudomonas aeruginosa PrhlAB was bioaugmented in simulated reservoir environments. P. aeruginosa PrhlAB could stably colonize in simulated reservoirs. Biosurfactants (200 mg L-1) were produced in simulated reservoirs after bio-augmenting strain PrhlAB. The surface tension of fluid was reduced to 32.1 mN m-1. Crude oil was emulsified with an emulsification index of 60.1%. Bio-augmenting strain PrhlAB stimulated the MEOR-related microbial activities. Hydrocarbons-degrading bacteria and biosurfactants-producing bacteria were activated, while the hydrogen sulfide producing bacteria were inhibited. Bio-augmenting P. aeruginosa PrhlAB reduced the diversity of bacterial community, and gradually simplified the species composition. Bacteria with oil displacement potential became dominant genera, such as Shewanella, Pseudomonas and Arcobacter.

CONCLUSIONS: Culture-based and sequence-based analysis reveal that genetically modified biosurfactants-producing strain P. aeruginosa PrhlAB are promising for in-situ MEOR as well.},
}

@article {pmid38962127,
year = {2024},
author = {Lange, E and Kranert, L and Krüger, J and Benndorf, D and Heyer, R},
title = {Microbiome modeling: a beginner's guide.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1368377},
pmid = {38962127},
issn = {1664-302X},
abstract = {Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.},
}

@article {pmid38960913,
year = {2024},
author = {Bischof, PSP and Bartolomaeus, TUP and Löber, U and Bleidorn, C},
title = {Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {91},
pmid = {38960913},
issn = {1432-184X},
support = {F01KI1909A//Bundesministerium für Bildung und Forschung/ ; },
mesh = {Animals ; *Diptera/microbiology ; *Larva/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; DNA Barcoding, Taxonomic ; Kelp/microbiology ; },
abstract = {Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies' microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this species have been subject of numerous studies, with debates whether they directly consume kelp or primarily feed on associated bacteria. By using a 16S rRNA metabarcoding approach, we found that the larval microbiota displayed considerably less diversity than adults, heavily dominated by only four operational taxonomic units (OTUs). Phylogenetic placement recovered the most dominant OTU of the larval microbiome, which is the source of more than half of all metabarcoding sequence reads, as an undescribed genus of Orbaceae (Gammaproteobacteria). Interestingly, this OTU is barely found among the 15 most abundant taxa of the adult microbiome, where it is responsible for less than 2% of the metabarcoding sequence reads. The other three OTUs dominating the larval microbiome have been assigned as Psychrobacter (Gammaproteobacteria), Wohlfahrtiimonas (Gammaproteobacteria), and Cetobacterium (Fusobacteriota). Moreover, we also uncovered a distinct shift in the functional composition between the larval and adult stages, where our taxonomic profiling suggests a significant decrease in functional diversity in larval samples. Our study offers insights into the microbiome dynamics and functional composition of Coelopa frigida.},
}

Animals
*Diptera/microbiology
*Larva/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Phylogeny
*Bacteria/classification/genetics/isolation & purification
DNA Barcoding, Taxonomic
Kelp/microbiology

@article {pmid38960411,
year = {2024},
author = {Mafune, KK and Kasson, MT and Winkler, MH},
title = {Building blocks towards sustainable biofertilizers: Variation in arbuscular mycorrhizal spore germination when immobilized with diazotrophic bacteria in biodegradable hydrogel beads.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae167},
pmid = {38960411},
issn = {1365-2672},
abstract = {AIM: We investigated whether there was interspecies and intraspecies variation in spore germination of twelve strains of arbuscular mycorrhizal fungi when co-entrapped with the diazotrophic plant growth promoting bacteria, Azospirillum brasilense Sp7 in alginate hydrogel beads.

METHODS AND RESULTS: Twelve Rhizophagus irregularis, Rhizophagus intraradices, and Funneliformis mosseae strains were separately combined with a live culture of Azospirillum brasilense Sp7. Each fungal-bacterial consortia was supplemented with sodium alginate to a 2% concentration (v/v) and cross-linked in calcium chloride (2% w/v) to form biodegradable hydrogel beads. 100 beads from each combination (total of 1,200) were fixed in solidified modified Strullu and Romand media. Beads were observed for successful spore germination and bacterial growth over 14 days. In all cases, successful growth of A. brasilense was observed. For arbuscular mycorrhizal fungi, interspecies variation in spore germination was observed, with R. intraradices having the highest germination rate (64.3%), followed by R. irregularis (45.5%) and F. mosseae (40.3%). However, a difference in intraspecies germination was only observed among strains of R. irregularis and F. mosseae. Despite having varying levels of germination, even the strains with the lowest potential were still able to establish with the plant host Brachypodium distachyon in a model system.

CONCLUSIONS: Arbuscular mycorrhizal spore germination varied across strains when co-entrapped with a diazotrophic plant-growth promoting bacteria. This demonstrates that hydrogel beads containing a mixed consortium hold potential as a sustainable biofertilizer and that compatibility tests remain an important building block when aiming to create a hydrogel biofertilizer that encases a diversity of bacteria and fungi. Moving forward, further studies should be conducted to test the efficacy of these hydrogel biofertilizers on different crops across varying climatic conditions in order to optimize their potential.},
}

@article {pmid38959887,
year = {2024},
author = {Perruzza, L and Rezzonico Jost, T and Raneri, M and Gargari, G and Palatella, M and De Ponte Conti, B and Seehusen, F and Heckmann, J and Viemann, D and Guglielmetti, S and Grassi, F},
title = {Protection from environmental enteric dysfunction and growth improvement in malnourished newborns by amplification of secretory IgA.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {101639},
doi = {10.1016/j.xcrm.2024.101639},
pmid = {38959887},
issn = {2666-3791},
abstract = {Environmental enteric dysfunction (EED) is a condition associated with malnutrition that can progress to malabsorption and villous atrophy. Severe EED results in linear growth stunting, slowed neurocognitive development, and unresponsiveness to oral vaccines. Prenatal exposure to malnutrition and breast feeding by malnourished mothers replicates EED. Pups are characterized by deprivation of secretory IgA (SIgA) and altered development of the gut immune system and microbiota. Extracellular ATP (eATP) released by microbiota limits T follicular helper (Tfh) cell activity and SIgA generation in Peyer's patches (PPs). Administration of a live biotherapeutic releasing the ATP-degrading enzyme apyrase to malnourished pups restores SIgA levels and ameliorates stunted growth. SIgA is instrumental in improving the growth and intestinal immune competence of mice while they are continuously fed a malnourished diet. The analysis of microbiota composition suggests that amplification of endogenous SIgA may exert a dominant function in correcting malnourishment dysbiosis and its consequences on host organisms, irrespective of the actual microbial ecology.},
}

@article {pmid38958675,
year = {2024},
author = {Dendooven, L and Pérez-Hernández, V and Navarro-Pérez, G and Tlalmis-Corona, J and Navarro-Noya, YE},
title = {Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. & Cham.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {90},
pmid = {38958675},
issn = {1432-184X},
support = {591213//Consejo Nacional de Humanidades Ciencia y Tecnología (CONAHCyT)/ ; INFR-2015-01-253217//Consejo Nacional de Humanidades Ciencia y Tecnología (CONAHCyT)/ ; },
mesh = {*Seedlings/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Endophytes/classification/isolation & purification/physiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Abies/microbiology ; *Plant Roots/microbiology ; Soil Microbiology ; Biodiversity ; Microbiota ; DNA, Bacterial/genetics ; },
abstract = {Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. & Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.},
}

*Seedlings/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification
*Endophytes/classification/isolation & purification/physiology/genetics
*RNA, Ribosomal, 16S/genetics
*Abies/microbiology
*Plant Roots/microbiology
Soil Microbiology
Biodiversity
Microbiota
DNA, Bacterial/genetics

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

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

@article {pmid38955821,
year = {2024},
author = {Weisse, T and Pröschold, T and Kammerlander, B and Sonntag, B and Schicker, L},
title = {Numerical and Thermal Response of the Bacterivorous Ciliate Colpidium kleini, a Species Potentially at Risk of Extinction by Rising Water Temperatures.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {89},
pmid = {38955821},
issn = {1432-184X},
support = {10.55776/P32714//Austrian Science Fund/ ; DOC fForte 22883//Österreichischen Akademie der Wissenschaften/ ; },
mesh = {*Ciliophora/physiology/growth & development/classification/isolation & purification ; Lakes/microbiology/parasitology ; Temperature ; Phylogeny ; Extinction, Biological ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {We investigated the food-dependent growth and thermal response of the freshwater ciliate Colpidium kleini using numerical response (NR) experiments. This bacterivorous ciliate occurs in lotic water and the pelagial of lakes and ponds. The C. kleini strain used in this work was isolated from a small alpine lake and identified by combining detailed morphological inspections with molecular phylogeny. Specific growth rates (rmax) were measured from 5 to 21 °C. The ciliate did not survive at 22 °C. The threshold bacterial food levels (0.3 - 2.2 × 10[6] bacterial cells mL[-1]) matched the bacterial abundance in the alpine lake from which C. kleini was isolated. The food threshold was notably lower than previously reported for C. kleini and two other Colpidium species. The threshold was similar to levels reported for oligotrich and choreotrich ciliates if expressed in terms of bacterial biomass (0.05 - 0.43 mg C L[-1]). From the NR results, we calculated physiological mortality rates at zero food concentration. The mean mortality (0.55 ± 0.17 d[-1]) of C. kleini was close to the mean estimate obtained for other planktonic ciliates that do not encyst. We used the data obtained by the NR experiments to fit a thermal performance curve (TPC). The TPC yielded a temperature optimum at 17.3 °C for C. kleini, a maximum upper thermal tolerance limit of 21.9 °C, and a thermal safety margin of 4.6 °C. We demonstrated that combining NR with TPC analysis is a powerful tool to predict better a species' fitness in response to temperature and food.},
}

*Ciliophora/physiology/growth & development/classification/isolation & purification
Lakes/microbiology/parasitology
Temperature
Phylogeny
Extinction, Biological
Bacteria/classification/isolation & purification/genetics

@article {pmid38954336,
year = {2024},
author = {Benammar, L and Menasria, T and Dibi, AR},
title = {Deciphering the geochemical influences on bacterial diversity and communities among two Algerian hot springs.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38954336},
issn = {1614-7499},
abstract = {Northeastern Algeria boasts numerous hot springs, yet these hydrothermal sites remain largely unexplored for their microbial ecology. The present study explores the bacterial abundance and diversity within two distinct Algerian hot springs (Hammam Saïda and Hammam Debagh) and investigates the link between the prevailing bacteria with geochemical parameters. High-throughput 16S rRNA gene sequencing of water and sediment samples revealed a bacterial dominance of 99.85-91.16% compared to Archaea (0.14-0.66%) in both springs. Interestingly, Saïda hot spring, characterized by higher temperatures and sodium content, harbored a community dominated by Pseudomonadota (51.13%), whereas Debagh, a Ca-Cl-SO4 type spring, was primarily populated by Bacillota with 55.33%. Bacteroidota displayed even distribution across both sites. Additional phyla, including Chloroflexota, Deinococcota, Cyanobacteriota, and Chlorobiota, were also present. Environmental factors, particularly temperature, sodium, potassium, and alkalinity, significantly influenced bacterial diversity and composition. These findings shed light on the interplay between distinct microbial communities and their associated geochemical properties, providing valuable insights for future research on biogeochemical processes in these unique ecosystems driven by distinct environmental conditions, including potential applications in bioremediation and enzyme discovery.},
}

@article {pmid38952448,
year = {2024},
author = {Aqueel, R and Badar, A and Ijaz, UZ and Malik, KA},
title = {Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1381883},
pmid = {38952448},
issn = {1664-302X},
abstract = {Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant's ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuD-resistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. This concept deciphers the diseased and healthy plant's response to viral disease, which may be microbially mediated.},
}

@article {pmid38946903,
year = {2024},
author = {Malfent, F and Zehl, M and Kirkegaard, RH and Oberhofer, M and Zotchev, SB},
title = {Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1408479},
pmid = {38946903},
issn = {1664-302X},
abstract = {Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.},
}

@article {pmid38946328,
year = {2024},
author = {Langlois, GA},
title = {Past-President address: My journey in microbial ecology-footprints in the sand, island hopping, supply chains, and technology bridges.},
journal = {The Journal of eukaryotic microbiology},
volume = {},
number = {},
pages = {e13037},
doi = {10.1111/jeu.13037},
pmid = {38946328},
issn = {1550-7408},
abstract = {This paper highlights and honors the connectivity among protistan researchers, using my own research journey as a backdrop, with attention to the supply chain of ideas, supporters, and other influencers who helped to shape and guide my career by sharing their ideas, protocols, skills, and enthusiasm. In looking back at the journey, the supply chain in my career has also included changes in the conceptual framework for my research studies, converging with a continuous flow of ideas and support from colleagues and mentors. To illustrate the complex map of ideas and supporters, this paper will examine technological advances, paradigm shifts in ecological constructs, geographical considerations, breakthroughs in peritrich biology, and the importance of an integrated perspective as we navigate the changing realities of today's scientific challenges.},
}

@article {pmid38946115,
year = {2024},
author = {Zayed, N and Vertommen, R and Simoens, K and Bernaerts, K and Boon, N and Srivastava, MG and Braem, A and Van Holm, W and Castro, AB and Teughels, W},
title = {How well do antimicrobial mouth rinses prevent dysbiosis in an in vitro periodontitis biofilm model?.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/JPER.23-0674},
pmid = {38946115},
issn = {1943-3670},
abstract = {BACKGROUND: Periodontal diseases are associated with dysbiosis in the oral microbial communities. Managing oral biofilms is therefore key for preventing these diseases. Management protocols often include over-the-counter antimicrobial mouth rinses, which lack data on their effects on the oral microbiome's ecology, bacterial composition, metabolic activity, and dysbiosis resilience. This study examined the efficacy of antimicrobial mouth rinses to halt dysbiosis in in vitro oral biofilms under periodontitis-simulating conditions.

METHODS: Multispecies oral biofilms were grown on hydroxyapatite discs (HADs) and rinsed daily with one of six mouth rinses. Positive and negative controls were included. After three rinses, biofilms were analyzed with viability quantitative polymerase chain reaction and visualized using scanning electron microscopy. Supernatants of rinsed biofilms were used for metabolic activity analysis. In addition, human oral keratinocytes were exposed to rinsed biofilms to assess their inflammatory response. All outputs were analyzed for correlation using Spearman coefficient.

RESULTS: Product-related changes were observed in the rinsed biofilms. Three of the six tested mouth rinses could significantly prevent dysbiosis with ≥30% reduction in pathobiont abundance relative to the control. These biofilms had lower metabolic activity, and the exposed human oral keratinocyte produced less interleukin-8. Interleukin-8 production correlated to both pathobiont quantity and the metabolic activity of the biofilms.

CONCLUSION: Some mouth rinses could support biofilm resilience and stop dysbiosis evolution in the biofilm model, with a clear product-related effect. Such mouth rinses can be considered for patients under maintenance/supportive periodontal therapy to prevent/delay disease recurrence. Others are more useful for different periodontal therapy stages.},
}

@article {pmid38943017,
year = {2024},
author = {Pires, CS and Costa, L and Barbosa, SG and Sequeira, JC and Cachetas, D and Freitas, JP and Martins, G and Machado, AV and Cavaleiro, AJ and Salvador, AF},
title = {Microplastics Biodegradation by Estuarine and Landfill Microbiomes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {88},
pmid = {38943017},
issn = {1432-184X},
support = {UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; 2023.01617.BD//Fundação para a Ciência e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; },
mesh = {*Biodegradation, Environmental ; *Microbiota ; *Microplastics/metabolism ; *Waste Disposal Facilities ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Water Pollutants, Chemical/metabolism ; Polyesters/metabolism ; Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Estuaries ; Polyethylene/metabolism ; Polyethylene Terephthalates/metabolism ; },
abstract = {Plastic pollution poses a worldwide environmental challenge, affecting wildlife and human health. Assessing the biodegradation capabilities of natural microbiomes in environments contaminated with microplastics is crucial for mitigating the effects of plastic pollution. In this work, we evaluated the potential of landfill leachate (LL) and estuarine sediments (ES) to biodegrade polyethylene (PE), polyethylene terephthalate (PET), and polycaprolactone (PCL), under aerobic, anaerobic, thermophilic, and mesophilic conditions. PCL underwent extensive aerobic biodegradation with LL (99 ± 7%) and ES (78 ± 3%) within 50-60 days. Under anaerobic conditions, LL degraded 87 ± 19% of PCL in 60 days, whereas ES showed minimal biodegradation (3 ± 0.3%). PE and PET showed no notable degradation. Metataxonomics results (16S rRNA sequencing) revealed the presence of highly abundant thermophilic microorganisms assigned to Coprothermobacter sp. (6.8% and 28% relative abundance in anaerobic and aerobic incubations, respectively). Coprothermobacter spp. contain genes encoding two enzymes, an esterase and a thermostable monoacylglycerol lipase, that can potentially catalyze PCL hydrolysis. These results suggest that Coprothermobacter sp. may be pivotal in landfill leachate microbiomes for thermophilic PCL biodegradation across varying conditions. The anaerobic microbial community was dominated by hydrogenotrophic methanogens assigned to Methanothermobacter sp. (21%), pointing at possible syntrophic interactions with Coprothermobacter sp. (a H2-producer) during PCL biodegradation. In the aerobic experiments, fungi dominated the eukaryotic microbial community (e.g., Exophiala (41%), Penicillium (17%), and Mucor (18%)), suggesting that aerobic PCL biodegradation by LL involves collaboration between fungi and bacteria. Our findings bring insights on the microbial communities and microbial interactions mediating plastic biodegradation, offering valuable perspectives for plastic pollution mitigation.},
}

*Biodegradation, Environmental
*Microbiota
*Microplastics/metabolism
*Waste Disposal Facilities
*Bacteria/classification/metabolism/genetics/isolation & purification
Water Pollutants, Chemical/metabolism
Polyesters/metabolism
Geologic Sediments/microbiology
RNA, Ribosomal, 16S/genetics
Estuaries
Polyethylene/metabolism
Polyethylene Terephthalates/metabolism

@article {pmid38942024,
year = {2024},
author = {Harder, CB and Miyauchi, S and Virágh, M and Kuo, A and Thoen, E and Andreopoulos, B and Lu, D and Skrede, I and Drula, E and Henrissat, B and Morin, E and Kohler, A and Barry, K and LaButti, K and Salamov, A and Lipzen, A and Merényi, Z and Hegedüs, B and Baldrian, P and Stursova, M and Weitz, H and Taylor, A and Koriabine, M and Savage, E and Grigoriev, IV and Nagy, LG and Martin, F and Kauserud, H},
title = {Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100586},
doi = {10.1016/j.xgen.2024.100586},
pmid = {38942024},
issn = {2666-979X},
abstract = {Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.},
}

@article {pmid38940921,
year = {2024},
author = {Picariello, E and De Nicola, F},
title = {Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {86},
pmid = {38940921},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Fagus/microbiology ; *Quercus/microbiology ; *Forests ; *Microbiota ; *Soil/chemistry ; *Seasons ; Bacteria/classification/metabolism/genetics/isolation & purification ; Biodiversity ; Forestry ; Trees/microbiology ; Ecosystem ; },
abstract = {Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.},
}

*Soil Microbiology
*Fagus/microbiology
*Quercus/microbiology
*Forests
*Microbiota
*Soil/chemistry
*Seasons
Bacteria/classification/metabolism/genetics/isolation & purification
Biodiversity
Forestry
Trees/microbiology
Ecosystem

@article {pmid38643981,
year = {2024},
author = {Haller, F and Jimenez, K and Baumgartner, M and Lang, M and Klotz, A and Jambrich, M and Busslinger, G and Müllauer, L and Khare, V and Gasche, C},
title = {Nfe2l2/NRF2 Deletion Attenuates Tumorigenesis and Increases Bacterial Diversity in a Mouse Model of Lynch Syndrome.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {17},
number = {7},
pages = {311-324},
doi = {10.1158/1940-6207.CAPR-23-0478},
pmid = {38643981},
issn = {1940-6215},
support = {P32302FW//Austrian Science Fund (FWF)/ ; },
mesh = {Animals ; *NF-E2-Related Factor 2/metabolism/genetics ; Mice ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology/metabolism ; *MutS Homolog 2 Protein/genetics/metabolism ; Humans ; *Mice, Inbred C57BL ; *Disease Models, Animal ; Carcinogenesis/genetics/pathology ; Mice, Knockout ; Female ; Intestinal Mucosa/pathology/metabolism/microbiology ; Male ; },
abstract = {Lynch syndrome (LS) is the most prevalent heritable form of colorectal cancer. Its early onset and high lifetime risk for colorectal cancer emphasize the necessity for effective chemoprevention. NFE2L2 (NRF2) is often considered a potential druggable target, and many chemopreventive compounds induce NRF2. However, although NRF2 counteracts oxidative stress, it is also overexpressed in colorectal cancer and may promote tumorigenesis. In this study, we evaluated the role of NRF2 in the prevention of LS-associated neoplasia. We found increased levels of NRF2 in intestinal epithelia of mice with intestinal epithelium-specific Msh2 deletion (MSH2ΔIEC) compared with C57BL/6 (wild-type) mice, as well as an increase in downstream NRF2 targets NAD(P)H dehydrogenase (quinone 1) and glutamate-cysteine ligase catalytic subunit. Likewise, NRF2 levels were increased in human MSH2-deficient LS tumors compared with healthy human controls. In silico analysis of a publicly accessible RNA sequencing LS dataset also found an increase in downstream NRF2 targets. Upon crossing MSH2ΔIEC with Nrf2null (MSH2ΔIECNrf2null) mice, we unexpectedly found reduced tumorigenesis in MSH2ΔIECNrf2null mice compared with MSH2ΔIEC mice after 40 weeks, which occurred despite an increase in oxidative damage in MSH2ΔIECNrf2null mice. The loss of NRF2 impaired proliferation as seen by Ki67 intestinal staining and in organoid cultures. This was accompanied by diminished WNT/β-catenin signaling, but apoptosis was unaffected. Microbial α-diversity increased over time with the loss of NRF2 based upon 16S rRNA gene amplicon sequencing of murine fecal samples. Altogether, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. Activation of NRF2 may not be a feasible strategy for chemoprevention in LS. Prevention Relevance: Patients with LS have an early onset and high lifetime risk for colorectal cancer. In this study, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. This suggests that NRF2 may not be a tumor suppressor in this specific context.},
}

Animals
*NF-E2-Related Factor 2/metabolism/genetics
Mice
*Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology/metabolism
*MutS Homolog 2 Protein/genetics/metabolism
Humans
*Mice, Inbred C57BL
*Disease Models, Animal
Carcinogenesis/genetics/pathology
Mice, Knockout
Female
Intestinal Mucosa/pathology/metabolism/microbiology
Male

@article {pmid38940862,
year = {2024},
author = {Ljaljević Grbić, M and Dimkić, I and Janakiev, T and Kosel, J and Tavzes, Č and Popović, S and Knežević, A and Legan, L and Retko, K and Ropret, P and Unković, N},
title = {Uncovering the Role of Autochthonous Deteriogenic Biofilm Community: Rožanec Mithraeum Monument (Slovenia).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {87},
pmid = {38940862},
issn = {1432-184X},
support = {451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; },
mesh = {*Biofilms ; *Lichens/microbiology/physiology ; *Calcium Carbonate ; Slovenia ; Ascomycota/physiology ; Mycobiome ; },
abstract = {The primary purpose of the study, as part of the planned conservation work, was to uncover all aspects of autochthonous biofilm pertaining to the formation of numerous deterioration symptoms occurring on the limestone Rožanec Mithraeum monument in Slovenia. Using state-of-the-art sequencing technologies combining mycobiome data with observations made via numerous light and spectroscopic (FTIR and Raman) microscopy analyses pointed out to epilithic lichen Gyalecta jenensis and its photobiont, carotenoid-rich Trentepohlia aurea, as the origin of salmon-hued pigmented alterations of limestone surface. Furthermore, the development of the main deterioration symptom on the monument, i.e., biopitting, was instigated by the formation of typical endolithic thalli and ascomata of representative Verrucariaceae family (Verrucaria sp.) in conjunction with the oxalic acid-mediated dissolution of limestone. The domination of lichenized fungi, as the main deterioration agents, both on the relief and surrounding limestone, was additionally supported by the high relative abundance of lichenized and symbiotroph groups in FUNGuild analysis. Obtained results not only upgraded knowledge of this frequently occurring but often overlooked group of extremophilic stone heritage deteriogens but also provided a necessary groundwork for the development of efficient biocontrol formulation applicable in situ for the preservation of similarly affected limestone monuments.},
}

*Biofilms
*Lichens/microbiology/physiology
*Calcium Carbonate
Slovenia
Ascomycota/physiology
Mycobiome

@article {pmid38940768,
year = {2024},
author = {Baroncelli, R and Cobo-Díaz, JF and Benocci, T and Peng, M and Battaglia, E and Haridas, S and Andreopoulos, W and LaButti, K and Pangilinan, J and Lipzen, A and Koriabine, M and Bauer, D and Le Floch, G and Mäkelä, MR and Drula, E and Henrissat, B and Grigoriev, IV and Crouch, JA and de Vries, RP and Sukno, SA and Thon, MR},
title = {Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {38940768},
issn = {2047-217X},
mesh = {*Colletotrichum/genetics/pathogenicity ; *Transcriptome ; *Genome, Fungal ; *Evolution, Molecular ; Phylogeny ; Adaptation, Physiological/genetics ; Gene Expression Profiling/methods ; Plant Diseases/microbiology/genetics ; },
abstract = {BACKGROUND: Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes.

RESULTS: Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation.

CONCLUSIONS: These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.},
}

*Colletotrichum/genetics/pathogenicity
*Transcriptome
*Genome, Fungal
*Evolution, Molecular
Phylogeny
Adaptation, Physiological/genetics
Gene Expression Profiling/methods
Plant Diseases/microbiology/genetics

@article {pmid38940583,
year = {2024},
author = {Xie, G and Sun, C and Luo, W and Gong, Y and Tang, X},
title = {Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0071424},
doi = {10.1128/aem.00714-24},
pmid = {38940583},
issn = {1098-5336},
abstract = {Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.},
}

@article {pmid38939048,
year = {2024},
author = {Shi, Q and Sun, L and Gao, J and Li, F and Chen, D and Shi, T and Tan, Y and Chang, H and Liu, X and Kang, J and Lu, F and Huang, Z and Zhao, H},
title = {Effects of sodium lauryl sulfate and postbiotic toothpaste on oral microecology.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2372224},
doi = {10.1080/20002297.2024.2372224},
pmid = {38939048},
issn = {2000-2297},
abstract = {The diversity and delicate balance of the oral microbiome contribute to oral health, with its disruption leading to oral and systemic diseases. Toothpaste includes elements like traditional additives such as sodium lauryl sulfate (SLS) as well as novel postbiotics derived from probiotics, which are commonly employed for maintaining oral hygiene and a healthy oral cavity. However, the response of the oral microbiota to these treatments remains poorly understood. In this study, we systematically investigated the impact of SLS, and toothpaste containing postbiotics (hereafter, postbiotic toothpaste) across three systems: biofilms, animal models, and clinical populations. SLS was found to kill bacteria in both preformed biofilms (mature biofilms) and developing biofilms (immature biofilms), and disturbed the microbial community structure by increasing the number of pathogenic bacteria. SLS also destroyed periodontal tissue, promoted alveolar bone resorption, and enhanced the extent of inflammatory response level. The postbiotic toothpaste favored bacterial homeostasis and the normal development of the two types of biofilms in vitro, and attenuated periodontitis and gingivitis in vivo via modulation of oral microecology. Importantly, the postbiotic toothpaste mitigated the adverse effects of SLS when used in combination, both in vitro and in vivo. Overall, the findings of this study describe the impact of toothpaste components on oral microflora and stress the necessity for obtaining a comprehensive understanding of oral microbial ecology by considering multiple aspects.},
}

@article {pmid38938005,
year = {2024},
author = {Chaudhary, DK and Kim, SE and Park, HJ and Kim, KH},
title = {Unveiling the Bacterial Community across the Stomach, Hepatopancreas, Anterior Intestine, and Posterior Intestine of Pacific Whiteleg Shrimp.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {6},
pages = {1260-1269},
doi = {10.4014/jmb.2403.03039},
pmid = {38938005},
issn = {1738-8872},
mesh = {Animals ; *Penaeidae/microbiology ; *Hepatopancreas/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Republic of Korea ; *Intestines/microbiology ; Phylogeny ; Stomach/microbiology ; Biodiversity ; Aquaculture ; DNA, Bacterial/genetics ; },
abstract = {The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.},
}

Animals
*Penaeidae/microbiology
*Hepatopancreas/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
Republic of Korea
*Intestines/microbiology
Phylogeny
Stomach/microbiology
Biodiversity
Aquaculture
DNA, Bacterial/genetics

@article {pmid38937989,
year = {2024},
author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W},
title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2400058},
doi = {10.1002/advs.202400058},
pmid = {38937989},
issn = {2198-3844},
support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; },
abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.},
}

@article {pmid38936927,
year = {2024},
author = {Shen, CL and Wankhade, UD and Shankar, K and Najjar, RS and Feresin, RG and Elmassry, MM and Dufour, JM and Kaur, G and Chintapalli, SV and Piccolo, BD and Dunn, DM and Cao, JJ},
title = {Effects of Statin and Annatto-extracted Tocotrienol Supplementation on Glucose Homeostasis, Bone Microstructure, and Gut Microbiota Composition in Obese Mice.},
journal = {In vivo (Athens, Greece)},
volume = {38},
number = {4},
pages = {1557-1570},
doi = {10.21873/invivo.13606},
pmid = {38936927},
issn = {1791-7549},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Tocotrienols/pharmacology/administration & dosage ; Mice ; *Homeostasis/drug effects ; *Obesity/drug therapy/metabolism ; Male ; *Dietary Supplements ; *Bone and Bones/drug effects/metabolism/pathology ; *Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology ; *Diet, High-Fat/adverse effects ; Bixaceae/chemistry ; Mice, Obese ; Plant Extracts/pharmacology/administration & dosage ; Glucose/metabolism ; Mice, Inbred C57BL ; Insulin Resistance ; Blood Glucose ; Disease Models, Animal ; Liver/drug effects/metabolism/pathology ; Biomarkers ; Carotenoids ; },
abstract = {BACKGROUND/AIM: This study examined the effects of tocotrienols (TT) in conjunction with statin on glucose homeostasis, bone microstructure, gut microbiome, and systemic and liver inflammatory markers in obese C57BL/6J mice.

MATERIALS AND METHODS: Forty male C57BL/6J mice were fed a high-fat diet (HFD) and assigned into four groups in a 2 (no statin vs. 120 mg statin/kg diet)×2 (no TT vs. 400 mg TT/kg diet) factorial design for 14 weeks.

RESULTS: Statin and TT improved glucose tolerance only when each was given alone, and only statin supplementation decreased insulin resistance. Consistently, only statin supplementation decreased serum insulin levels and HOMA-IR. Pancreatic insulin was also increased with statin treatment. Statin and TT, alone or in combination, reduced the levels of serum IL-6, but only TT attenuated the increased serum leptin levels induced by a HFD. Statin supplementation increased bone area/total area and connectivity density at LV-4, while TT supplementation increased bone area/total area and trabecular number, but decreased trabecular separation at the distal femur. Statin supplementation, but not TT, reduced hepatic inflammatory cytokine gene expression. Neither TT supplementation nor statin supplementation statistically altered microbiome species evenness or richness. However, they altered the relative abundance of certain microbiome species. Most notably, both TT and statin supplementation increased the relative abundance of Lachnospiraceae UCG-006.

CONCLUSION: TT and statin collectively benefit bone microstructure, glucose homeostasis, and microbial ecology in obese mice. Such changes may be, in part, associated with suppression of inflammation in the host.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Tocotrienols/pharmacology/administration & dosage
Mice
*Homeostasis/drug effects
*Obesity/drug therapy/metabolism
Male
*Dietary Supplements
*Bone and Bones/drug effects/metabolism/pathology
*Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology
*Diet, High-Fat/adverse effects
Bixaceae/chemistry
Mice, Obese
Plant Extracts/pharmacology/administration & dosage
Glucose/metabolism
Mice, Inbred C57BL
Insulin Resistance
Blood Glucose
Disease Models, Animal
Liver/drug effects/metabolism/pathology
Biomarkers
Carotenoids

@article {pmid38936916,
year = {2024},
author = {Morikawa, T and Paudel, D and Uehara, O and Ariwansa, D and Kobayashi, Y and Yang, J and Yoshida, K and Abiko, Y},
title = {Effects of Laurus nobilis Leaf Extract (LAURESH[®]) on Oral and Gut Microbiota Diversity in Mice.},
journal = {In vivo (Athens, Greece)},
volume = {38},
number = {4},
pages = {1758-1766},
doi = {10.21873/invivo.13626},
pmid = {38936916},
issn = {1791-7549},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves/chemistry ; Mice ; *Plant Extracts/pharmacology ; *Laurus/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Biodiversity ; Feces/microbiology ; Bacteria/classification/drug effects/genetics/isolation & purification ; Male ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND/AIM: The leaves of Laurus nobilis have been used for culinary purposes for many years and have recently been shown to have beneficial effects on human health by altering microbiota composition. However, the effects of L. nobilis on the diversity of microbiomes in the oral cavity and gut remain unknown. Therefore, in this study, we examined the effects of an extract of L. nobilis on the diversity of microbiomes in the oral cavity and gut in mice.

MATERIALS AND METHODS: C57BL/6J mice were randomly divided into two groups and fed a standard diet (SD) and a standard diet containing 5% LAURESH[®], a laurel extract (SDL). After 10 weeks, oral swabs and fecal samples were collected. The bacterial DNA extracted from the oral swabs and feces was used for microbiota analysis using 16S rRNA sequencing. The sequencing data were analyzed using the Quantitative Insights into Microbial Ecology 2 in the DADA2 pipeline and 16S rRNA database.

RESULTS: The α-diversity of the oral microbiome was significantly greater in the SDL group than in the SD group. The β-diversity of the oral microbiome was also significantly different between the groups. Moreover, the taxonomic abundance analysis showed that five bacteria in the gut were significantly different among the groups. Furthermore, the SDL diet increased the abundance of beneficial gut bacteria, such as Akkermansia sp.

CONCLUSION: Increased diversity of the oral microbiome and proportion of Akkermansia sp. in the gut microbiome induced by L. nobilis consumption may benefit oral and gut health.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Plant Leaves/chemistry
Mice
*Plant Extracts/pharmacology
*Laurus/chemistry
*RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
Biodiversity
Feces/microbiology
Bacteria/classification/drug effects/genetics/isolation & purification
Male
Mice, Inbred C57BL

@article {pmid38936824,
year = {2024},
author = {Chen, YC and Destouches, L and Cook, A and Fedorec, AJH},
title = {Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae158},
pmid = {38936824},
issn = {1365-2672},
abstract = {Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.},
}

@article {pmid38935596,
year = {2024},
author = {O'Brien, JM and Blais, N and Butler, C and White, N and Bustead, A and Figler, C and Wells, M and Anderson, G and Yuhas, A and Ernakovich, JG},
title = {Ten "simple" rules for non-Indigenous researchers engaging Indigenous communities in Arctic research.},
journal = {PLoS computational biology},
volume = {20},
number = {6},
pages = {e1012093},
doi = {10.1371/journal.pcbi.1012093},
pmid = {38935596},
issn = {1553-7358},
mesh = {Arctic Regions ; Humans ; *Indigenous Peoples ; Research Personnel ; },
}

Arctic Regions
Humans
*Indigenous Peoples
Research Personnel

@article {pmid38935504,
year = {2024},
author = {Luo, S and Zhang, X and Zhou, X},
title = {Temporospatial dynamics and host specificity of honeybee gut bacteria.},
journal = {Cell reports},
volume = {43},
number = {7},
pages = {114408},
doi = {10.1016/j.celrep.2024.114408},
pmid = {38935504},
issn = {2211-1247},
abstract = {Honeybees are important pollinators worldwide, with their gut microbiota playing a crucial role in maintaining their health. The gut bacteria of honeybees consist of primarily five core lineages that are spread through social interactions. Previous studies have provided a basic understanding of the composition and function of the honeybee gut microbiota, with recent advancements focusing on analyzing diversity at the strain level and changes in bacterial functional genes. Research on honeybee gut microbiota across different regions globally has provided insights into microbial ecology. Additionally, recent findings have shed light on the mechanisms of host specificity of honeybee gut bacteria. This review explores the temporospatial dynamics in honeybee gut microbiota, discussing the reasons and mechanisms behind these fluctuations. This synopsis provides insights into host-microbe interactions and is invaluable for honeybee health.},
}

@article {pmid38935220,
year = {2024},
author = {Parra, B and Lutz, VT and Brøndsted, L and Carmona, JL and Palomo, A and Nesme, J and Van Hung Le, V and Smets, BF and Dechesne, A},
title = {Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {85},
pmid = {38935220},
issn = {1432-184X},
support = {101026675//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant/ ; 002200000279//VRID Postdoctorado from Vicerrectoría de Investigación y Desarrollo, Universidad de Concepción/ ; P-PhanFARE (23046)//Villum Fonden/ ; },
mesh = {*Plasmids/genetics ; *Wastewater/virology/microbiology ; *Bacteriophages/genetics/isolation & purification/physiology/classification ; Genome, Viral ; Escherichia coli/virology/genetics ; Host Specificity ; Pseudomonas putida/virology/genetics ; Salmonella enterica/virology/genetics ; Phylogeny ; },
abstract = {Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.},
}

*Plasmids/genetics
*Wastewater/virology/microbiology
*Bacteriophages/genetics/isolation & purification/physiology/classification
Genome, Viral
Escherichia coli/virology/genetics
Host Specificity
Pseudomonas putida/virology/genetics
Salmonella enterica/virology/genetics
Phylogeny

@article {pmid38933974,
year = {2024},
author = {Rezende, GS and Rocha, FI and Funnicelli, MIG and Malavazi, I and Crauwels, S and Brandao, MM and Cunha, AF},
title = {Metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e32283},
doi = {10.1016/j.heliyon.2024.e32283},
pmid = {38933974},
issn = {2405-8440},
abstract = {Grapes are globally popular with wine production being one of the most well-known uses of grapes worldwide. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production. Nonetheless, other states are increasing their relevance in this segment. Environmental factors and the soil microbiome (bacteria and fungi) heavily influence grape quality, shaping the crucial "terroir" for wines. Here, soil quality was assessed through nutrient analysis and bacteria microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent chemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses including PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analysis pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analysis revealed varied co-occurrence patterns, with Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding how these specific microorganisms are associated with grapes can improve vineyard management, grape quality, and wine production. It can also potentially optimize soil health, bolster grapevine resilience against pests and diseases, and contribute to the unique character of wines known as terroir.},
}

@article {pmid38933028,
year = {2024},
author = {Stemple, B and Gulliver, D and Sarkar, P and Tinker, K and Bibby, K},
title = {Metagenome-assembled genomes provide insight into the metabolic potential during early production of Hydraulic Fracturing Test Site 2 in the Delaware Basin.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1376536},
doi = {10.3389/fmicb.2024.1376536},
pmid = {38933028},
issn = {1664-302X},
abstract = {Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a "shut-in" period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.},
}

@article {pmid38932970,
year = {2024},
author = {Ponce, MA and Maille, JM and Stoll, I and James, A and Bruce, A and Kim, TN and Scully, ED and Morrison, WR},
title = {Microbial vectoring capacity by internal- and external-infesting stored product insects after varying dispersal periods between novel food patches: An underestimated risk.},
journal = {Ecology and evolution},
volume = {14},
number = {6},
pages = {e11368},
doi = {10.1002/ece3.11368},
pmid = {38932970},
issn = {2045-7758},
abstract = {Understanding the ability of internal- and external-infesting stored product insects to vector microbes is important for estimating the relative risk that insects pose to postharvest commodities as they move between habitat patches and in the landscape. Thus, the aim of the current study was to evaluate and compare the microbial growth in novel food patches at different dispersal periods by different populations of Sitophilus oryzae (e.g., internal-infesting) and Lasioderma serricorne (e.g., external-infesting). Adults of both species collected from laboratory colonies or field-captured populations were either placed immediately in a novel food patch, or given a dispersal period of 24 or 72 h in a sterilized environment before entering a surrogate food patch. Vectored microbes in new food patches were imaged after 3 or 5 days of foraging, and microbial growth was processed using ImageJ while fungal species were identified through sequencing the ITS4/5 ribosomal subunit. We found that increasing dispersal time resulted in multiple-fold reductions in microbial growth surrogate food patches by L. serricorne but not S. oryzae. This was likely attributable to higher mobility by S. oryzae than L. serricorne. A total of 20 morphospecies were identified from 13 genera among the 59 sequences, with a total of 23% and 16% classified as Aspergillus and Penicillium spp. Our data suggest that there is a persistent risk of microbial contamination by both species, which has important food safety implications at food facilities.},
}

@article {pmid38930577,
year = {2024},
author = {Hernández-Zulueta, J and Rubio-Bueno, S and Zamora-Tavares, MDP and Vargas-Ponce, O and Rodríguez-Troncoso, AP and Rodríguez-Zaragoza, FA},
title = {Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific.},
journal = {Microorganisms},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/microorganisms12061195},
pmid = {38930577},
issn = {2076-2607},
abstract = {The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species' physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus' holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.},
}

@article {pmid38928853,
year = {2024},
author = {Tata, A and Massaro, A and Miano, B and Petrin, S and Antonelli, P and Peruzzo, A and Pezzuto, A and Favretti, M and Bragolusi, M and Zacometti, C and Losasso, C and Piro, R},
title = {A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/foods13121912},
pmid = {38928853},
issn = {2304-8158},
support = {RC IZSVe 11/2018//Ministero della Salute/ ; },
abstract = {Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms.},
}

@article {pmid38928813,
year = {2024},
author = {Vale, ADS and Pereira, CMT and De Dea Lindner, J and Rodrigues, LRS and Kadri, NKE and Pagnoncelli, MGB and Kaur Brar, S and Soccol, CR and Pereira, GVM},
title = {Exploring Microbial Influence on Flavor Development during Coffee Processing in Humid Subtropical Climate through Metagenetic-Metabolomics Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/foods13121871},
pmid = {38928813},
issn = {2304-8158},
support = {440343/2022-4//National Council for Scientific and Technological Development/ ; },
abstract = {Research into microbial interactions during coffee processing is essential for developing new methods that adapt to climate change and improve flavor, thus enhancing the resilience and quality of global coffee production. This study aimed to investigate how microbial communities interact and contribute to flavor development in coffee processing within humid subtropical climates. Employing Illumina sequencing for microbial dynamics analysis, and high-performance liquid chromatography (HPLC) integrated with gas chromatography-mass spectrometry (GC-MS) for metabolite assessment, the study revealed intricate microbial diversity and associated metabolic activities. Throughout the fermentation process, dominant microbial species included Enterobacter, Erwinia, Kluyvera, and Pantoea from the prokaryotic group, and Fusarium, Cladosporium, Kurtzmaniella, Leptosphaerulina, Neonectria, and Penicillium from the eukaryotic group. The key metabolites identified were ethanol, and lactic, acetic, and citric acids. Notably, the bacterial community plays a crucial role in flavor development by utilizing metabolic versatility to produce esters and alcohols, while plant-derived metabolites such as caffeine and linalool remain stable throughout the fermentation process. The undirected network analysis revealed 321 interactions among microbial species and key substances during the fermentation process, with Enterobacter, Kluyvera, and Serratia showing strong connections with sugar and various volatile compounds, such as hexanal, benzaldehyde, 3-methylbenzaldehyde, 2-butenal, and 4-heptenal. These interactions, including inhibitory effects by Fusarium and Cladosporium, suggest microbial adaptability to subtropical conditions, potentially influencing fermentation and coffee quality. The sensory analysis showed that the final beverage obtained a score of 80.83 ± 0.39, being classified as a specialty coffee by the Specialty Coffee Association (SCA) metrics. Nonetheless, further enhancements in acidity, body, and aftertaste could lead to a more balanced flavor profile. The findings of this research hold substantial implications for the coffee industry in humid subtropical regions, offering potential strategies to enhance flavor quality and consistency through controlled fermentation practices. Furthermore, this study contributes to the broader understanding of how microbial ecology interplays with environmental factors to influence food and beverage fermentation, a topic of growing interest in the context of climate change and sustainable agriculture.},
}

@article {pmid38927252,
year = {2024},
author = {Huang, Y and Chen, Y and Xie, H and Feng, Y and Chen, S and Bao, B},
title = {Effects of Inducible Nitric Oxide Synthase (iNOS) Gene Knockout on the Diversity, Composition, and Function of Gut Microbiota in Adult Zebrafish.},
journal = {Biology},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biology13060372},
pmid = {38927252},
issn = {2079-7737},
support = {2022YFD2400103//the National Key R&D Program of China/ ; 2021N3016//the Regional Development Project of Fujian/ ; },
abstract = {The gut microbiota constitutes a complex ecosystem that has an important impact on host health. In this study, genetically engineered zebrafish with inducible nitric oxide synthase (iNOS or NOS2) knockout were used as a model to investigate the effects of nos2a/nos2b gene single knockout and nos2 gene double knockout on intestinal microbiome composition and function. Extensive 16S rRNA sequencing revealed substantial changes in microbial diversity and specific taxonomic abundances, yet it did not affect the functional structure of the intestinal tissues. Notably, iNOS-deficient zebrafish demonstrated a decrease in Vibrio species and an increase in Aeromonas species, with more pronounced effects observed in double knockouts. Further transcriptomic analysis of the gut in double iNOS knockout zebrafish indicated significant alterations in immune-related and metabolic pathways, including the complement and PPAR signaling pathways. These findings underscore the crucial interplay between host genetics and gut microbiota, indicating that iNOS plays a key role in modulating the gut microbial ecology, host immune system, and metabolic responses.},
}

@article {pmid38926469,
year = {2024},
author = {Martin, LC and O'Hare, MA and Ghielmetti, G and Twesigomwe, D and Kerr, TJ and Gumbo, R and Buss, PE and Kitchin, N and Hemmings, SMJ and Miller, MA and Goosen, WJ},
title = {Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14768},
pmid = {38926469},
issn = {2045-2322},
support = {MND200409511840//National Research Foundation/ ; PMDS22052113333//National Research Foundation/ ; 86949//National Research Foundation, South Africa/ ; S005651//American Association of Zoo Veterinarians/ ; S007355//American Association of Zoo Veterinarians/ ; 222941/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Elephants/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Respiratory System/microbiology ; Animals, Zoo/microbiology ; Sequence Analysis, DNA/methods ; Animals, Wild/microbiology ; Phylogeny ; },
abstract = {Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.},
}

Animals
*Elephants/microbiology/genetics
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Microbiota/genetics
High-Throughput Nucleotide Sequencing/methods
Respiratory System/microbiology
Animals, Zoo/microbiology
Sequence Analysis, DNA/methods
Animals, Wild/microbiology
Phylogeny

@article {pmid38926391,
year = {2024},
author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A},
title = {Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5412},
pmid = {38926391},
issn = {2041-1723},
support = {1545756//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; 2125798//National Science Foundation (NSF)/ ; 4813//Water Research Foundation (WRF)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Sewage/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism ; Water Purification/methods ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; Drug Resistance, Bacterial/genetics ; Selection, Genetic ; },
abstract = {Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.},
}

*Gene Transfer, Horizontal
*Sewage/microbiology
*Wastewater/microbiology
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/classification/metabolism
Water Purification/methods
Metagenomics/methods
Drug Resistance, Microbial/genetics
Waste Disposal, Fluid/methods
Drug Resistance, Bacterial/genetics
Selection, Genetic

@article {pmid38923208,
year = {2024},
author = {Bosch, J and Lebre, PH and Marais, E and Maggs-Kölling, G and Cowan, DA},
title = {Kinetics and pathways of sub-lithic microbial community (hypolithon) development.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13290},
doi = {10.1111/1758-2229.13290},
pmid = {38923208},
issn = {1758-2229},
support = {//University of Pretoria/ ; 113308//National Research Foundation/ ; 137954//National Research Foundation/ ; 95565//National Research Foundation/ ; },
mesh = {*Soil Microbiology ; *Cyanobacteria/genetics/isolation & purification/growth & development/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Desert Climate ; Namibia ; Kinetics ; Phylogeny ; DNA, Bacterial/genetics ; Soil/chemistry ; },
abstract = {Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.},
}

*Soil Microbiology
*Cyanobacteria/genetics/isolation & purification/growth & development/classification/metabolism
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Desert Climate
Namibia
Kinetics
Phylogeny
DNA, Bacterial/genetics
Soil/chemistry

@article {pmid38922748,
year = {2024},
author = {Pérez-Pazos, E and Beidler, KV and Narayanan, A and Beatty, BH and Maillard, F and Bancos, A and Heckman, KA and Kennedy, PG},
title = {Fungi rather than bacteria drive early mass loss from fungal necromass regardless of particle size.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13280},
doi = {10.1111/1758-2229.13280},
pmid = {38922748},
issn = {1758-2229},
support = {SCW1632//Department of Energy Office of Biological and Environmental Research Genomic Science Program/ ; 2038293//National Science Foundation/ ; },
mesh = {*Bacteria/classification/genetics/isolation & purification/growth & development/metabolism ; *Particle Size ; Fungi/growth & development/classification/genetics/physiology ; Soil Microbiology ; Hydrogen-Ion Concentration ; Ascomycota/growth & development/physiology ; },
abstract = {Microbial necromass is increasingly recognized as an important fast-cycling component of the long-term carbon present in soils. To better understand how fungi and bacteria individually contribute to the decomposition of fungal necromass, three particle sizes (>500, 250-500, and <250 μm) of Hyaloscypha bicolor necromass were incubated in laboratory microcosms inoculated with individual strains of two fungi and two bacteria. Decomposition was assessed after 15 and 28 days via necromass loss, microbial respiration, and changes in necromass pH, water content, and chemistry. To examine how fungal-bacterial interactions impact microbial growth on necromass, single and paired cultures of bacteria and fungi were grown in microplates containing necromass-infused media. Microbial growth was measured after 5 days through quantitative PCR. Regardless of particle size, necromass colonized by fungi had higher mass loss and respiration than both bacteria and uninoculated controls. Fungal colonization increased necromass pH, water content, and altered chemistry, while necromass colonized by bacteria remained mostly unaltered. Bacteria grew significantly more when co-cultured with a fungus, while fungal growth was not significantly affected by bacteria. Collectively, our results suggest that fungi act as key early decomposers of fungal necromass and that bacteria may require the presence of fungi to actively participate in necromass decomposition.},
}

*Bacteria/classification/genetics/isolation & purification/growth & development/metabolism
*Particle Size
Fungi/growth & development/classification/genetics/physiology
Soil Microbiology
Hydrogen-Ion Concentration
Ascomycota/growth & development/physiology

@article {pmid38922446,
year = {2024},
author = {Filek, K and Vuković, BB and Žižek, M and DiBello, A and Kanjer, L and Trotta, A and Corrente, M and Bosak, S},
title = {Correction to: Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {84},
doi = {10.1007/s00248-024-02405-z},
pmid = {38922446},
issn = {1432-184X},
}

@article {pmid38921731,
year = {2024},
author = {Wang, C and Defoirdt, T and Rajkovic, A},
title = {The Effect of Caco-2 Cells on Sporulation and Enterotoxin Expression by Foodborne Clostridium perfringens.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
pmid = {38921731},
issn = {2076-0817},
support = {201808630020//China Scholarship Council/ ; BOF20/BAS/120//Special Research Fund of Ghent University/ ; 1506419N//Research Foundation - Flanders/ ; },
abstract = {Clostridium perfringens enterotoxin (Cpe)-producing strains cause gastrointestinal infections in humans and account for the second-largest number of all foodborne outbreaks caused by bacterial toxins. The Cpe toxin is only produced during sporulation; this process might be affected when C. perfringens comes into contact with host cells. The current study determined how the cpe expression levels and spore formation changed over time during co-culture with Caco-2 cells (as a model of intestinal epithelial cells). In co-culture with Caco-2 cells, total C. perfringens cell counts first decreased and then remained more or less stable, whereas spore counts were stable over the whole incubation period. The cpe mRNA level in the co-culture with Caco-2 cells increased more rapidly than in the absence of Caco-2 cells (3.9-fold higher levels in coculture than in the absence of Caco-2 cells after 8 h of incubation). Finally, we found that cpe expression is inhibited by a cue released by Caco-2 cells (8.3-fold lower levels in the presence of supernatants of Caco-2 cells than in the absence of the supernatants after 10 h of incubation); as a consequence, the increased expression in co-culture with Caco-2 cells must be caused by a factor associated with the Caco-2 cells.},
}

@article {pmid38816227,
year = {2024},
author = {Carrillo-Barragan, P},
title = {Clean your own house first: integrating sustainability into microbiology labs.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {7},
pages = {},
doi = {10.1093/femsec/fiae084},
pmid = {38816227},
issn = {1574-6941},
support = {//University of Basel/ ; },
mesh = {*Laboratories ; Environmental Microbiology ; Sustainable Development ; Microbiology ; Conservation of Natural Resources ; },
abstract = {Microbiology laboratories are pivotal hubs for exploring the potential of microorganisms and addressing global challenges. Particularly, Environmental Microbiology facilities hold substantial influence in advancing knowledge and capabilities crucial for achieving the United Nations Sustainable Development Goals. This raises the imperative of integrating sustainable practices to mitigate the environmental impact of research activities and foster a culture of responsibility. Such an approach not only aligns with global sustainability objectives but also catalyses innovative, eco-conscious methodologies in scientific research aimed at tackling pressing environmental issues. Concerns regarding the environmental footprint of laboratory practices have stimulated innovative improvements within the scientific community, ranging from resource-efficient initiatives to the management of essential commodities like water and energy. This perspective discusses specific areas where microbiology laboratories can enhance their sustainability efforts, drawing on reports and case studies of pioneering groups. Additionally, it explores potential collaborators to support these endeavours and emphasises the pivotal role of early career researchers in driving this transition. By initiating discussions and sparking curiosity within the environmental microbial community, this commentary seeks to propel the microbial ecology field toward a greener future, starting from within the laboratory environment.},
}

*Laboratories
Environmental Microbiology
Sustainable Development
Microbiology
Conservation of Natural Resources

@article {pmid38920365,
year = {2024},
author = {Givati, S and Forchielli, E and Aharonovich, D and Barak, N and Weissberg, O and Belkin, N and Rahav, E and Segrè, D and Sher, D},
title = {Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0025624},
doi = {10.1128/aem.00256-24},
pmid = {38920365},
issn = {1098-5336},
abstract = {UNLABELLED: Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be used by different heterotrophic clades. Here, we ask how a natural microbial community from the Eastern Mediterranean Sea (EMS) responds to different molecular classes of DOM (peptides, amino acids, amino sugars, disaccharides, monosaccharides, and organic acids) comprising much of the biomass of living organisms. Bulk bacterial activity increased after 24 h for all treatments relative to the control, while glucose and ATP uptake decreased or remained unchanged. Moreover, while the per-cell uptake rate of glucose and ATP decreased, that of Leucin significantly increased for amino acids, reflecting their importance as common metabolic currencies in the marine environment. Pseudoalteromonadaceae dominated the peptides treatment, while different Vibrionaceae strains became dominant in response to amino acids and amino sugars. Marinomonadaceae grew well on organic acids, and Alteromonadaseae on disaccharides. A comparison with a recent laboratory-based study reveals similar peptide preferences for Pseudoalteromonadaceae, while Alteromonadaceae, for example, grew well in the lab on many substrates but dominated in seawater samples only when disaccharides were added. We further demonstrate a potential correlation between the genetic capacity for degrading amino sugars and the dominance of specific clades in these treatments. These results highlight the diversity in DOM utilization among heterotrophic bacteria and complexities in the response of natural communities.

IMPORTANCE: A major goal of microbial ecology is to predict the dynamics of natural communities based on the identity of the organisms, their physiological traits, and their genomes. Our results show that several clades of heterotrophic bacteria each grow in response to one or more specific classes of organic matter. For some clades, but not others, growth in a complex community is similar to that of isolated strains in laboratory monoculture. Additionally, by measuring how the entire community responds to various classes of organic matter, we show that these results are ecologically relevant, and propose that some of these resources are utilized through common uptake pathways. Tracing the path between different resources to the specific microbes that utilize them, and identifying commonalities and differences between different natural communities and between them and lab cultures, is an important step toward understanding microbial community dynamics and predicting how communities will respond to perturbations.},
}

@article {pmid38918384,
year = {2024},
author = {Dueholm, MKD and Andersen, KS and Korntved, AC and Rudkjøbing, V and Alves, M and Bajón-Fernández, Y and Batstone, D and Butler, C and Cruz, MC and Davidsson, Å and Erijman, L and Holliger, C and Koch, K and Kreuzinger, N and Lee, C and Lyberatos, G and Mutnuri, S and O'Flaherty, V and Oleskowicz-Popiel, P and Pokorna, D and Rajal, V and Recktenwald, M and Rodríguez, J and Saikaly, PE and Tooker, N and Vierheilig, J and De Vrieze, J and Wurzbacher, C and Nielsen, PH},
title = {MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5361},
pmid = {38918384},
issn = {2041-1723},
support = {Dark Matter and grant 13351//Villum Fonden (Villum Foundation)/ ; 6111-00617 A//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; },
mesh = {*Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; *Biodiversity ; *Phylogeny ; Wastewater/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Sequence Analysis, DNA ; },
abstract = {Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.},
}

*Archaea/genetics/classification/metabolism
*RNA, Ribosomal, 16S/genetics
Anaerobiosis
*Bacteria/genetics/classification/metabolism
*Microbiota/genetics
*Biodiversity
*Phylogeny
Wastewater/microbiology
Bioreactors/microbiology
Methane/metabolism
Sequence Analysis, DNA

@article {pmid38918217,
year = {2024},
author = {Duong, HL and Paufler, S and Harms, H and Maskow, T and Schlosser, D},
title = {Biocalorimetry-aided monitoring of fungal pretreatment of lignocellulosic agricultural residues.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {394},
pmid = {38918217},
issn = {1432-0614},
support = {911 Program//Bộ Giáo dục và Ðào tạo/ ; },
mesh = {*Lignin/metabolism ; *Triticum/microbiology/chemistry ; *Fungi/metabolism ; Fermentation ; Hydrolysis ; Agriculture/methods ; },
abstract = {The present study aimed to investigate whether and how non-invasive biocalorimetric measurements could serve for process monitoring of fungal pretreatment during solid-state fermentation (SSF) of lignocellulosic agricultural residues such as wheat straw. Seven filamentous fungi representing different lignocellulose decay types were employed. Water-soluble sugars being immediately available after fungal pretreatment and those becoming water-extractable after enzymatic digestion of pretreated wheat straw with hydrolysing (hemi)cellulases were considered to constitute the total bioaccessible sugar fraction. The latter was used to indicate the success of pretreatments and linked to corresponding species-specific metabolic heat yield coefficients (YQ/X) derived from metabolic heat flux measurements during fungal wheat straw colonisation. An YQ/X range of about 120 to 140 kJ/g was seemingly optimal for pretreatment upon consideration of all investigated fungi and application of a non-linear Gaussian fitting model. Upon exclusion from analysis of the brown-rot basidiomycete Gloeophyllum trabeum, which differs from all other here investigated fungi in employing extracellular Fenton chemistry for lignocellulose decomposition, a linear relationship where amounts of total bioaccessible sugars were suggested to increase with increasing YQ/X values was obtained. It remains to be elucidated whether an YQ/X range being optimal for fungal pretreatment could firmly be established, or if the sugar accessibility for post-treatment generally increases with increasing YQ/X values as long as "conventional" enzymatic, i.e. (hemi)cellulase-based, lignocellulose decomposition mechanisms are operative. In any case, metabolic heat measurement-derived parameters such as YQ/X values may become very valuable tools supporting the assessment of the suitability of different fungal species for pretreatment of lignocellulosic substrates. KEY POINTS: • Biocalorimetry was used to monitor wheat straw pretreatment with seven filamentous fungi. • Metabolic heat yield coefficients (YQ/X) seem to indicate pretreatment success. • YQ/X values may support the selection of suitable fungal strains for pretreatment.},
}

*Lignin/metabolism
*Triticum/microbiology/chemistry
*Fungi/metabolism
Fermentation
Hydrolysis
Agriculture/methods

@article {pmid38917910,
year = {2024},
author = {Gao, Y and Heng, S and Wang, J and Liu, Z and Liu, Y and Chen, B and Han, Y and Li, W and Lu, X and Zhen, G},
title = {Bioelectrochemically altering microbial ecology in upflow anaerobic sludge blanket to enhance methanogenesis fed with high-sulfate methanolic wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131026},
doi = {10.1016/j.biortech.2024.131026},
pmid = {38917910},
issn = {1873-2976},
abstract = {A bioelectrochemical upflow anaerobic sludge blanket (BE-UASB) was constructed and compared with the traditional UASB to investigate the role of bioelectrocatalysis in modulating methanogenesis and sulfidogensis involved within anaerobic treatment of high-sulfate methanolic wastewater (COD/SO4[2-] ratio ≤ 2). Methane production rate for BE-UASB was 1.4 times higher than that of the single UASB, while SO4[2-] removal stabilized at 16.7 %. Bioelectrocatalysis selectively enriched key functional anaerobes and stimulated the secretion of extracellular polymeric substances, especially humic acids favoring electron transfer, thereby accelerating the electroactive biofilms development of electrodes. Methanomethylovorans was the dominant genus (35 %) to directly convert methanol to CH4. Methanobacterium as CO2 electroreduction methane-producing archaea appeared only on electrodes. Acetobacterium exhibited anode-dependence, which provided acetate for sulfate-reducing bacteria (norank Syntrophobacteraceae and Desulfomicrobium) through synergistic coexistence. This study confirmed that BE-UASB regulated the microbial ecology to achieve efficient removal and energy recovery of high-sulfate methanolic wastewater.},
}

@article {pmid38917500,
year = {2024},
author = {Zhang, D and Calmanovici, B and Marican, H and Reisser, J and Summers, S},
title = {The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef.},
journal = {Marine pollution bulletin},
volume = {205},
number = {},
pages = {116651},
doi = {10.1016/j.marpolbul.2024.116651},
pmid = {38917500},
issn = {1879-3363},
abstract = {Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.},
}

@article {pmid38915372,
year = {2024},
author = {Levi, EE and Jeppesen, E and Nejstgaard, JC and Davidson, TA},
title = {High resolution chlorophyll- a in-situ fluorescence sensors versus in-vitro chlorophyll- a measurements in mesocosms with contrasting nutrient and temperature treatments.},
journal = {Open research Europe},
volume = {4},
number = {},
pages = {69},
pmid = {38915372},
issn = {2732-5121},
abstract = {Harmful algal blooms (HABs) are a significant threat to freshwater ecosystems, and monitoring for changes in biomass is therefore important. Fluorescence in-situ sensors enable rapid and high frequency real-time data collection and have been widely used to determine chlorophyll- a (Chla) concentrations that are used as an indicator of the total algal biomass. However, conversion of fluorescence to equivalent Chla concentrations is often complicated due to biofouling, phytoplankton composition and the type of equipment used. Here, we validated measurements from 24 Chla and 12 phycocyanin (cyanobacteria indicator) fluorescence in-situ sensors (Cyclops-7F, Turner Designs) against spectrophotometrically (in-vitro) determined Chla and tested a data-cleaning procedure for eliminating data errors and impacts of non-photochemical quenching. The test was done across a range of freshwater plankton communities in 24 mesocosms (i.e. experimental tanks) with a 2x3 (high and low nutrient x ambient, IPCC-A2 and IPCC-A2+50% temperature scenarios) factorial design. For most mesocosms (tanks), we found accurate (r [2] ≥ 0.7) calibration of in-situ Chla fluorescence data using simple linear regression. An exception was tanks with high in-situ phycocyanin fluorescence, for which multiple regressions were employed, which increased the explained variance by >16%. Another exception was the low Chla concentration tanks (r [2] < 0.3). Our results also show that the high frequency in-situ fluorescence data recorded the timing of sudden Chla variations, while less frequent in-vitro sampling sometimes missed these or, when recorded, the duration of changes was inaccurately determined. Fluorescence in-situ sensors are particularly useful to detect and quantify sudden phytoplankton biomass variations through high frequency measurements, especially when using appropriate data-cleaning methods and accounting for factors that can impact the fluorescence readings.},
}

@article {pmid38912052,
year = {2024},
author = {Goldman, SL and Sanders, JG and Sprockett, DD and Landers, A and Yan, W and Moeller, AH},
title = {Hackflex library preparation enables low-cost metagenomic profiling.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae075},
pmid = {38912052},
issn = {2730-6151},
abstract = {Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.},
}

@article {pmid38910491,
year = {2024},
author = {Kommana, G and Hupfer, M and Woodhouse, JN and Grossart, HP and Goldhammer, T},
title = {Reduced greenhouse gas emissions from particulate organic matter degradation in iron-enriched sediments.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4em00185k},
pmid = {38910491},
issn = {2050-7895},
abstract = {Iron (Fe) plays an important role in the biogeochemical cycling of carbon and nutrients in aquatic systems. Reactive Fe phases can interact with organic carbon and facilitate the removal of carbon from the biogeochemical cycle; however, this important ecosystem function is often strongly controlled by Fe availability. Due to pollution from lignite mining in the Lusatian province in Northeast Germany, large amounts of iron and sulfate are released into the fluvial-lacustrine system of the Spree River. It was hypothesized that the input of freshly precipitated iron oxyhydroxides from mining areas (e.g., ferrihydrite) alter the biodegradation of particulate organic matter (POM) in downstream lacustrine sediments. To investigate the Fe-dependent degradation of POM, slurries mimicking iron-polluted sediments (85 mg Fe per g, 116 mg Fe per g, and 149 mg Fe per g dry weight) were incubated with plankton or leaf POM under anoxic and oxic headspace conditions, and CO2 and CH4 emissions, water chemistry, and stable isotopes of dissolved inorganic carbon were measured. The experiments revealed that (i) with an increasing Fe content, the CO2 and CH4 emissions were gradually reduced, (ii) CO2 and CH4 production was higher during plankton degradation than during leaf decomposition, and (iii) under oxic conditions, CO2 production was higher and CH4 production was lower when compared to the treatments under anoxic conditions. These findings demonstrate that while benthic mineralization of fresh POM typically releases greenhouse gases into the water column, the availability of iron oxyhydroxides can contribute to reduced greenhouse gas emissions from sediments. This is of considerable relevance for future carbon budgets of similar mining-affected, iron-polluted fluvial-lacustrine river systems.},
}

@article {pmid38909617,
year = {2024},
author = {Kullberg, RFJ and Wikki, I and Haak, BW and Kauko, A and Galenkamp, H and Peters-Sengers, H and Butler, JM and Havulinna, AS and Palmu, J and McDonald, D and Benchraka, C and Abdel-Aziz, MI and Prins, M and Maitland van der Zee, AH and van den Born, BJ and Jousilahti, P and de Vos, WM and Salomaa, V and Knight, R and Lahti, L and Nieuwdorp, M and Niiranen, T and Wiersinga, WJ},
title = {Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2666-5247(24)00079-X},
pmid = {38909617},
issn = {2666-5247},
abstract = {BACKGROUND: Microbiota alterations are common in patients hospitalised for severe infections, and preclinical models have shown that anaerobic butyrate-producing gut bacteria protect against systemic infections. However, the relationship between microbiota disruptions and increased susceptibility to severe infections in humans remains unclear. We investigated the relationship between gut microbiota and the risk of future infection-related hospitalisation in two large population-based cohorts.

METHODS: In this observational microbiome study, gut microbiota were characterised using 16S rRNA gene sequencing in independent population-based cohorts from the Netherlands (HELIUS study; derivation cohort) and Finland (FINRISK 2002 study; validation cohort). HELIUS was conducted in Amsterdam, Netherlands, and included adults (aged 18-70 years at inclusion) who were randomly sampled from the municipality register of Amsterdam. FINRISK 2002 was conducted in six regions in Finland and is a population survey that included a random sample of adults (aged 25-74 years). In both cohorts, participants completed questionnaires, underwent a physical examination, and provided a faecal sample at inclusion (Jan 3, 2013, to Nov 27, 2015, for HELIUS participants and Jan 21 to April 19, 2002, for FINRISK participants. For inclusion in our study, a faecal sample needed to be provided and successfully sequenced, and national registry data needed to be available. Primary predictor variables were microbiota composition, diversity, and relative abundance of butyrate-producing bacteria. Our primary outcome was hospitalisation or mortality due to any infectious disease during 5-7-year follow-up after faecal sample collection, based on national registry data. We examined associations between microbiota and infection risk using microbial ecology and Cox proportional hazards.

FINDINGS: We profiled gut microbiota from 10 699 participants (4248 [39·7%] from the derivation cohort and 6451 [60·3%] from the validation cohort). 602 (5·6%) participants (152 [3·6%] from the derivation cohort; 450 [7·0%] from the validation cohort) were hospitalised or died due to infections during follow-up. Gut microbiota composition of these participants differed from those without hospitalisation for infections (derivation p=0·041; validation p=0·0002). Specifically, higher relative abundance of butyrate-producing bacteria was associated with a reduced risk of hospitalisation for infections (derivation cohort cause-specific hazard ratio 0·75 [95% CI 0·60-0·94] per 10% increase in butyrate producers, p=0·013; validation cohort 0·86 [0·77-0·96] per 10% increase, p=0·0077). These associations remained unchanged following adjustment for demographics, lifestyle, antibiotic exposure, and comorbidities.

INTERPRETATION: Gut microbiota composition, specifically colonisation with butyrate-producing bacteria, was associated with protection against hospitalisation for infectious diseases in the general population across two independent European cohorts. Further studies should investigate whether modulation of the microbiome can reduce the risk of severe infections.

FUNDING: Amsterdam UMC, Porticus, National Institutes of Health, Netherlands Organisation for Health Research and Development (ZonMw), and Leducq Foundation.},
}

@article {pmid38906896,
year = {2024},
author = {Schorn, S and Graf, JS and Littmann, S and Hach, PF and Lavik, G and Speth, DR and Schubert, CJ and Kuypers, MMM and Milucka, J},
title = {Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5293},
pmid = {38906896},
issn = {2041-1723},
mesh = {*Methane/metabolism ; *Lakes/microbiology ; *Oxidation-Reduction ; Anaerobiosis ; Methylococcaceae/metabolism/genetics ; Metagenomics ; Oxygen/metabolism ; },
abstract = {Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d[-1]. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.},
}

*Methane/metabolism
*Lakes/microbiology
*Oxidation-Reduction
Anaerobiosis
Methylococcaceae/metabolism/genetics
Metagenomics
Oxygen/metabolism

@article {pmid38904568,
year = {2024},
author = {Ganier, C and Callewaert, C and Matos, TR and Sonkoly, E and Dyring-Andersen, B and Rajan, N},
title = {Young ESDR: Engaging and Nurturing the Next-Generation Skin Research Community.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2024.05.004},
pmid = {38904568},
issn = {1523-1747},
}

@article {pmid38902915,
year = {2024},
author = {Kerr, BJ and Anderson, CL and Pearce, SC and Schweer, WP},
title = {Dietary isoacids effects on growth, nitrogen, and energy digestibility, and fecal VFA and microbial ecology in finishing pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skae170},
pmid = {38902915},
issn = {1525-3163},
abstract = {Isoacids are branched ketoacids which when fed to ruminants have been shown to enhance the growth of fiber-digesting organisms. Ninety finishing gilts were individually fed dietary treatments consisting of diet type: corn-soybean meal (CSBM), a diet containing 40% distillers dried grains with solubles (DDGS), or a diet containing 40% sugar beet pulp (SBP); in combination with either no feed additive (CNT), the addition of 0.50% isobutyrate (IB), or the addition of a 0.88% mix of isobutyrate, isovalerate, and 2-methylbutyrate (MX). Gilts consumed an average of 2.171 kg/d over the 28-d trial. On d 26, fresh fecal samples were collected for determination of apparent total tract digestibility (ATTD) of gross energy (GE) and nitrogen (N), determination of fecal volatile fatty acids (VFA), and evaluation of microbial ecology. There was no interaction between diet type and isoacid addition, and no main effect of isoacid or diet type on alpha or Shannon microbial diversity measures (P > 0.05). There was no interaction between isoacid addition and diet type, and no main effect of isoacid addition on microbial beta diversity (P > 0.05), but differences were observed in microbial beta diversity due to diet type (P ≤ 0.05). There was no interaction between diet type and isoacid addition observed in fecal VFA concentrations (P > 0.05), with only minor differences in fecal VFA concentrations noted due to isoacid addition (P ≤ 0.05). The interaction between diet type and isoacid addition on ATTD of dietary GE and N (P ≤ 0.01) was largely because the addition of IB did not affect ATTD of GE or N in pigs fed the CSBM diet, but increased ATTD of GE and N in pigs fed diets containing DDGS and decreased the ATTD of GE and N in pigs fed diets containing SBP. In contrast, adding a blend of isoacids (i.e., MX) reduced the ATTD of GE and N, regardless of diet type. There was no interaction between diet type and isoacid addition, and no effect of isoacid addition was observed on pig performance (P > 0.05). Diet type did not affect ADG (P > 0.05), but pigs fed diets containing DDGS or SBP consumed less feed (P = 0.01) and exhibited greater GF ratios compared to pigs fed the low-fiber CSBM diet (P ≤ 0.05). In conclusion, there was little to no effect of isoacid addition on microbial ecology, fecal VFA concentrations, ATTD of GE or N, or pig performance, but the improvement in ATTD of GE and N in pigs fed diets containing DDGS when IB was added warrants further investigation.},
}