@article {pmid38628677,
year = {2024},
author = {Kim, M and Park, T and Park, C and Baek, YC and Cho, A and Lee, HG and Kim, E and Bok, EY and Jung, YH and Hur, TY and Do, YJ},
title = {Impact of rumen cannulation surgery on rumen microbiota composition in Hanwoo steers.},
journal = {Journal of animal science and technology},
volume = {66},
number = {2},
pages = {353-365},
pmid = {38628677},
issn = {2055-0391},
abstract = {Rumen cannulation is a surgical technique used to collect rumen contents from ruminants. However, rumen cannulation surgery may potentially impact the composition of the rumen microbiota. This study aimed to examine the longitudinal alterations in the rumen microbiota composition of Hanwoo steers after cannulation surgery. In this study, eight Hanwoo steers were used; four steers underwent rumen cannulation surgery (cannulation group), while the remaining four were left intact (control group). Rumen samples were collected from all eight steers using the stomach tubing method on the day before surgery (day 0) and on postoperative days 1, 4, 7, 10, 14, 17, 21, 24, and 28, resulting in 80 samples (10 timepoints × 8 animals). The microbiota of all 80 samples were analyzed using 16S rRNA gene amplicon sequencing with Quantitative Insights into Microbial Ecology version 2 (QIIME2). There were no significant differences (p > 0.05) in all major phyla and most major genera representing at least 0.5% of total sequences across all 80 samples between the control and cannulation groups on the preoperative and postoperative days. However, while the alpha diversity indices did not differ (p > 0.05) between the two groups on the preoperative day, they significantly differed (p < 0.05) between the two groups on the postoperative days. Further, the overall microbial distribution based on both unweighted and weighted principal coordinate analysis plots significantly differed (p < 0.05) between the two groups on both the preoperative and postoperative days. Orthogonal polynomial contrasts indicated that major genera and microbial diversity in the cannulation group decreased following surgery but returned to their initial states by postoperative day 28. In conclusion, this study demonstrates that rumen cannulation surgery affects some major taxa and microbial diversity, suggesting that the rumen cannulation method can alter the composition of rumen microbiota in Hanwoo steers.},
}

@article {pmid38627476,
year = {2024},
author = {Ridley, RS and Conrad, RE and Lindner, BG and Woo, S and Konstantinidis, KT},
title = {Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8798},
pmid = {38627476},
issn = {2045-2322},
support = {2136146//National Science Foundation/ ; },
abstract = {Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.},
}

@article {pmid38626537,
year = {2024},
author = {Ali, A and Wang, N and Wang, Q and Xu, G and Xu, H},
title = {An approach to evaluating seasonal responses to acute toxicity of antibiotic nitrofurazone on periphytic ciliated protist communities in marine environments.},
journal = {European journal of protistology},
volume = {94},
number = {},
pages = {126081},
doi = {10.1016/j.ejop.2024.126081},
pmid = {38626537},
issn = {1618-0429},
abstract = {Periphytic protists including ciliates are the primary components of microbial communities in which they play a vital role in the progression of food webs by moving resources from lower to higher trophic levels. However, the toxic effects of veterinary antibiotics on periphytic protists across four seasons are minimally understood. Therefore, in this study, a 1-year survey was conducted with the antibiotic nitrofurazone (NFZ) applied at concentrations of 0.0, 1.5, 3.0, 6.0, and 12.0 mg/L. Samples of protist communities were collected using microscope glass slides during four seasons in the coastal waters of the Yellow Sea, Qingdao, northern China. The abundance of protists dropped with an increase in NFZ concentrations, and almost all species were dead at a concentration of 12.0 mg/L. The 12 h-LC50 values of NFZ for the protist biota were similar among the four seasons, despite significant seasonal variability in the community structure. The present results suggest that the periphytic protist biota may be used as a biomarker for assessing the ecotoxicity of NFZ in marine environments regardless of the year season.},
}

@article {pmid38625060,
year = {2024},
author = {Garvin, ZK and Abades, SR and Trefault, N and Alfaro, FD and Sipes, K and Lloyd, KG and Onstott, TC},
title = {Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae062},
pmid = {38625060},
issn = {1751-7370},
abstract = {High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing the spatial reach of their impact on trace gas-oxidizing microbes in the surrounding soils. This study assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA quantities and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest that this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy and/or carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests that the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.},
}

@article {pmid38622815,
year = {2024},
author = {Riquelme Del Río, B and Sepulveda-Jauregui, A and Salas-Rabaza, JA and Mackenzie, R and Thalasso, F},
title = {Fine-Scale Spatial Variability of Greenhouse Gas Emissions From a Subantarctic Peatland Bog.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.3c10746},
pmid = {38622815},
issn = {1520-5851},
abstract = {Peatlands are recognized as crucial greenhouse gas sources and sinks and have been extensively studied. Their emissions exhibit high spatial heterogeneity when measured on site using flux chambers. However, the mechanism by which this spatial variability behaves on a very fine scale remains unclear. This study investigates the fine-scale spatial variability of greenhouse gas emissions from a subantarctic Sphagnum peatland bog. Using a recently developed skirt chamber, methane emissions and ecosystem respiration (as carbon dioxide) were measured at a submeter scale resolution, at five specific 3 × 3 m plots, which were examined across the site throughout a single campaign during the Austral summer season. The results indicated that methane fluxes were significantly less homogeneously distributed compared with ecosystem respiration. Furthermore, we established that the spatial variation scale, i.e., the minimum spatial domain over which notable changes in methane emissions and ecosystem respiration occur, was <0.56 m[2]. Factors such as ground height relative to the water table and vegetation coverage were analyzed. It was observed that Tetroncium magellanicum exhibited a notable correlation with higher methane fluxes, likely because of the aerenchymatous nature of this species, facilitating gas transport. This study advances understanding of gas exchange patterns in peatlands but also emphasizes the need for further efforts for characterizing spatial dynamics at a very fine scale for precise greenhouse gas budget assessment.},
}

@article {pmid38621490,
year = {2024},
author = {Cheng, J and Robles-Lecompte, A and McKenna, AM and Chang, NB},
title = {Deciphering Linkages between DON and the Microbial Community for Nitrogen Removal Using Two Green Sorption Media in a Surface Water Filtration System.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {142042},
doi = {10.1016/j.chemosphere.2024.142042},
pmid = {38621490},
issn = {1879-1298},
abstract = {The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 tesla Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 tesla FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.},
}

@article {pmid38619794,
year = {2024},
author = {Van Holm, W and Zayed, N and Lauwens, K and Saghi, M and Axelsson, J and Aktan, MK and Braem, A and Simoens, K and Vanbrabant, L and Proost, P and Van Holm, B and Maes, P and Boon, N and Bernaerts, K and Teughels, W},
title = {Oral Biofilm Composition, Dissemination to Keratinocytes, and Inflammatory Attenuation Depend on Probiotic and Synbiotic Strain Specificity.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38619794},
issn = {1867-1314},
support = {C24/17/086//KU Leuven/ ; C16/17/010//KU Leuven/ ; C16/17/010//KU Leuven/ ; C24/17/086//KU Leuven/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {Several inflammatory diseases are characterized by a disruption in the equilibrium between the host and its microbiome. Due to the increase in resistance, the use of antibiotics for the widespread, nonspecific killing of microorganisms is at risk. Pro-microbial approaches focused on stimulating or introducing beneficial species antagonistic toward pathobionts may be a viable alternative for restoring the host-microbiome equilibrium. Unfortunately, not all potential probiotic or synbiotic species and even subspecies (to strain level) are equally effective for the designated pathology, leading to conflicting accounts of their efficacy. To assess the extent of these species- and strain-specific effects, 13 probiotic candidates were evaluated for their probiotic and synbiotic potential with glycerol on in vitro oral biofilms, dissemination from biofilms to keratinocytes, and anti-inflammatory activity. Species- and strain-specific effects and efficacies were observed in how they functioned as probiotics or synbiotics by influencing oral pathobionts and commensals within biofilms and affected the dissemination of pathobionts to keratinocytes, ranging from ineffective strains to strains that reduced pathobionts by 3 + log. In addition, a minority of the candidates exhibited the ability to mitigate the inflammatory response of LPS-stimulated monocytes. For a comprehensive assessment of probiotic therapy for oral health, a judicious selection of fully characterized probiotic strains that are specifically tailored to the designated pathology is required. This approach aims to challenge the prevailing perception of probiotics, shifting the focus away from "form over function." Rather than using unproven, hypothetical probiotic strains from known genera or species, one should choose strains that are actually functional in resolving the desired pathology before labelling them probiotics.},
}

@article {pmid38619730,
year = {2024},
author = {Zhu, H and Li, S and Wu, Z and Xiong, X and Lin, P and Liu, B and He, D and Liu, G},
title = {Diversity Patterns of Eukaryotic Phytoplankton in the Medog Section of the Yarlung Zangbo River.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {59},
pmid = {38619730},
issn = {1432-184X},
mesh = {*Ecosystem ; *Rivers ; Biodiversity ; Biomass ; Phytoplankton ; },
abstract = {As one of the important biodiversity conservation areas in China, the ecosystem in the lower reaches of the Yarlung Zangbo River is fragile, and is particularly sensitive to global changes. To reveal the diversity pattern of phytoplankton, the metabarcode sequencing was employed in the Medog section of the lower reaches of the Yarlung Zangbo River during autumn 2019 in present study. The phytoplankton assemblies can be significantly divided into the main stem and the tributaries; there are significant differences in the phytoplankton biomass, alpha and beta diversity between the main stem and the tributaries. While both the main stem and the tributaries are affected by dispersal limitation, the phytoplankton assemblages in the entire lower reaches are primarily influenced by heterogeneous selection. Community dissimilarity and assembly process were significantly correlated with turbidity, electrical conductivity, and nitrogen nutrition. The tributaries were the main source of the increase in phytoplankton diversity in the lower reaches of the Yarlung Zangbo River. Such diversity pattern of phytoplankton in the lower reach may be caused by the special habitat in Medog, that is, the excessive flow velocity, and the significant spatial heterogeneity in physical and chemical factors between stem and tributaries. Based on the results and conclusions obtained in present study, continuous long-term monitoring is essential to assess and quantify the impact of global changes on phytoplankton.},
}

*Ecosystem
*Rivers
Biodiversity
Biomass
Phytoplankton

@article {pmid38618866,
year = {2024},
author = {Zha, Z and Wang, R and Wang, Q and Chen, F and Ye, Z and Li, Y},
title = {A fast and efficient liquid chromatography-tandem mass spectrometry method for measuring l- and d-amino acids in the urine of patients with immunoglobulin A nephropathy.},
journal = {Biomedical chromatography : BMC},
volume = {},
number = {},
pages = {e5866},
doi = {10.1002/bmc.5866},
pmid = {38618866},
issn = {1099-0801},
support = {82170716//National Science Foundation of China/ ; 81870333//National Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; //College Science and Technology Innovation Project of Shanxi Education Department/ ; },
abstract = {Immunoglobulin nephropathy (IgAN) stands as the most prevalent primary glomerular nephropathy globally, typically diagnosed through an invasive renal biopsy. Emerging research suggests the significant involvement of chiral amino acids in kidney disease progression. This study introduces a nonderivative LC-tandem mass spectrometry approach, offering efficient separation outcomes within 15 min for identifying chiral amino acids in human urine samples. Subsequently, using this method, the analysis of l- and d-amino acids in the urine of both patients with IgAN and healthy individuals was conducted. Fourteen d-amino acids and 20 l-amino acids were identified in the urine samples obtained from 17 patients with IgAN and 21 healthy individuals. The results indicated notable variances in the concentrations of both l- and d-amino acids between the IgAN and healthy control groups. In contrast to the healthy group, the IgAN group exhibited higher mean urine concentrations of most l-amino acids and lower concentrations of d-amino acids. Furthermore, correlations between amino acids and clinical markers were investigated. These results propose a novel method for monitoring trace amino acids in urine samples and introduce a new concept for potential markers of IgAN.},
}

@article {pmid38617439,
year = {2024},
author = {Ogaya, Y and Kadota, T and Hamada, M and Nomura, R and Nakano, K},
title = {Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2339158},
pmid = {38617439},
issn = {2000-2297},
abstract = {OBJECTIVE: Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.

METHODS: Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).

RESULTS: Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of α-diversity (p < 0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in β-diversity between H. pylori-positive and negative child specimens (p < 0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p < 0.01 and p < 0.05, respectively).

CONCLUSION: These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.},
}

@article {pmid38613756,
year = {2024},
author = {Costa, JL and Silva, LG and Veras, STS and Gavazza, S and Florencio, L and Motteran, F and Kato, MT},
title = {Use of nitrate, sulphate, and iron (III) as electron acceptors to improve the anaerobic degradation of linear alkylbenzene sulfonate: effects on removal potential and microbiota diversification.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38613756},
issn = {1614-7499},
support = {APQ-0603-3.07/14//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; CAPES-PrInt//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; finance code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; process number 88887.467533/2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {Linear alkylbenzene sulfonate (LAS) is a synthetic anionic surfactant that is found in certain amounts in wastewaters and even in water bodies, despite its known biodegradability. This study aimed to assess the influence of nitrate, sulphate, and iron (III) on LAS anaerobic degradation and biomass microbial diversity. Batch reactors were inoculated with anaerobic biomass, nutrients, LAS (20 mg L[-1]), one of the three electron acceptors, and ethanol (40 mg L[-1]) as a co-substrate. The control treatments, with and without co-substrate, showed limited LAS biodegradation efficiencies of 10 ± 2% and 0%, respectively. However, when nitrate and iron (III) were present without co-substrate, biodegradation efficiencies of 53 ± 4% and 75 ± 3% were achieved, respectively, which were the highest levels observed. Clostridium spp. was prominent in all treatments, while Alkaliphilus spp. and Bacillus spp. thrived in the presence of iron, which had the most significant effect on LAS biodegradation. Those microorganisms were identified as crucial in affecting the LAS anaerobic degradation. The experiments revealed that the presence of electron acceptors fostered the development of a more specialised microbiota, especially those involved in the LAS biodegradation. A mutual interaction between the processes of degradation and adsorption was also shown.},
}

@article {pmid38613638,
year = {2024},
author = {Cai, Y and Chen, Z and Chen, E and Zhang, D and Wei, T and Sun, M and Lian, Y},
title = {Succinic Acid Ameliorates Concanavalin A-Induced Hepatitis by Altering the Inflammatory Microenvironment and Expression of BCL-2 Family Proteins.},
journal = {Inflammation},
volume = {},
number = {},
pages = {},
pmid = {38613638},
issn = {1573-2576},
support = {2021J05278//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//The Health Science Foundation of Fujian Youth Program/ ; 82303109//National Natural Science Foundation of China/ ; 2022J05299//Natural Science Foundation of Fujian Province, China/ ; 2021B002//Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China/ ; },
abstract = {Autoimmune hepatitis (AIH) is a severe immune-mediated inflammatory liver disease that currently lacks feasible drug treatment methods. Our study aimed to evaluate the protective effect of succinic acid against AIH and provide a reliable method for the clinical treatment of AIH. We performed an in vivo study of the effects of succinic acid on concanavalin A (ConA)-induced liver injury in mice. We examined liver transaminase levels, performed hematoxylin and eosin (HE) staining, and observed apoptotic phenotypes in mice. We performed flow cytometry to detect changes in the number of neutrophils and monocytes, and used liposomes to eliminate the liver Kupffer cells and evaluate their role. We performed bioinformatics analysis, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and western blotting to detect mitochondrial apoptosis-induced changes in proteins from the B-cell lymphoma 2(Bcl-2) family. Succinic acid ameliorated ConA-induced AIH in a concentration-dependent manner, as reflected in the survival curve. HE and TUNEL staining and terminal deoxynucleotidyl transferase dUTP nick end labeling revealed decreased alanine transaminase and aspartate aminotransferase levels, and reduced liver inflammation and apoptosis. RT-qPCR and enzyme-linked immunosorbent assay revealed that succinic acid significantly reduced liver pro-inflammatory cytokine levels. Flow cytometry revealed significantly decreased levels of liver neutrophils. Moreover, the protective effect of succinic acid disappeared after the Kupffer cells were eliminated, confirming their important role in the effect. Bioinformatics analysis, RT-qPCR, and western blotting showed that succinic acid-induced changes in proteins from the Bcl-2 family involved mitochondrial apoptosis, indicating the molecular mechanism underlying the protective effect of succinic acid. Succinic acid ameliorated ConA-induced liver injury by regulating immune balance, inhibiting pro-inflammatory factors, and promoting anti-apoptotic proteins in the liver. This study provides novel insights into the biological functions and therapeutic potential of succinic acid in the treatment of autoimmune liver injury.},
}

@article {pmid38606974,
year = {2024},
author = {Cardoso, PM and Hill, LJ and Villela, HDM and Vilela, CLS and Assis, JM and Rosado, PM and Rosado, JG and Chacon, MA and Majzoub, ME and Duarte, GAS and Thomas, T and Peixoto, RS},
title = {Localization and symbiotic status of probiotics in the coral holobiont.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0026124},
doi = {10.1128/msystems.00261-24},
pmid = {38606974},
issn = {2379-5077},
abstract = {UNLABELLED: Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.

IMPORTANCE: Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.},
}

@article {pmid38602612,
year = {2024},
author = {Xie, Y and Fan, Y and Su, M and Wang, Y and Zhang, G},
title = {Characteristics of the oral microbiota in patients with primary Sjögren's syndrome.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {38602612},
issn = {1434-9949},
support = {2019-106-21//Shantou Medical Health Science and Technology Plan/ ; A2019244//Medical Science Research Foundation of Guangdong Province/ ; },
abstract = {OBJECTIVE: Primary Sjögren's syndrome (pSS) is an autoimmune disease with unknown etiology that is considered to be related to environmental and genetic factors. The aim of this study was to clarify the oral microflora characteristics of pSS patients and to reveal the connection between oral bacterial composition and dental caries using a high-throughput sequencing technique.

METHODS: Thirty-five pSS patients and 20 healthy controls were enrolled in this study. We collected saliva and plaque samples from pSS patients and saliva samples from healthy controls. We used 16S ribosomal DNA (16S rDNA) high-throughput sequencing targeting the V3-V4 hypervariable region to determine the composition and structure of the microbiota in the three sample sets. Finally, bioinformatics analyses, including the diversity of the microbiota, species differences, and functional prediction were performed.

RESULTS: In the alpha diversity and beta diversity analysis, the Chao1 (P < 0.01), observed species (P < 0.01), and PD whole tree indices (P < 0.01) were significantly lower in the saliva and plaque samples of pSS patients than in the saliva samples of healthy controls, but the Shannon (P < 0.01) and Simpson indices (P < 0.01) were significantly higher in the healthy controls, and their total diversity significantly differed. In the main flora composition at the genus level (top 10), we identified Prevotella and Veillonella as more enriched in the saliva of pSS patients and Fusobacterium, Actinomyces, and Leptotrichia as more enriched in the plaque of pSS patients. Predictive functional analysis showed that the oral microbiota of pSS patients was related to translation, metabolism of cofactors and vitamins, and nucleotide metabolism.

CONCLUSIONS: The oral microbial ecology of patients with pSS is dysregulated, resulting in a decrease in overall diversity. Prevotella and Veillonella may be related to pSS, while Fusobacterium, Actinomyces, and Leptotrichia may be related to dental caries in pSS patients. Key Points • This study revealed differences in the oral microbial composition of patients with pSS compared to healthy controls. • We included a plaque group of pSS patients to identify the microbiota related to pSS and dental caries. • Prevotella and Veillonella may contribute to pSS, and Fusobacterium, Actinomyces, and Leptotrichia are associated with dental caries in pSS patients.},
}

@article {pmid38602532,
year = {2024},
author = {Xing, H and Chen, W and Liu, Y and Cahill, JF},
title = {Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {58},
pmid = {38602532},
issn = {1432-184X},
support = {31670531 and 32071645//National Natural Science Foundation of China/ ; 2022JBGS04 and 2023JBGS06//Research Project of Baishanzu National Park/ ; },
mesh = {China ; Forests ; Gamma Rays ; *Microbiota ; *Mycorrhizae ; Soil ; },
abstract = {Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.},
}

China
Forests
Gamma Rays
*Microbiota
*Mycorrhizae
Soil

@article {pmid38602492,
year = {2024},
author = {Machushynets, NV and Al Ayed, K and Terlouw, BR and Du, C and Buijs, NP and Willemse, J and Elsayed, SS and Schill, J and Trebosc, V and Pieren, M and Alexander, FM and Cochrane, SA and Liles, MR and Medema, MH and Martin, NI and van Wezel, GP},
title = {Discovery and Derivatization of Tridecaptin Antibiotics with Altered Host Specificity and Enhanced Bioactivity.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.4c00034},
pmid = {38602492},
issn = {1554-8937},
abstract = {The prevalence of multidrug-resistant (MDR) pathogens combined with a decline in antibiotic discovery presents a major challenge for health care. To refill the discovery pipeline, we need to find new ways to uncover new chemical entities. Here, we report the global genome mining-guided discovery of new lipopeptide antibiotics tridecaptin A5 and tridecaptin D, which exhibit unusual bioactivities within their class. The change in the antibacterial spectrum of Oct-TriA5 was explained solely by a Phe to Trp substitution as compared to Oct-TriA1, while Oct-TriD contained 6 substitutions. Metabolomic analysis of producer Paenibacillus sp. JJ-21 validated the predicted amino acid sequence of tridecaptin A5. Screening of tridecaptin analogues substituted at position 9 identified Oct-His9 as a potent congener with exceptional efficacy against Pseudomonas aeruginosa and reduced hemolytic and cytotoxic properties. Our work highlights the promise of tridecaptin analogues to combat MDR pathogens.},
}

@article {pmid38598334,
year = {2024},
author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C},
title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114078},
doi = {10.1016/j.celrep.2024.114078},
pmid = {38598334},
issn = {2211-1247},
abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.},
}

@article {pmid38593340,
year = {2024},
author = {Suárez-Moo, P and Prieto-Davó, A},
title = {Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications.},
journal = {MicrobiologyOpen},
volume = {13},
number = {2},
pages = {e1407},
pmid = {38593340},
issn = {2045-8827},
support = {//Consejo Nacional de Humanidades Ciencias y Tecnologías (CONAHCYT), México project A1-S-10785 (APD) and postdoctoral fellowship (362331) (PSM)/ ; },
mesh = {Bacteria/genetics ; Metagenome ; *Microbiota ; Multigene Family ; *Bacillaceae/genetics ; *Biological Products ; Biosynthetic Pathways/genetics ; },
abstract = {Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.},
}

Bacteria/genetics
Metagenome
*Microbiota
Multigene Family
*Bacillaceae/genetics
*Biological Products
Biosynthetic Pathways/genetics

@article {pmid38593079,
year = {2024},
author = {Zhong, Q and Liao, B and Liu, J and Shen, W and Wang, J and Wei, L and Ma, Y and Dong, PT and Bor, B and McLean, JS and Chang, Y and Shi, W and Cen, L and Wu, M and Liu, J and Li, Y and He, X and Le, S},
title = {Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {16},
pages = {e2319790121},
doi = {10.1073/pnas.2319790121},
pmid = {38593079},
issn = {1091-6490},
support = {R01DE023810//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R01DE030943//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; 31870167//MOST | National Natural Science Foundation of China (NSFC)/ ; R01AI087946//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI132818//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Humans ; *Bacteriophages/physiology ; Symbiosis ; Bacteria/genetics ; },
abstract = {Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.},
}

Humans
*Bacteriophages/physiology
Symbiosis
Bacteria/genetics

@article {pmid38591008,
year = {2024},
author = {Kang, M and Liu, L and Grossart, HP},
title = {Spatio-temporal variations of methane fluxes in sediments of a deep stratified temperate lake.},
journal = {iScience},
volume = {27},
number = {4},
pages = {109520},
pmid = {38591008},
issn = {2589-0042},
abstract = {Spatio-temporal variability of sediment-mediated methane (CH4) production in freshwater lakes causes large uncertainties in predicting global lake CH4 emissions under different climate change and eutrophication scenarios. We conducted extensive sediment incubation experiments to investigate CH4 fluxes in Lake Stechlin, a deep, stratified temperate lake. Our results show contrasting spatial patterns in CH4 fluxes between littoral and profundal sites. The littoral sediments, ∼33% of the total sediment surface area, contributed ∼86.9% of the annual CH4 flux at the sediment-water interface. Together with sediment organic carbon quality, seasonal stratification is responsible for the striking spatial difference in sediment CH4 production between littoral and profundal zones owing to more sensitive CH4 production than oxidation to warming. While profundal sediments produce a relatively small amount of CH4, its production increases markedly as anoxia spreads in late summer. Our measurements indicate that future lake CH4 emissions will increase due to climate warming and concomitant hypoxia/anoxia.},
}

@article {pmid38587642,
year = {2024},
author = {Srinivasan, S and Jnana, A and Murali, TS},
title = {Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {56},
pmid = {38587642},
issn = {1432-184X},
support = {CRG/2022/003227//Science and Engineering Research Board/ ; },
mesh = {Humans ; *Microbial Interactions ; *Microbiota ; Microbial Consortia ; Coculture Techniques ; Community Networks ; },
abstract = {Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.},
}

Humans
*Microbial Interactions
*Microbiota
Microbial Consortia
Coculture Techniques
Community Networks

@article {pmid38587527,
year = {2024},
author = {Garcia Mendez, DF and Egan, S and Wist, J and Holmes, E and Sanabria, J},
title = {Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {57},
pmid = {38587527},
issn = {1432-184X},
support = {FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bioreactors ; Feces ; },
abstract = {Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota. Community structure comparison between samples using t-distributed stochastic neighbour embedding and the Hellinger distance revealed a high variation between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Moreover, there was no overlap in the structure of the microbial communities between studies using the same bioreactor platform. In addition, α-diversity analysis using Hill numbers showed that highly complex bioreactors did not exhibit higher diversities than simpler designs. However, analyses of five projects in which the samples from the faecal inoculum were also provided revealed an amplicon sequence variants enrichment in bioreactors compared to the inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and the GMRepo database revealed bacterial families exclusively found in the bioreactor models. These findings highlight the potential of bioreactors to enrich low-abundance microorganisms from faecal samples, contributing to uncovering the gut microbial "dark matter".},
}

Humans
*Gastrointestinal Microbiome
*Microbiota
Bioreactors
Feces

@article {pmid38585661,
year = {2024},
author = {Hill, LJ and Messias, CSMA and Vilela, CLS and Garritano, AN and Villela, HDM and do Carmo, FL and Thomas, T and Peixoto, RS},
title = {Bacteria associated with the in hospite Symbiodiniaceae's phycosphere.},
journal = {iScience},
volume = {27},
number = {4},
pages = {109531},
pmid = {38585661},
issn = {2589-0042},
abstract = {Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.},
}

@article {pmid38585291,
year = {2023},
author = {Hobusch, U and Scheuch, M and Heuckmann, B and Hodžić, A and Hobusch, GM and Rammel, C and Pfeffer, A and Lengauer, V and Froehlich, DE},
title = {One Health Education Nexus: enhancing synergy among science-, school-, and teacher education beyond academic silos.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1337748},
pmid = {38585291},
issn = {2296-2565},
mesh = {Humans ; Ecosystem ; *One Health ; *Teacher Training ; Students ; Schools ; Health Education ; Educational Status ; },
abstract = {INTRODUCTION: The fact that the daily lives of billions of people were affected by the medical, social, and political aspects of the SARS-CoV-2 pandemic shows the need to anchor the understanding of One Health in society. Hence, promoting awareness and deepening the understanding of the interrelation between human health, animal health, and ecosystems must be accomplished through quality education, as advocated by UN Sustainable Development Goal 4. The often-questioned and discussed measures taken by governments to control the global pandemic between 2020 and 2023 can be seen as an opportunity to meet the educational needs of civil society solutions in multi-stakeholder settings between public, universities, and schools.

METHODS: This paper focuses on the integration of One Health principles in educational frameworks, particularly within the context of the higher education teaching framework "Teaching Clinic." This master-level course in the domain of pre-service teacher education serves as a potent vehicle for facilitating One Health Education, bridging the gap between research, higher education, and schools. Through the presentation of two case studies, this article demonstrates how the Teaching Clinic approach fosters interdisciplinary perspectives and provides a dynamic learning environment for pre-service teachers, as well as for pupils involved in the educational process.

RESULTS: In both cases, the integration of educational One Health school teaching-learning settings effectively enhanced pupils' understanding of complex topics and engaged them in active learning experiences. Pre-service teachers played a crucial role in developing, implementing, and evaluating these interventions. In Case I, pupils demonstrated proficiency in analyzing data and evaluating mathematical models, while in Case II, the chosen instructional approach facilitated One Health knowledge acquisition and enjoyment among pupils. These results underscore the potential of the One Health Teaching Clinic as a valuable educational framework for enhancing teaching and learning outcomes for pre-service teachers and fostering pupil engagement in socio-scientific One Health-related topics.

DISCUSSION: The discussion delves into the significance of breaking down disciplinary silos and the crucial role of teacher education in promoting a holistic approach to education, emphasizing the intersectionality of One Health Education and Education for Sustainable Development. This article underpins the significance of collaborative efforts across multiple (scientific) disciplines and across secondary and tertiary education levels to reach a nexus. Moreover, it emphasizes the alignment of this approach with the 2030 Agenda, Education for Sustainable Development, and Sustainable Development Goals, highlighting the potential for collective action toward a more sustainable future.},
}

Humans
Ecosystem
*One Health
*Teacher Training
Students
Schools
Health Education
Educational Status

@article {pmid38581683,
year = {2024},
author = {Loos, D and Filho, APDC and Dutilh, BE and Barber, AE and Panagiotou, G},
title = {A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114046},
doi = {10.1016/j.celrep.2024.114046},
pmid = {38581683},
issn = {2211-1247},
abstract = {Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.},
}

@article {pmid38581020,
year = {2024},
author = {Douillard, FP and Derman, Y and Jian, C and Korpela, K and Saxén, H and Salonen, A and de Vos, WM and Korkeala, H and Lindström, M},
title = {Case report: Aberrant fecal microbiota composition of an infant diagnosed with prolonged intestinal botulism.},
journal = {Gut pathogens},
volume = {16},
number = {1},
pages = {20},
pmid = {38581020},
issn = {1757-4749},
abstract = {BACKGROUND: Intestinal botulism is primarily reported in small babies as a condition known as infant botulism. The condition results from the ingestion of environmental or foodborne spores of botulinum neurotoxin (BoNT) producing Clostridia, usually Clostridium botulinum, and subsequent spore germination into active botulinum neurotoxinogenic cultures in the gut. It is generally considered that small babies are susceptible to C. botulinum colonization because of their immature gut microbiota. Yet, it is poorly understood which host factors contribute to the clinical outcome of intestinal botulism. We previously reported a case of infant botulism where the infant recovered clinically in six weeks but continued to secrete C. botulinum cells and/or BoNT in the feces for seven months.

CASE PRESENTATION: To further understand the microbial ecology behind this exceptionally long-lasting botulinum neurotoxinogenic colonization, we characterized the infant fecal microbiota using 16S rRNA gene amplicon sequencing over the course of disease and recovery. C. botulinum could be detected in the infant fecal samples at low levels through the acute phase of the disease and three months after recovery. Overall, we observed a temporal delay in the maturation of the infant fecal microbiota associated with a persistently high-level bifidobacterial population and a low level of Lachnospiraceae, Bacteroidaceae and Ruminococcaceae compared to healthy infants over time.

CONCLUSION: This study brings novel insights into the infant fecal composition associated with intestinal botulism and provides a basis for a more systematic analysis of the gut microbiota of infants diagnosed with botulism. A better understanding of the gut microbial ecology associated with infant botulism may support the development of prophylactic strategies against this life-threatening disease in small babies.},
}

@article {pmid38579997,
year = {2024},
author = {Cao, Y and Li, Y and Jia, L and Wang, Q and Niu, T and Yang, Q and Wang, Q and Zeng, X and Wang, R and Yue, L},
title = {Long-term and combined heavy-metal contamination forms a unique microbiome and resistome: A case study in a Yellow River tributary sediments.},
journal = {Environmental research},
volume = {252},
number = {Pt 1},
pages = {118861},
doi = {10.1016/j.envres.2024.118861},
pmid = {38579997},
issn = {1096-0953},
abstract = {Microorganisms have developed mechanisms to adapt to environmental stress, but how microbial communities adapt to long-term and combined heavy-metal contamination under natural environmental conditions remains unclear. Specifically, this study analyzed the characteristics of heavy metal composition, microbial community, and heavy metal resistance genes (MRGs) in sediments along Mang River, a tributary of the Yellow River, which has been heavily polluted by industrial production for more than 40 years. The results showed that the concentrations of Cr, Zn, Pb, Cu and As in most sediments were higher than the ambient background values. Bringing the heavy metals speciation and concentration into the risk evaluation method, two-thirds of the sediment samples were at or above the moderate risk level, and the ecological risk of combined heavy metals in the sediments decreased along the river stream. The high ecological risk of heavy metals affected the microbial community structure, metabolic pathways and MRG distribution. The formation of a HM-resistant microbiome possibly occurred through the spread of insertion sequences (ISs) carrying multiple MRGs, the types of ISs carrying MRGs outnumber those of plasmids, and the quantity of MRGs on ISs is also higher than that on plasmids. These findings could improve our understanding of the adaptation mechanism of microbial communities to long-term combined heavy metal contamination.},
}

@article {pmid38578091,
year = {2024},
author = {Morrison, BH and Jones, JL and Dzwonkowski, B and Krause, JW},
title = {Tracking Vibrio: population dynamics and ecology of Vibrio parahaemolyticus and V. vulnificus in an Alabama estuary.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0367423},
doi = {10.1128/spectrum.03674-23},
pmid = {38578091},
issn = {2165-0497},
abstract = {UNLABELLED: Vibrio is a genus of halophilic, gram-negative bacteria found in estuaries around the globe. Integral parts of coastal cultures often involve contact with vectors of pathogenic Vibrio spp. (e.g., consuming raw shellfish). High rates of mortality from certain Vibrio spp. infections demonstrate the need for an improved understanding of Vibrio spp. dynamics in estuarine regions. Our study assessed meteorological, hydrographic, and biological correlates of Vibrio parahaemolyticus and V. vulnificus at 10 sites in the Eastern Mississippi Sound System (EMSS) from April to October 2019. During the sampling period, median abundances of V. parahaemolyticus and V. vulnificus were 2.31 log MPN/L and 2.90 log MPN/L, respectively. Vibrio spp. dynamics were largely driven by site-based variation, with sites closest to freshwater inputs having the highest abundances. The E-W wind scalar, which affects Ekman transport, was a novel Vibrio spp. correlate observed. A potential salinity effect on bacterial-particle associations was identified, where V. vulnificus was associated with larger particles in conditions outside of their optimal salinity. Additionally, V. vulnificus abundances were correlated to those of harmful algal species that did not dominate community chlorophyll. Correlates from this study may be used to inform the next iteration of regionally predictive Vibrio models and may lend additional insight to Vibrio spp. ecology in similar systems.

IMPORTANCE: Vibrio spp. are bacteria found in estuaries worldwide; some species can cause illness and infections in humans. Relationships between Vibrio spp. abundance, salinity, and temperature are well documented, but correlations to other environmental parameters are less understood. This study identifies unique correlates (e.g., E-W wind scalar and harmful algal species) that could potentially inform the next iteration of predictive Vibrio models for the EMSS region. Additionally, these correlates may allow existing environmental monitoring efforts to be leveraged in providing data inputs for future Vibrio risk models. An observed correlation between salinity and V. vulnificus/particle-size associations suggests that predicted environmental changes may affect the abundance of Vibrio spp. in certain reservoirs, which may alter which vectors present the greatest vibrio risk.},
}

@article {pmid38575035,
year = {2024},
author = {Zheng, W and Wu, Q and Guo, X and Zhou, P and Wu, J and Yan, W},
title = {Rocky desertification succession alters soil microbial communities and survival strategies in the karst context.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172171},
doi = {10.1016/j.scitotenv.2024.172171},
pmid = {38575035},
issn = {1879-1026},
abstract = {Rocky desertification is one of the most ecological problems in the karst context. Although extensive research has been conducted to explore how to restore and protect, the responses of soil fungi and archaea to rocky desertification succession remain limited. Here, four grades of rocky desertification in a karst ecosystem were selected, amplicon sequencing analysis was conducted to investigate fungal and archaeal community adaptation in response to rocky desertification succession. Our findings revealed that the diversity and community structure of fungi and archaea in soils declined with the aggravation of rocky desertification. As the rocky desertification succession intensified, microbial interactions shifted from cooperation to competition. Microbial survival strategies were K-strategist and r-strategist dominated in the early and late stages of succession, respectively. Additionally, the driving factors affecting microorganisms have shifted from vegetation diversity to soil properties as the intensification of rocky desertification. Collectively, our study highlighted that plant diversity and soil properties play important roles on soil microbiomes in fragile karst ecosystems and that environmental factors induced by human activities might still be the dominant factor exacerbating rocky desertification, which could significantly enrich our understanding of microbial ecology within karst ecosystems.},
}

@article {pmid38574431,
year = {2024},
author = {Cunha, ICMD and Silva, AVRD and Boleta, EHM and Pellegrinetti, TA and Zagatto, LFG and Zagatto, SDSS and Chaves, MG and Mendes, R and Patreze, CM and Tsai, SM and Mendes, LW},
title = {The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype.},
journal = {Microbiological research},
volume = {283},
number = {},
pages = {127706},
doi = {10.1016/j.micres.2024.127706},
pmid = {38574431},
issn = {1618-0623},
abstract = {Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.},
}

@article {pmid38571798,
year = {2024},
author = {Rani, V and Horváth, Z and Nejstgaard, JC and Fierpasz, Á and Pálffy, K and Vad, CF},
title = {Food density drives diet shift of the invasive mysid shrimp, Limnomysis benedeni.},
journal = {Ecology and evolution},
volume = {14},
number = {4},
pages = {e11202},
pmid = {38571798},
issn = {2045-7758},
abstract = {Understanding the diet preferences and food selection of invasive species is crucial to better predict their impact on community structure and ecosystem functioning. Limnomysis benedeni, a Ponto-Caspian invasive mysid shrimp, is one of the most successful invaders in numerous European river and lake ecosystems. While existing studies suggest potentially strong trophic impact due to high predation pressure on native plankton communities, little is known of its food selectivity between phyto- and zooplankton, under different food concentrations. Here, we therefore investigated the feeding selectivity of L. benedeni on two commonly occurring prey organisms in freshwaters, the small rotifer zooplankton Brachionus calyciflorus together with the microphytoplankton Cryptomonas sp. present in increasing densities. Our results demonstrated a clear shift in food selection, with L. benedeni switching from B. calyciflorus to Cryptomonas sp. already when the two prey species were provided in equal biomasses. Different functional responses were observed for the two food types, indicating somewhat different foraging mechanisms for each food type. These findings provide experimental evidence on the feeding flexibility of invasive mysid shrimps and potential implications for trophic interactions in invaded ecosystems.},
}

@article {pmid38567263,
year = {2023},
author = {Crous, PW and Osieck, ER and Shivas, RG and Tan, YP and Bishop-Hurley, SL and Esteve-Raventós, F and Larsson, E and Luangsa-Ard, JJ and Pancorbo, F and Balashov, S and Baseia, IG and Boekhout, T and Chandranayaka, S and Cowan, DA and Cruz, RHSF and Czachura, P and De la Peña-Lastra, S and Dovana, F and Drury, B and Fell, J and Flakus, A and Fotedar, R and Jurjević, Ž and Kolecka, A and Mack, J and Maggs-Kölling, G and Mahadevakumar, S and Mateos, A and Mongkolsamrit, S and Noisripoom, W and Plaza, M and Overy, DP and Piątek, M and Sandoval-Denis, M and Vauras, J and Wingfield, MJ and Abell, SE and Ahmadpour, A and Akulov, A and Alavi, F and Alavi, Z and Altés, A and Alvarado, P and Anand, G and Ashtekar, N and Assyov, B and Banc-Prandi, G and Barbosa, KD and Barreto, GG and Bellanger, JM and Bezerra, JL and Bhat, DJ and Bilański, P and Bose, T and Bozok, F and Chaves, J and Costa-Rezende, DH and Danteswari, C and Darmostuk, V and Delgado, G and Denman, S and Eichmeier, A and Etayo, J and Eyssartier, G and Faulwetter, S and Ganga, KGG and Ghosta, Y and Goh, J and Góis, JS and Gramaje, D and Granit, L and Groenewald, M and Gulden, G and Gusmão, LFP and Hammerbacher, A and Heidarian, Z and Hywel-Jones, N and Jankowiak, R and Kaliyaperumal, M and Kaygusuz, O and Kezo, K and Khonsanit, A and Kumar, S and Kuo, CH and Læssøe, T and Latha, KPD and Loizides, M and Luo, SM and Maciá-Vicente, JG and Manimohan, P and Marbach, PAS and Marinho, P and Marney, TS and Marques, G and Martín, MP and Miller, AN and Mondello, F and Moreno, G and Mufeeda, KT and Mun, HY and Nau, T and Nkomo, T and Okrasińska, A and Oliveira, JPAF and Oliveira, RL and Ortiz, DA and Pawłowska, J and Pérez-De-Gregorio, MÀ and Podile, AR and Portugal, A and Privitera, N and Rajeshkumar, KC and Rauf, I and Rian, B and Rigueiro-Rodríguez, A and Rivas-Torres, GF and Rodriguez-Flakus, P and Romero-Gordillo, M and Saar, I and Saba, M and Santos, CD and Sarma, PVSRN and Siquier, JL and Sleiman, S and Spetik, M and Sridhar, KR and Stryjak-Bogacka, M and Szczepańska, K and Taşkın, H and Tennakoon, DS and Thanakitpipattana, D and Trovão, J and Türkekul, I and van Iperen, AL and van 't Hof, P and Vasquez, G and Visagie, CM and Wingfield, BD and Wong, PTW and Yang, WX and Yarar, M and Yarden, O and Yilmaz, N and Zhang, N and Zhu, YN and Groenewald, JZ},
title = {Fungal Planet description sheets: 1478-1549.},
journal = {Persoonia},
volume = {50},
number = {},
pages = {158-310},
pmid = {38567263},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia, Penicillium nudgee from soil under Melaleuca quinquenervia, Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata, and Pseudocercospora dalyelliae on leaf spot of Senna alata. Bolivia, Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum on a twig. Brazil, Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria, Amanita abscondita on sandy soil in a plantation of Quercus suber. Canada, Penicillium acericola on dead bark of Acer saccharum, and Penicillium corticola on dead bark of Acer saccharum. China, Colletotrichum qingyuanense on fruit lesion of Capsicum annuum. Denmark, Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos), Phaeosphaeria scalesiae on Scalesia sp. Finland, Inocybe jacobssonii on calcareous soils in dry forests and park habitats. France, Cortinarius rufomyrrheus on sandy soil under Pinus pinaster, and Periconia neominutissima on leaves of Poaceae. India, Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica, and Poronia nagaraholensis on elephant dung. Iran, Neosetophoma fici on infected leaves of Ficus elastica. Israel, Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata. Italy, Lyophyllum obscurum on acidic soil. Namibia, Aureobasidium faidherbiae on dead leaf of Faidherbia albida, and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis. Netherlands, Gaeumannomycella caricigena on dead culms of Carex elongata, Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha, Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis, Niesslia phragmiticola on dead standing culms of Phragmites australis, Pseudopyricularia caricicola on culms of Carex disticha, and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway, Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grown path. Pakistan, Mallocybe ahmadii on soil. Poland, Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica, Lapidomyces epipinicola from sooty mould community on Pinus nigra, and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies. Portugal, Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica, and Lunasporangiospora lusitanica from a biofilm covering a biodeteriorated limestone wall. Qatar, Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa, Alfaria thamnochorti on culm of Thamnochortus fraternus, Knufia aloeicola on Aloe gariepensis, Muriseptatomyces restionacearum (incl. Muriseptatomyces gen. nov.) on culms of Restionaceae, Neocladosporium arctotis on nest of cases of bag worm moths (Lepidoptera, Psychidae) on Arctotis auriculata, Neodevriesia scadoxi on leaves of Scadoxus puniceus, Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris, Tulasnella epidendrea from the roots of Epidendrum × obrienianum, and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora. South Korea, Lemonniera fraxinea on decaying leaves of Fraxinus sp. from pond. Spain, Atheniella lauri on the bark of fallen trees of Laurus nobilis, Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula, Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris, Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae from soil. Sweden, Inocybe bidumensis on calcareous soil. Thailand, Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buried in soil. Taiwan region (China), Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia. Türkiye, Melanogaster anatolicus on clay loamy soils. UK, Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum. Ukraine, Xenosphaeropsis corni on recently dead stem of Cornus alba. USA, Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Shivas RG, et al. 2023. Fungal Planet description sheets: 1478-1549. Persoonia 50: 158- 310. https://doi.org/10.3767/persoonia.2023.50.05.},
}

@article {pmid38562743,
year = {2024},
author = {Matz, LM and Shah, NS and Porterfield, L and Stuyck, OM and Jochum, MD and Kayed, R and Taglialatela, G and Urban, RJ and Buffington, SA},
title = {Microbial determinants of dementia risk in subjects of Mexican descent with type 2 diabetes living in South Texas.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.20.24304637},
pmid = {38562743},
abstract = {Type 2 diabetes (T2D) is a common forerunner of neurodegeneration and dementia, including Alzheimer's Disease (AD), yet the underlying mechanisms remain unresolved. Individuals of Mexican descent living in South Texas have increased prevalence of comorbid T2D and early onset AD, despite low incidence of the predisposing APOE-e4 variant and an absence of the phenotype among relatives residing in Mexico - suggesting a role for environmental factors in coincident T2D and AD susceptibility. Here, in a small clinical trial, we show dysbiosis of the human gut microbiome could contribute to neuroinflammation and risk for AD in this population. Divergent Gastrointestinal Symptom Rating Scale (GSRS) responses, despite no differences in expressed dietary preferences, provided the first evidence for altered gut microbial ecology among T2D subjects (sT2D) versus population-matched healthy controls (HC). Metataxonomic 16S rRNA sequencing of participant stool revealed a decrease in alpha diversity of sT2D versus HC gut communities and identified BMI as a driver of gut community structure. Linear discriminant analysis effect size (LEfSe) identified a significant decrease in the relative abundance of the short-chain fatty acid-producing taxa Lachnospiraceae, Faecalibacterium, and Alistipes and an increase in pathobionts Escherichia-Shigella, Enterobacter, and Clostridia innocuum among sT2D gut microbiota, as well as differentially abundant gene and metabolic pathways. These results suggest characterization of the gut microbiome of individuals with T2D could identify key actors among "disease state" microbiota which may increase risk for or accelerate the onset of neurodegeneration. Furthermore, they identify candidate microbiome-targeted approaches for prevention and treatment of neuroinflammation in AD.},
}

@article {pmid38562476,
year = {2024},
author = {Zhang, R and Zhang, H and Yang, C and Li, H and Wu, J},
title = {Effects of water stress on nutrients and enzyme activity in rhizosphere soils of greenhouse grape.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1376849},
pmid = {38562476},
issn = {1664-302X},
abstract = {In grape cultivation, incorrect water regulation will lead to significant water wastage, which in turn will change soil structure and disrupt soil nutrient cycling processes. This study aimed to investigate the effects of different water regulation treatments [by setting moderate water stress (W1), mild water stress (W2), and adequate water availability (CK)] on soil physical-chemical properties and enzyme activity in greenhouse grape during the growing season. The result showed that the W2 treatment had a negative impact on the build-up of dissolved organic carbon (DOC), nitrate nitrogen (NO3-N), and available phosphorus (AP). Throughout the reproductive period, the W1 and W2 treatments decreased the soil's microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) contents, and MBC was more vulnerable to water stress. During the growth period, the trends of urease, catalase, and sucrase activities in different soil depth were ranked as 10-20 cm > 0-10 cm > 20-40 cm. The urease activity in 0-10 cm soil was suppressed by both W1 and W2 treatments, while the invertase activity in various soil layers under W1 treatment differed substantially. The W1 treatment also reduced the catalase activity in the 20-40 cm soil layer in the grape growth season. These findings suggested that W2 treatment can conserve water and enhance microbial ecology of greenhouse grape soils. Therefore, W2 treatment was the most effective water regulation measure for local greenhouse grape cultivation.},
}

@article {pmid38562261,
year = {2024},
author = {Zünd, JN and Plüss, S and Mujezinovic, D and Menzi, C and von Bieberstein, PR and de Wouters, T and Lacroix, C and Leventhal, GE and Pugin, B},
title = {A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae035},
pmid = {38562261},
issn = {2730-6151},
abstract = {The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.},
}

@article {pmid38555787,
year = {2024},
author = {Mugani, R and El Khalloufi, F and Redouane, EM and Haida, M and Aba, RP and Essadki, Y and El Amrani Zerrifi, S and Hejjaj, A and Ouazzani, N and Campos, A and Grossart, HP and Mandi, L and Vasconcelos, V and Oudra, B},
title = {Unlocking the potential of bacterioplankton-mediated microcystin degradation and removal: A bibliometric analysis of sustainable water treatment strategies.},
journal = {Water research},
volume = {255},
number = {},
pages = {121497},
doi = {10.1016/j.watres.2024.121497},
pmid = {38555787},
issn = {1879-2448},
abstract = {Microcystins (MCs) constitute a significant threat to human and environmental health, urging the development of effective removal methods for these toxins. In this review, we explore the potential of MC-degrading bacteria as a solution for the removal of MCs from water. The review insights into the mechanisms of action employed by these bacteria, elucidating their ability to degrade and thus remove MCs. After, the review points out the influence of the structural conformation of MCs on their removal, particularly their stability at different water depths within different water bodies. Then, we review the crucial role played by the production of MCs in ensuring the survival and safeguarding of the enzymatic activities of Microcystis cells. This justifies the need for developing effective and sustainable methods for removing MCs from aquatic ecosystems, given their critical ecological function and potential toxicity to humans and animals. Thereafter, challenges and limitations associated with using MC-degrading bacteria in water treatment are discussed, emphasizing the need for further research to optimize the selection of bacterial strains used for MCs biodegradation. The interaction of MCs-degrading bacteria with sediment particles is also crucial for their toxin removal potential and its efficiency. By presenting critical information, this review is a valuable resource for researchers, policymakers, and stakeholders involved in developing sustainable and practical approaches to remove MCs. Our review highlights the potential of various applications of MC-degrading bacteria, including multi-soil-layering (MSL) technologies. It emphasizes the need for ongoing research to optimize the utilization of MC-degrading bacteria in water treatment, ultimately ensuring the safety and quality of water sources. Moreover, this review highlights the value of bibliometric analyses in revealing research gaps and trends, providing detailed insights for further investigations. Specifically, we discuss the importance of employing advanced genomics, especially combining various OMICS approaches to identify and optimize the potential of MCs-degrading bacteria.},
}

@article {pmid38555472,
year = {2024},
author = {Pan, J and Zhang, Z and Li, Y and Yu, J and You, Z and Li, C and Wang, S and Zhu, M and Ren, F and Zhang, X and Sun, Y and Wang, S},
title = {A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {3},
pages = {},
pmid = {38555472},
issn = {1477-4054},
support = {2022FY101100//Science & Technology Fundamental Resources Investigation Program/ ; 62325308//National Science Fund for Distinguished Young Scholars of China/ ; 32170114//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Deep Learning ; Pattern Recognition, Automated ; Neural Networks, Computer ; Algorithms ; Bacteria ; },
abstract = {Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.},
}

Humans
*Deep Learning
Pattern Recognition, Automated
Neural Networks, Computer
Algorithms
Bacteria

@article {pmid38555095,
year = {2024},
author = {Brame, JE and Warbrick, I and Heke, D and Liddicoat, C and Breed, MF},
title = {Short-term passive greenspace exposures have little effect on nasal microbiomes: A cross-over exposure study of a Māori cohort.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118814},
doi = {10.1016/j.envres.2024.118814},
pmid = {38555095},
issn = {1096-0953},
abstract = {Indigenous health interventions have emerged in New Zealand aimed at increasing people's interactions with and exposure to macro and microbial diversity. Urban greenspaces provide opportunities for people to gain such exposures. However, the dynamics and pathways of microbial transfer from natural environments onto a person remain poorly understood. Here, we analysed bacterial 16S rRNA amplicons in air samples (n = 7) and pre- and post-exposure nasal samples (n = 238) from 35 participants who had 30-min exposures in an outdoor park. The participants were organised into two groups: over eight days each group had two outdoor park exposures and two indoor office exposures, with a cross-over study design and washout days between exposure days. We investigated the effects of participant group, location (outdoor park vs. indoor office), and exposures (pre vs. post) on the nasal bacterial community composition and three key suspected health-associated bacterial indicators (alpha diversity, generic diversity of Gammaproteobacteria, and read abundances of butyrate-producing bacteria). The participants had distinct nasal bacterial communities, but these communities did not display notable shifts in composition following exposures. The community composition and key health bacterial indicators were stable throughout the trial period, with no clear or consistent effects of group, location, or exposure. We conclude that 30-min exposure periods to urban greenspaces are unlikely to create notable changes in the nasal microbiome of visitors, which contrasts with previous research. Our results suggest that longer exposures or activities that involves closer interaction with microbial rich ecological components (e.g., soil) are required for greenspace exposures to result in noteworthy changes in the nasal microbiome.},
}

@article {pmid38554019,
year = {2024},
author = {Hohagen, M and Sánchez, L and Herbst, AJ and Kählig, H and Shin, JW and Berry, D and Del Favero, G and Kleitz, F},
title = {MANNosylation of Mesoporous Silica Nanoparticles Modifies TLR4 Localization and NF-κB Translocation in T24 Bladder Cancer Cells.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2304150},
doi = {10.1002/adhm.202304150},
pmid = {38554019},
issn = {2192-2659},
support = {//University of Vienna/ ; IBS-R004//Institute for Basic Science/ ; },
abstract = {D-mannose is widely used as non-antibiotic treatment for bacterial urinary tract infections. This application is based on a well-studied mechanism of binding to the type 1 bacterial pili and, therefore, blocking bacteria adhesion to the uroepithelial cells. To implement D-mannose into carrier systems, the mechanism of action of the sugar in the bladder environment is also relevant and requires investigation. Herein, two different MANNosylation strategies using mesoporous silica nanoparticles (MSNs) are described. The impact of different chemical linkers on bacterial adhesion and bladder cell response is studied via confocal microscopy imaging of the MSN interactions with the respective organisms. Cytotoxicity is assessed and the expression of Toll-like receptor 4 (TLR4) and caveolin-1 (CAV-1), in the presence or absence of simulated infection with bacterial lipopolysaccharide (LPS), is evaluated using the human urinary bladder cancer cell line T24. Further, localisation of the transcription factor NF-κB due to the MANNosylated materials is examined over time. The results show that MANNosylation modifies bacterial adhesion to the nanomaterials and significantly affects TLR4, caveolin-1, and NF-κB in bladder cells. These elements are essential components of the inflammatory cascade/pathogens response during urinary tract infections. These findings demonstrate that MANNosylation is a versatile tool to design hybrid nanocarriers for targeted biomedical applications.},
}

@article {pmid38553666,
year = {2024},
author = {Ma, ZS},
title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {137},
pmid = {38553666},
issn = {1471-2105},
abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus & Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.

RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.

CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.},
}

@article {pmid38552803,
year = {2024},
author = {Petra de Oliveira Barros, V and Macedo Silva, JR and Maciel Melo, VM and Terceiro, PS and Nunes de Oliveira, I and Duarte de Freitas, J and Francisco da Silva Moura, O and Xavier de Araújo-Júnior, J and Erlanny da Silva Rodrigues, E and Maraschin, M and Thompson, FL and Landell, MF},
title = {Biosurfactants production by marine yeasts isolated from zoanthids and characterization of an emulsifier produced by Yarrowia lipolytica LMS 24B.},
journal = {Chemosphere},
volume = {355},
number = {},
pages = {141807},
doi = {10.1016/j.chemosphere.2024.141807},
pmid = {38552803},
issn = {1879-1298},
abstract = {The present study investigates the potential for biosurfactant production of 19 marine yeast species obtained from zoanthids. Using the emulsification index test to screen the samples produced by the marine yeasts, we verified that five isolates exhibited an emulsification index ≥50%. Additional tests were performed on such isolates, including oil displacement, drop collapse, Parafilm M assay, and surface tension measurement. The tolerance of produced biosurfactants for environmental conditions was also analyzed, especially considering the media's temperature, pH, and salinity. Moreover, the surfactant's ability to emulsify different hydrocarbon sources and to metabolize kerosene as the sole carbon source was evaluated in vitro. Our results demonstrate that yeast biosurfactants can emulsify hydrocarbon sources under different physicochemical conditions and metabolize kerosene as a carbon source. Considering the Yarrowia lipolytica LMS 24B as the yeast model for biosurfactant production from the cell's wall biomass, emulsification indexes of 61.2% were obtained, even at a high temperature of 120 °C. Furthermore, the Fourier-transform middle infrared spectroscopy (FTIR) analysis of the biosurfactant's chemical composition revealed the presence of distinct functional groups assigned to a glycoprotein complex. Considering the status of developing new bioproducts and bioprocesses nowadays, our findings bring a new perspective to biosurfactant production by marine yeasts, especially Y. lipolytica LMS 24B. In particular, the presented results validate the relevance of marine environments as valuable sources of genetic resources, i.e., yeast strains capable of metabolizing and emulsifying petroleum derivatives.},
}

@article {pmid38549428,
year = {2024},
author = {Männistö, MK and Ahonen, SHK and Ganzert, L and Tiirola, M and Stark, S and Häggblom, MM},
title = {Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae036},
pmid = {38549428},
issn = {1574-6941},
abstract = {Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early and late growing season. Phospholipid fatty acid (PLFA) and qPCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.},
}

@article {pmid38548725,
year = {2024},
author = {Giordano, N and Gaudin, M and Trottier, C and Delage, E and Nef, C and Bowler, C and Chaffron, S},
title = {Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2721},
pmid = {38548725},
issn = {2041-1723},
support = {862923//European Commission (EC)/ ; },
abstract = {Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.},
}

@article {pmid38548158,
year = {2024},
author = {Yang, S and Zuo, J and Grossart, HP and Dai, G and Liu, J and Song, L and Gan, N},
title = {Evaluating microcystinase A-based approach on microcystins degradation during harvested cyanobacterial blooms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {123878},
doi = {10.1016/j.envpol.2024.123878},
pmid = {38548158},
issn = {1873-6424},
abstract = {Addressing notorious and worldwide Microcystis blooms, mechanical algae harvesting is an effective emergency technology for bloom mitigation and removal of nutrient loads in waterbodies. However, the absence of effective methods for removal of cyanobacterial toxins, e.g., microcystins (MCs), poses a challenge to recycle the harvested Microcystis biomass. In this study, we therefore introduced a novel approach, the "captured biomass-MlrA enzymatic MC degradation", by enriching microcystinase A (MlrA) via fermentation and spraying it onto salvaged Microcystis slurry to degrade all MCs. After storing the harvested Microcystis slurry, a rapid release of extracellular MCs occurred within the initial 8 hours, reaching a peak concentration of 5.33 μg/mL at 48 hours during the composting process. Upon spraying the recombinant MlrA crude extract (about 3.36 U) onto the Microcystis slurry in a ratio of 0.1% (v/v), over 95% of total MCs were degraded within a 24-hour period. Importantly, we evaluated the reliability and safety of using MlrA extracts to degrade MCs. Results showed that organic matter/nutrient contents, e.g. soluble proteins, polysaccharides, phycocyanin and carotenoids, were not significantly altered. Furthermore, the addition of MlrA extracts did not significantly change the bacterial community composition and diversity in the Microcystis slurry, indicating that the MlrA extracts did not increase the risk of pathogenic bacteria. Our study provides an effective and promising method for the pre-treatment of harvested Microcystis biomass, highlighting an ecologically sustainable framework for addressing Microcystis blooms.},
}

@article {pmid38547998,
year = {2024},
author = {Li, Y and Schütte, W and Dekeukeleire, M and Janssen, C and Boon, N and Asselman, J and Lebeer, S and Spacova, I and De Rijcke, M},
title = {The immunostimulatory activity of sea spray aerosols: bacteria and endotoxins activate TLR4, TLR2/6, NF-κB and IRF in human cells.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {171969},
doi = {10.1016/j.scitotenv.2024.171969},
pmid = {38547998},
issn = {1879-1026},
abstract = {Frequent exposure to sea spray aerosols (SSA) containing marine microorganisms and bioactive compounds may influence human health. However, little is known about potential immunostimulation by SSA exposure. This study focuses on the effects of marine bacteria and endotoxins in SSA on several receptors and transcription factors known to play a key role in the human innate immune system. SSA samples were collected in the field (Ostend, Belgium) or generated in the lab using a marine aerosol reference tank (MART). Samples were characterized by their sodium contents, total bacterial counts, and endotoxin concentrations. Human reporter cells were exposed to SSA to investigate the activation of toll-like receptor 4 (TLR4) in HEK-Blue hTLR4 cells and TLR2/6 in HEK-Blue hTLR2/6 cells, as well as the activation of nuclear factor kappa B (NF-κB) and interferon regulatory factors (IRF) in THP1-Dual monocytes. These responses were then correlated to the total bacterial counts and endotoxin concentrations to explore dose-effect relationships. Field SSA contained from 3.0 × 10[3] to 6.0 × 10[5] bacteria/m[3] air (averaging 2.0 ± 1.9 × 10[5] bacteria/m[3] air) and an endotoxin concentration ranging from 7 to 1217 EU/m[3] air (averaging 389 ± 434 EU/m[3] air). In contrast, MART SSA exhibited elevated levels of total bacterial count (from 2.0 × 10[5] to 2.4 × 10[6], averaging 7.3 ± 5.5 × 10[5] cells/m[3] air) and endotoxin concentration from 536 to 2191 (averaging 1310 ± 513 EU/m[3] air). SSA samples differentially activated TLR4, TLR2/6, NF-κB and IRF. These immune responses correlated dose-dependently with the total bacterial counts, endotoxin levels, or both. This study sheds light on the immunostimulatory potential of SSA and its underlying mechanisms, highlighting the need for further research to deepen our understanding of the health implications of SSA exposure.},
}

@article {pmid38544331,
year = {2024},
author = {Wang, C and Defoirdt, T and Rajkovic, A},
title = {The impact of indole and mucin on sporulation, biofilm formation and enterotoxin production in foodborne Clostridium perfringens.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae083},
pmid = {38544331},
issn = {1365-2672},
abstract = {AIMS: Indole and mucin are compounds found in the host environment as they are produced by the host or by the host-associated microbiota. This study investigated whether indole and mucin impact C. perfringens growth and sporulation, as well as enterotoxin production and biofilm formation.

METHODS AND RESULTS: There was no impact on growth of C. perfringens for up to 400 µM indole and 240 mg/L mucin, and neither indole nor mucin affected sporulation. Reverse-transcriptase qPCR showed that mucin strongly upregulated the expression of C. perfringens enterotoxin (up to 121-fold increase), whereas indole had a much more modest effect (2-fold). This was also reflected in increased C. perfringens enterotoxin levels in mucin-treated C. perfringens (as assessed by a reversed passive latex agglutination assay). Finally, mucin and indole significanly increased biofilm formation of C. perfringens, although the effect size was relatively small (less than 1.5 fold).

CONCLUSION: These results indicate that C. perfringens can sense its presence in a host environment by responding to mucin and thereby markedly increased enterotoxin production.},
}

@article {pmid38543583,
year = {2024},
author = {Pandey, S and Blache, A and Achouak, W},
title = {Insights into Bacterial Extracellular Vesicle Biogenesis, Functions, and Implications in Plant-Microbe Interactions.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543583},
issn = {2076-2607},
abstract = {Plant-microbe interactions play a crucial role in shaping plant health and survival. In recent years, the role of extracellular vesicles (EVs) in mediating intercellular communication between plants and microbes has emerged as an intriguing area of research. EVs serve as important carriers of bioactive molecules and genetic information, facilitating communication between cells and even between different organisms. Pathogenic bacteria leverage extracellular vesicles (EVs) to amplify their virulence, exploiting their cargo rich in toxins and virulence factors. Conversely, beneficial microbes initiate EV secretion to stimulate plant immune responses and nurture symbiotic relationships. The transfer of EV-packed small RNAs (sRNAs) has been demonstrated to facilitate the modulation of immune responses. Furthermore, harnessing the potential of EVs holds promise for the development of innovative diagnostic tools and sustainable crop protection strategies. This review highlights the biogenesis and functions of EVs in bacteria and their importance in plant defense, and paves the way for future research in this exciting field.},
}

@article {pmid38543493,
year = {2024},
author = {Heczko, P},
title = {Editorial for Special Issue "Effects of Probiotics on Health".},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/microorganisms12030442},
pmid = {38543493},
issn = {2076-2607},
abstract = {Since 1987, when Professor Sherwood Gorbach discovered, characterized, and commercialized the first probiotic Lactobacillus rhamnosus GG, a total of over 17,000 publications have been indexed in PubMed under "probiotic" and "health", which is an extensive amount of research on the specific bacteria and yeasts defined as "live microorganisms that, when administered in adequate amounts, exert a health benefit on the host" [...].},
}

@article {pmid38543484,
year = {2024},
author = {Rosa-Masegosa, A and Rodriguez-Sanchez, A and Gorrasi, S and Fenice, M and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B},
title = {Microbial Ecology of Granular Biofilm Technologies for Wastewater Treatment: A Review.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/microorganisms12030433},
pmid = {38543484},
issn = {2076-2607},
abstract = {Nowadays, the discharge of wastewater is a global concern due to the damage caused to human and environmental health. Wastewater treatment has progressed to provide environmentally and economically sustainable technologies. The biological treatment of wastewater is one of the fundamental bases of this field, and the employment of new technologies based on granular biofilm systems is demonstrating success in tackling the environmental issues derived from the discharge of wastewater. The granular-conforming microorganisms must be evaluated as functional entities because their activities and functions for removing pollutants are interconnected with the surrounding microbiota. The deep knowledge of microbial communities allows for the improvement in system operation, as the proliferation of microorganisms in charge of metabolic roles could be modified by adjustments to operational conditions. This is why engineering must consider the intrinsic microbiological aspects of biological wastewater treatment systems to obtain the most effective performance. This review provides an extensive view of the microbial ecology of biological wastewater treatment technologies based on granular biofilms for mitigating water pollution.},
}

@article {pmid38543271,
year = {2024},
author = {Srivastava, MG and Kamarudin, NHN and Aktan, MK and Zheng, K and Zayed, N and Yongabi, D and Wagner, P and Teughels, W and Boccaccini, AR and Braem, A},
title = {pH-Triggered Controlled Release of Chlorhexidine Using Chitosan-Coated Titanium Silica Composite for Dental Infection Prevention.},
journal = {Pharmaceutics},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/pharmaceutics16030377},
pmid = {38543271},
issn = {1999-4923},
support = {STG/17/024, C32/18/059//KU Leuven/ ; },
abstract = {Peri-implantitis is a growing pathological concern for dental implants which aggravates the occurrence of revision surgeries. This increases the burden on both hospitals and the patients themselves. Research is now focused on the development of materials and accompanying implants designed to resist biofilm formation. To enhance this endeavor, a smart method of biofilm inhibition coupled with limiting toxicity to the host cells is crucial. Therefore, this research aims to establish a proof-of-concept for the pH-triggered release of chlorhexidine (CHX), an antiseptic commonly used in mouth rinses, from a titanium (Ti) substrate to inhibit biofilm formation on its surface. To this end, a macroporous Ti matrix is filled with mesoporous silica (together referred to as Ti/SiO2), which acts as a diffusion barrier for CHX from the CHX feed side to the release side. To limit release to acidic conditions, the release side of Ti/SiO2 is coated with crosslinked chitosan (CS), a pH-responsive and antimicrobial natural polymer. Scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM/EDX) and Fourier transform infrared (FTIR) spectroscopy confirmed successful CS film formation and crosslinking on the Ti/SiO2 disks. The presence of the CS coating reduced CHX release by 33% as compared to non-coated Ti/SiO2 disks, thus reducing the antiseptic exposure to the environment in normal conditions. Simultaneous differential scanning calorimetry and thermogravimetric analyzer (SDT) results highlighted the thermal stability of the crosslinked CS films. Quartz crystal microbalance with dissipation monitoring (QCM-D) indicated a clear pH response for crosslinked CS coatings in an acidic medium. This pH response also influenced CHX release through a Ti/SiO2/CS disk where the CHX release was higher than the average trend in the neutral medium. Finally, the antimicrobial study revealed a significant reduction in biofilm formation for the CS-coated samples compared to the control sample using viability quantitative polymerase chain reaction (v-qPCR) measurements, which were also corroborated using SEM imaging. Overall, this study investigates the smart triggered release of pharmaceutical agents aimed at inhibiting biofilm formation, with potential applicability to implant-like structures.},
}

@article {pmid38542054,
year = {2024},
author = {Barathan, M and Ng, SL and Lokanathan, Y and Ng, MH and Law, JX},
title = {Unseen Weapons: Bacterial Extracellular Vesicles and the Spread of Antibiotic Resistance in Aquatic Environments.},
journal = {International journal of molecular sciences},
volume = {25},
number = {6},
pages = {},
doi = {10.3390/ijms25063080},
pmid = {38542054},
issn = {1422-0067},
support = {DIP-2023-011//National University of Malaysia/ ; FF-2021-518//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; },
abstract = {This paper sheds light on the alarming issue of antibiotic resistance (ABR) in aquatic environments, exploring its detrimental effects on ecosystems and public health. It examines the multifaceted role of antibiotic use in aquaculture, agricultural runoff, and industrial waste in fostering the development and dissemination of resistant bacteria. The intricate interplay between various environmental factors, horizontal gene transfer, and bacterial extracellular vesicles (BEVs) in accelerating the spread of ABR is comprehensively discussed. Various BEVs carrying resistance genes like blaCTX-M, tetA, floR, and sul/I, as well as their contribution to the dominance of multidrug-resistant bacteria, are highlighted. The potential of BEVs as both a threat and a tool in combating ABR is explored, with promising strategies like targeted antimicrobial delivery systems and probiotic-derived EVs holding significant promise. This paper underscores the urgency of understanding the intricate interplay between BEVs and ABR in aquatic environments. By unraveling these unseen weapons, we pave the way for developing effective strategies to mitigate the spread of ABR, advocating for a multidisciplinary approach that includes stringent regulations, enhanced wastewater treatment, and the adoption of sustainable practices in aquaculture.},
}

@article {pmid38539868,
year = {2024},
author = {M'hir, S and Ayed, L and De Pasquale, I and Fanizza, E and Tlais, AZA and Comparelli, R and Verni, M and Latronico, R and Gobbetti, M and Di Cagno, R and Filannino, P},
title = {Comparison of Milk Kefirs Obtained from Cow's, Ewe's and Goat's Milk: Antioxidant Role of Microbial-Derived Exopolysaccharides.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/antiox13030335},
pmid = {38539868},
issn = {2076-3921},
abstract = {Different types of milk are used in the production of milk kefir, but little information is available on the release of potentially antioxidant exopolysaccharides (EPS). The aim of this study was to investigate whether the microbial dynamics and EPS release are dependent on the milk substrate. In our study, the inoculated microbial consortium was driven differently by each type of milk (cow, ewe, and goat). This was evident in the sugar consumption, organic acid production, free amino release, and EPS production. The amount and the composition of the secreted EPS varied depending on the milk type, with implications for the structure and functional properties of the EPS. The low EPS yield in ewe's milk was associated with a higher lactic acid production and thus with the use of carbon sources oriented towards energy production. Depending on the milk used as substrate, the EPS showed different monosaccharide and FT-IR profiles, microstructures, and surface morphologies. These differences affected the antiradical properties and reducing power of the EPS. In particular, EPS extracted from cow's milk had a higher antioxidant activity than other milk types, and the antioxidant activity was concentration dependent.},
}

@article {pmid38539229,
year = {2024},
author = {Villena-Alemany, C and Mujakić, I and Fecskeová, LK and Woodhouse, J and Auladell, A and Dean, J and Hanusová, M and Socha, M and Gazulla, CR and Ruscheweyh, HJ and Sunagawa, S and Silva Kavagutti, V and Andrei, AŞ and Grossart, HP and Ghai, R and Koblížek, M and Piwosz, K},
title = {Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {65},
pmid = {38539229},
issn = {2049-2618},
support = {19-28778X//Grantová Agentura České Republiky/ ; 19-28778X//Grantová Agentura České Republiky/ ; 19-28778X//Grantová Agentura České Republiky/ ; 19-28778X//Grantová Agentura České Republiky/ ; 19-28778X//Grantová Agentura České Republiky/ ; 2021/03/Y/NZ8/00076//Polska Akademia Nauk/ ; },
abstract = {BACKGROUND: Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake.

RESULTS: AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM genes, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource, we demonstrated that the majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. AAP community presented an indigenous freshwater nature characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment.

CONCLUSIONS: Our findings highlight the substantial contribution of AAP bacteria to the carbon flow and ecological dynamics of lakes and unveil a recurrent and dynamic seasonal succession of the AAP community. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom. We suggest a potential role of AAP bacteria within the context of the PEG model and their consideration in further ecological models.},
}

@article {pmid38537828,
year = {2024},
author = {Pimentel, IM and Baikova, D and Buchner, D and Castellanos, AB and David, GM and Deep, A and Doliwa, A and Hadžiomerović, U and Serge Mayombo, NA and Prati, S and Spyra, MA and Vermiert, AM and Beisser, D and Dunthorn, M and Piggott, JJ and Sures, B and Tiegs, SD and Leese, F and Beermann, AJ},
title = {Assessing the response of an urban stream ecosystem to salinization under different flow regimes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {171849},
doi = {10.1016/j.scitotenv.2024.171849},
pmid = {38537828},
issn = {1879-1026},
abstract = {Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.},
}

@article {pmid38537819,
year = {2024},
author = {Tobias-Hünefeldt, SP and van Beusekom, JEE and Russnak, V and Dähnke, K and Streit, WR and Grossart, HP},
title = {Seasonality, rather than estuarine gradient or particle suspension/sinking dynamics, determines estuarine carbon distributions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {171962},
doi = {10.1016/j.scitotenv.2024.171962},
pmid = {38537819},
issn = {1879-1026},
abstract = {Estuaries are important components of the global carbon cycle; exchanging carbon between aquatic, atmospheric, and terrestrial environments, representing important loci for blue carbon storage and greenhouse gas emissions. However, how estuarine gradients affect sinking/suspended particles, and dissolved organic matter dynamic interactions remains unexplored. We fractionated suspended/sinking particles to assess and characterise carbon fate differences. We investigated bacterial colonisation (SYBR Green I) and exopolymer concentrations (TEP/CSP) with microscopy staining techniques. C/H/N and dry weight analysis identified particle composition differences. Meanwhile, nutrient and carbon analysis, and excitation and emission matrix evaluations with a subsequent parallel factor (PARAFAC) analysis characterised dissolved organic matter. The lack of clear salinity driven patterns in our study are presumably due to strong mixing forces and high particle heterogeneity along the estuary, with only density differences between suspended and sinking particles. Elbe estuary particles' organic portion is made up of marine-like (sinking) and terrestrial-like (suspended) signatures. Salinity did not have a significant role in microbial degradation and carbon composition, although brackish estuary portions were more biologically active. Indicative of increased degradation rates, leading to decreased greenhouse gas emissions, which are especially relevant for estuaries, with their disproportionate greenhouse gas emissions. Bacterial colonisation decreased seawards, indicative of decreased degradation, and shifts in microbial community composition and functions. Our findings span diverse strands of research, concerning steady carbon contributions from both marine and terrestrial sources, carbon aromaticity, humification index, and bioavailability. Their integration highlights the importance of the Elbe estuary as a model system, providing robust information for future policy decisions affecting dissolved and particulate matter dynamics within the Elbe Estuary.},
}

@article {pmid38537644,
year = {2024},
author = {Kawa, D and Thiombiano, B and Shimels, MZ and Taylor, T and Walmsley, A and Vahldick, HE and Rybka, D and Leite, MFA and Musa, Z and Bucksch, A and Dini-Andreote, F and Schilder, M and Chen, AJ and Daksa, J and Etalo, DW and Tessema, T and Kuramae, EE and Raaijmakers, JM and Bouwmeester, H and Brady, SM},
title = {The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.},
journal = {Cell reports},
volume = {},
number = {},
pages = {113971},
doi = {10.1016/j.celrep.2024.113971},
pmid = {38537644},
issn = {2211-1247},
abstract = {Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.},
}

@article {pmid38537571,
year = {2024},
author = {Jing, J and Garbeva, P and Raaijmakers, JM and Medema, MH},
title = {Strategies for tailoring functional microbial synthetic communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae049},
pmid = {38537571},
issn = {1751-7370},
abstract = {Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While synthetic communities have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional synthetic communities to reveal common principles and discuss multi-dimensional approaches for community design. We propose a strategy for tailoring the design of functional synthetic communities based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.},
}

@article {pmid38535593,
year = {2024},
author = {Cristino, S and Pascale, MR and Marino, F and Derelitto, C and Salaris, S and Orsini, M and Squarzoni, S and Grottola, A and Girolamini, L},
title = {Characterization of a Novel Species of Legionella Isolated from a Healthcare Facility: Legionella resiliens sp. nov.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/pathogens13030250},
pmid = {38535593},
issn = {2076-0817},
abstract = {Two Legionella-like isolates, 8cVS16[T] and 9fVS26, were isolated from a water distribution system (WDS) in a healthcare facility. Cells were Gram- and Ziehl Neelsen-stain-negative, rod-shaped, motile, and exhibited a blue-white fluorescence under Wood's lamp at 365 nm. The strains grew in a range of 32-37 °C on BCYE with L-cysteine (Cys+), GVPC, and MWY agar medium, with a positive reaction for oxidase, catalase, and gelatinase. The dominant fatty acids were summed features 3 (C16:1ω7c/C16:1ω6c) (27.7%), C16:0 iso (17.5%), and C16:0 (16.3%), and Q13 as the major ubiquinone. The mip and rpoB gene sequences showed a similarity of 96.7% and 92.4%, with L. anisa (ATCC 35292[T]). The whole genomes sequencing (WGS) performed displayed a GC content of 38.21 mol% for both. The digital DNA-DNA hybridization (dDDH) analysis demonstrated the separation of the two strains from the phylogenetically most related L. anisa (ATCC 35292[T]), with ≤43% DNA-DNA relatedness. The Average Nucleotide Identity (ANI) between the two strains and L. anisa (ATCC 35292[T]) was 90.74%, confirming that the two isolates represent a novel species of the genus Legionella. The name proposed for this species is Legionella resiliens sp. nov., with 8cVS16[T] (=DSM 114356[T] = CCUG 76627[T]) as the type strain.},
}

@article {pmid38531380,
year = {2024},
author = {Skinner, JP and Palar, S and Allen, C and Raderstorf, A and Blake, P and Morán Reyes, A and Berg, RN and Muse, C and Robles, A and Hamdan, N and Chu, MY and Delgado, AG},
title = {Acetylene Tunes Microbial Growth During Aerobic Cometabolism of Trichloroethene.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.3c08068},
pmid = {38531380},
issn = {1520-5851},
abstract = {Microbial aerobic cometabolism is a possible treatment approach for large, dilute trichloroethene (TCE) plumes at groundwater contaminated sites. Rapid microbial growth and bioclogging pose a persistent problem in bioremediation schemes. Bioclogging reduces soil porosity and permeability, which negatively affects substrate distribution and contaminant treatment efficacy while also increasing the operation and maintenance costs of bioremediation. In this study, we evaluated the ability of acetylene, an oxygenase enzyme-specific inhibitor, to decrease biomass production while maintaining aerobic TCE cometabolism capacity upon removal of acetylene. We first exposed propane-metabolizing cultures (pure and mixed) to 5% acetylene (v v[-1]) for 1, 2, 4, and 8 d and we then verified TCE aerobic cometabolic activity. Exposure to acetylene overall decreased biomass production and TCE degradation rates while retaining the TCE degradation capacity. In the mixed culture, exposure to acetylene for 1-8 d showed minimal effects on the composition and relative abundance of TCE cometabolizing bacterial taxa. TCE aerobic cometabolism and incubation conditions exerted more notable effects on microbial ecology than did acetylene. Acetylene appears to be a viable approach to control biomass production that may lessen the likelihood of bioclogging during TCE cometabolism. The findings from this study may lead to advancements in aerobic cometabolism remediation technologies for dilute plumes.},
}

@article {pmid38530469,
year = {2024},
author = {Maraci, Ö and Antonatou-Papaioannou, A and Jünemann, S and Schneeberger, K and Schulze, M and Scheffler, I and Caspers, BA},
title = {Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {55},
pmid = {38530469},
issn = {1432-184X},
support = {SCHN 1584/2-1//Deutsche Forschungsgemeinschaft/ ; SCHN 1584/2-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Reproducibility is a fundamental principle in science, ensuring reliable and valid findings. However, replication studies are scarce, particularly in ecology, due to the emphasis on novelty for publication. We explored the possibility of replicating original findings in the field of microbial and chemical ecology by conducting a conceptual replication of a previous study analysing the sex-specific differences in the microbial communities inhabiting the wing sacs, a scent organ with crucial functions in olfactory communication, of greater sac-winged bat (Saccopteryx bilineata). In the original study, the skin swabs from the antebrachial wing sacs of the males and wing sac rudiments of the females were analysed using culture-dependent methods to test sex-specific differences. The authors demonstrated that males have lower microbial richness and different microbial composition than females. We attempted to reproduce these findings using 16S rRNA sequencing, which offers improved accuracy in pinpointing microbial members than culture-dependent methods because of advanced statistical methods. Our study validated the original study's findings: Males had a lower microbial richness, and the community composition differed between the sexes. Furthermore, in the current study, males had an increased abundance of bacteria that might potentially be involved in odour production and degradation of malodorous substances and antimicrobial production. Our conceptual replication study corroborated that microbes can play a role in shaping their host's olfactory phenotype and consequently influence sexual selection. Furthermore, the current study emphasises the importance of replication efforts and hopefully encourages a culture that values replication studies in scientific practice.},
}

@article {pmid38528797,
year = {2024},
author = {Avila Santos, AP and de Almeida, BLS and Bonidia, RP and Stadler, PF and Stefanic, P and Mandic-Mulec, I and Rocha, U and Sanches, DS and de Carvalho, ACPLF},
title = {BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.},
journal = {RNA biology},
volume = {21},
number = {1},
pages = {1-12},
doi = {10.1080/15476286.2024.2329451},
pmid = {38528797},
issn = {1555-8584},
mesh = {*Deep Learning ; RNA, Untranslated/genetics ; Algorithms ; RNA ; Neural Networks, Computer ; },
abstract = {The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.},
}

*Deep Learning
RNA, Untranslated/genetics
Algorithms
RNA
Neural Networks, Computer

@article {pmid38526664,
year = {2024},
author = {Roy, R and Paul, P and Chakraborty, P and Malik, M and Das, S and Chatterjee, S and Maity, A and Dasgupta, M and Sarker, RK and Sarkar, S and Das Gupta, A and Tribedi, P},
title = {Cuminaldehyde and Tobramycin Forestall the Biofilm Threats of Staphylococcus aureus: A Combinatorial Strategy to Evade the Biofilm Challenges.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {38526664},
issn = {1559-0291},
support = {R&D/2020/F2//The Neotia University/ ; },
abstract = {Staphylococcus aureus, an opportunistic Gram-positive pathogen, is known for causing various infections in humans, primarily by forming biofilms. The biofilm-induced antibiotic resistance has been considered a significant medical threat. Combinatorial therapy has been considered a reliable approach to combat antibiotic resistance by using multiple antimicrobial agents simultaneously, targeting bacteria through different mechanisms of action. To this end, we examined the effects of two molecules, cuminaldehyde (a natural compound) and tobramycin (an antibiotic), individually and in combination, against staphylococcal biofilm. Our experimental observations demonstrated that cuminaldehyde (20 μg/mL) in combination with tobramycin (0.05 μg/mL) exhibited efficient reduction in biofilm formation compared to their individual treatments (p < 0.01). Additionally, the combination showed an additive interaction (fractional inhibitory concentration value 0.66) against S. aureus. Further analysis revealed that the effective combination accelerated the buildup of reactive oxygen species (ROS) and increased the membrane permeability of the bacteria. Our findings also specified that the cuminaldehyde in combination with tobramycin efficiently reduced biofilm-associated pathogenicity factors of S. aureus, including fibrinogen clumping ability, hemolysis property, and staphyloxanthin production. The selected concentrations of tobramycin and cuminaldehyde demonstrated promising activity against the biofilm development of S. aureus on catheter models without exerting antimicrobial effects. In conclusion, the combination of tobramycin and cuminaldehyde presented a successful strategy for combating staphylococcal biofilm-related healthcare threats. This combinatorial approach holds the potential for controlling biofilm-associated infections caused by S. aureus.},
}

@article {pmid38524670,
year = {2023},
author = {Yount, TA and Murtha, AN and Cecere, AG and Miyashiro, TI},
title = {Quorum sensing facilitates interpopulation signaling by Vibrio fischeri within the light organ of Euprymna scolopes.},
journal = {Israel journal of chemistry},
volume = {63},
number = {5-6},
pages = {},
pmid = {38524670},
issn = {0021-2148},
support = {R01 GM129133/GM/NIGMS NIH HHS/United States ; },
abstract = {Quorum sensing is an intercellular signaling mechanism that enables bacterial cells to coordinate population-level behaviors. How quorum sensing functions in natural habitats remains poorly understood. Vibrio fischeri is a bacterial symbiont of the Hawaiian bobtail squid Euprymna scolopes and depends on LuxI/LuxR quorum sensing to produce the symbiotic trait of bioluminescence. A previous study demonstrated that animals emit light when co-colonized by a Δlux mutant, which lacks several genes within the lux operon that are necessary for bioluminescence production, and a LuxI[-] mutant, which cannot synthesize the quorum signaling molecule N-3-oxohexanoyl-homoserine lactone. Here, we build upon that observation and show that populations of LuxI[-] feature elevated promoter activity for the lux operon. We find that population structures comprising of Δlux and LuxI[-] are attenuated within the squid, but a wild-type strain enables the LuxI[-] strain type to be maintained in vivo. These experimental results support a model of interpopulation signaling, which provides basic insight into how quorum sensing functions within the natural habitats found within a host.},
}

@article {pmid38521905,
year = {2024},
author = {Wu, J and Lv, Y and Hao, P and Zhang, Z and Zheng, Y and Chen, E and Fan, Y},
title = {Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {300},
pmid = {38521905},
issn = {1479-5876},
support = {82300630//National Natural Science Foundation of China/ ; 2022GGB011//Project of Young and Middle-aged Backbone Talents Cultivation/ ; 2021J011329//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//Health Science Foundation of Fujian Youth Program/ ; },
mesh = {Humans ; *Crohn Disease/genetics ; Databases, Factual ; Lactic Acid ; Sequence Analysis, RNA ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.

METHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.

RESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.

CONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.},
}

Humans
*Crohn Disease/genetics
Databases, Factual
Lactic Acid
Sequence Analysis, RNA

@article {pmid38519354,
year = {2024},
author = {, and Jurburg, SD and Álvarez Blanco, MJ and Chatzinotas, A and Kazem, A and König-Ries, B and Babin, D and Smalla, K and Cerecetto, V and Fernandez-Gnecco, G and Covacevich, F and Viruel, E and Bernaschina, Y and Leoni, C and Garaycochea, S and Terra, JA and Fresia, P and Figuerola, ELM and Wall, LG and Covelli, JM and Agnello, AC and Nieto, EE and Festa, S and Dominici, LE and Allegrini, M and Zabaloy, MC and Morales, ME and Erijman, L and Coniglio, A and Cassán, FD and Nievas, S and Roldán, DM and Menes, R and Jauri, PV and Marrero, CS and Massa, AM and Revetria, MAM and Fernández-Scavino, A and Pereira-Mora, L and Martínez, S and Frene, JP},
title = {Datathons: fostering equitability in data reuse in ecology.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.02.010},
pmid = {38519354},
issn = {1878-4380},
abstract = {Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis.},
}

@article {pmid38518769,
year = {2024},
author = {Pristner, M and Wasinger, D and Seki, D and Klebermaß-Schrehof, K and Berger, A and Berry, D and Wisgrill, L and Warth, B},
title = {Neuroactive metabolites and bile acids are altered in extremely premature infants with brain injury.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {101480},
doi = {10.1016/j.xcrm.2024.101480},
pmid = {38518769},
issn = {2666-3791},
abstract = {The gut microbiome is associated with pathological neurophysiological evolvement in extremely premature infants suffering from brain injury. The exact underlying mechanism and its associated metabolic signatures in infants are not fully understood. To decipher metabolite profiles linked to neonatal brain injury, we investigate the fecal and plasma metabolome of samples obtained from a cohort of 51 extremely premature infants at several time points, using liquid chromatography (LC)-high-resolution mass spectrometry (MS)-based untargeted metabolomics and LC-MS/MS-based targeted analysis for investigating bile acids and amidated bile acid conjugates. The data are integrated with 16S rRNA gene amplicon gut microbiome profiles as well as patient cytokine, growth factor, and T cell profiles. We find an early onset of differentiation in neuroactive metabolites between infants with and without brain injury. We detect several bacterially derived bile acid amino acid conjugates in plasma and feces. These results provide insights into the early-life metabolome of extremely premature infants.},
}

@article {pmid38516656,
year = {2024},
author = {Brait, N and Hackl, T and Morel, C and Exbrayat, A and Gutierrez, S and Lequime, S},
title = {A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {vead088},
pmid = {38516656},
issn = {2057-1577},
abstract = {Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.},
}

@article {pmid38514851,
year = {2024},
author = {Silva, DEO and Costa, RM and Campos, JR and Rocha, SMB and de Araujo Pereira, AP and Melo, VMM and Oliveira, FAS and de Alcantara Neto, F and Mendes, LW and Araujo, ASF},
title = {Short-term restoration practices change the bacterial community in degraded soil from the Brazilian semiarid.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6845},
pmid = {38514851},
issn = {2045-2322},
abstract = {Land degradation by deforestation adversely impacts soil properties, and long-term restoration practices have been reported to potentially reverse these effects, particularly on soil microorganisms. However, there is limited knowledge regarding the short-term effects of restoration on the soil bacterial community in semiarid areas. This study evaluates the bacterial community in soils experiencing degradation (due to slash-and-burn deforestation) and restoration (utilizing stone cordons and revegetation), in comparison to a native soil in the Brazilian semiarid region. Three areas were selected: (a) under degradation; (b) undergoing short-term restoration; and (c) a native area, and the bacterial community was assessed using 16S rRNA sequencing on soil samples collected during both dry and rainy seasons. The dry and rainy seasons exhibited distinct bacterial patterns, and native sites differed from degraded and restoration sites. Chloroflexi and Proteobacteria phyla exhibited higher prevalence in degraded and restoration sites, respectively, while Acidobacteria and Actinobacteria were more abundant in sites undergoing restoration compared to degraded sites. Microbial connections varied across sites and seasons, with an increase in nodes observed in the native site during the dry season, more edges and positive connections in the restoration site, and a higher occurrence of negative connections in the degradation site during the rainy season. Niche occupancy analysis revealed that degradation favored specialists over generalists, whereas restoration exhibited a higher prevalence of generalists compared to native sites. Specifically, degraded sites showed a higher abundance of specialists in contrast to restoration sites. This study reveals that land degradation impacts the soil bacterial community, leading to differences between native and degraded sites. Restoring the soil over a short period alters the status of the bacterial community in degraded soil, fostering an increase in generalist microbes that contribute to enhanced soil stability.},
}

@article {pmid38512483,
year = {2024},
author = {Zhan, Y and Wang, E and Zhou, Y and He, G and Lv, P and Wang, L and Zhou, T and Miao, X and Chen, C and Li, Q},
title = {Facilitating Effects of Reductive Soil Disinfestation on Soil Health and Physiological Properties of Panax ginseng.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {54},
pmid = {38512483},
issn = {1432-184X},
abstract = {Chemical soil fumigation (CSF) and reductive soil disinfestation (RSD) have been proven to be effective agricultural strategies to improve soil quality, restructure microbial communities, and promote plant growth in soil degradation remediation. However, it is still unclear how RSD and CSF ensure soil and plant health by altering fungal communities. Field experiments were conducted to investigate the effects of CSF with chloropicrin, and RSD with animal feces on soil properties, fungal communities and functional composition, and plant physiological characteristics were evaluated. Results showed that RSD and CSF treatment improved soil properties, restructured fungal community composition and structure, enhanced fungal interactions and functions, and facilitated plant growth. There was a significant increase in OM, AN, and AP contents in the soil with both CSF and RSD treatments compared to CK. Meanwhile, compared with CK and CSF, RSD treatment significantly increased biocontrol Chaetomium relative abundance while reducing pathogenic Neonectria relative abundance, indicating that RSD has strong inhibition potential. Furthermore, the microbial network of RSD treatment was more complex and interconnected, and the functions of plant pathogens, and animal pathogen were decreased. Importantly, RSD treatment significantly increased plant SOD, CAT, POD activity, SP, Ca, Zn content, and decreased MDA, ABA, Mg, K, and Fe content. In summary, RSD treatment is more effective than CSF treatment, by stimulating the proliferation of probiotic communities to further enhance soil health and plant disease resistance.},
}

@article {pmid38509266,
year = {2024},
author = {Djotan, AKG and Matsushita, N and Fukuda, K},
title = {Year-round dynamics of arbuscular mycorrhizal fungi communities in the roots and surrounding soils of Cryptomeria japonica.},
journal = {Mycorrhiza},
volume = {},
number = {},
pages = {},
pmid = {38509266},
issn = {1432-1890},
support = {JP22H02382//Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) live simultaneously inside and outside of host plant roots for a functional mycorrhizal symbiosis. Still, the year-round dynamics and relationships between soil properties and AMF communities of trees in forest ecosystems remain unclear. We collected paired root and soil samples of the same Cryptomeria japonica trees at two forest sites (five trees at each site) every 2 months over a year. Total DNA was extracted from roots and soil separately and soil physicochemical properties were measured. With Illumina's next-generation amplicon sequencing targeting the small subunit of fungal ribosomal DNA, we clarified seasonal dynamics of soil properties and AMF communities. Soil pH and total phosphorus showed significant seasonality while total carbon, nitrogen, and C/N did not. Only pH was a good predictor of the composition and dynamics of the AMF community. The total AMF community (roots + soil) showed significant seasonality because of variation from May to September. Root and soil AMF communities were steady year-round, however, with similar species richness but contained significantly different AMF assemblages in any sampling month. Despite the weak seasonality in the communities, the top two dominant OTUs showed significant but different shifts between roots and soils across seasons with strong antagonistic relationships. In conclusion, few dominant AMF taxa are dynamically shifting between the roots and soils of C. japonica to respond to seasonal and phenological variations in their microhabitats. AMF inhabiting forest ecosystems may have high environmental plasticity to sustain a functional symbiosis regardless of seasonal variations that occur in the soil.},
}

@article {pmid38508742,
year = {2024},
author = {Nishimura, Y and Yamada, K and Okazaki, Y and Ogata, H},
title = {DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics.},
journal = {Microbes and environments},
volume = {39},
number = {1},
pages = {},
doi = {10.1264/jsme2.ME23061},
pmid = {38508742},
issn = {1347-4405},
mesh = {*Software ; *User-Computer Interface ; Sequence Alignment ; Genomics ; Genome ; },
abstract = {With the explosion of available genomic information, comparative genomics has become a central approach to understanding microbial ecology and evolution. We developed DiGAlign (https://www.genome.jp/digalign/), a web server that provides versatile functionality for comparative genomics with an intuitive interface. It allows the user to perform the highly customizable visualization of a synteny map by simply uploading nucleotide sequences of interest, ranging from a specific region to the whole genome landscape of microorganisms and viruses. DiGAlign will serve a wide range of biological researchers, particularly experimental biologists, with multifaceted features that allow the rapid characterization of genomic sequences of interest and the generation of a publication-ready figure.},
}

*Software
*User-Computer Interface
Sequence Alignment
Genomics
Genome

@article {pmid38508273,
year = {2024},
author = {O'Donnell, C and Thorn, C and Roskam, E and Friel, R and Kirwan, SF and Waters, SM and O'Flaherty, V},
title = {Novel oxidising feed additives reduce in vitro methane emissions using the rumen simulation technique.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {171808},
doi = {10.1016/j.scitotenv.2024.171808},
pmid = {38508273},
issn = {1879-1026},
abstract = {Enteric methane (CH4) produced by ruminant livestock is a potent greenhouse gas and represents significant energy loss for the animal. The novel application of oxidising compounds as antimethanogenic agents with future potential to be included in ruminant feeds was assessed across two separate experiments in this study. Low concentrations of oxidising agents, namely urea hydrogen peroxide (UHP) with and without potassium iodide (KI), and magnesium peroxide (MgO2), were investigated for their effects on CH4 production, total gas production (TGP), volatile fatty acid (VFA) profiles, and nutrient disappearance in vitro using the rumen simulation technique. In both experiments, the in vitro diet consisted of 50:50 grass silage:concentrate on a dry matter basis. Treatment concentrations were based on the amount of oxygen delivered and expressed in terms of fold concentration. In Experiment 1, four treatments were tested (Control, 1× UHP + KI, 1× UHP, and 0.5× UHP + KI), and six treatments were assessed in Experiment 2 (Control, 0.5× UHP + KI, 0.5× UHP, 0.25× UHP + KI, 0.25× UHP, and 0.12× MgO2). All treatments in this study had a reducing effect on CH4 parameters. A dose-dependent reduction of TGP and CH4 parameters was observed, where treatments delivering higher levels of oxygen resulted in greater CH4 suppression. 1× UHP + KI reduced TGP by 28 % (p = 0.611), CH4% by 64 % (p = 0.075) and CH4 mmol/g digestible organic matter by 71 % (p = 0.037). 0.12× MgO2 reduced CH4 volume by 25 % (p > 0.05) without affecting any other parameters. Acetate-to-propionate ratios were reduced by treatments in both experiments (p < 0.01). Molar proportions of acetate and butyrate were reduced, while propionate and valerate were increased in UHP treatments. High concentrations of UHP affected the degradation of neutral detergent fibre in the forage substrate. Future in vitro work should investigate alternative slow-release oxygen sources aimed at prolonging CH4 suppression.},
}

@article {pmid38508106,
year = {2024},
author = {Luo, Y and Pang, J and Pan, S and Wang, J and Jiang, X and Xu, Q and Zhang, H and Ruan, C and Ren, J and Zhang, C and Shi, J},
title = {Penicillium oxalicum SL2-enhanced nanoscale zero-valent iron effectively reduces Cr(VI) and shifts soil microbiota.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {134058},
doi = {10.1016/j.jhazmat.2024.134058},
pmid = {38508106},
issn = {1873-3336},
abstract = {Most current researches focus solely on reducing soil chromium availability. It is difficult to reduce soil Cr(VI) concentration below 5.0 mg kg[-1] using single remediation technology. This study introduced a sustainable soil Cr(VI) reduction and stabilization system, Penicillium oxalicum SL2-nanoscale zero-valent iron (nZVI), and investigated its effect on Cr(VI) reduction efficiency and microbial ecology. Results showed that P. oxalicum SL2-nZVI effectively reduced soil total Cr(VI) concentration from 187.1 to 3.4 mg kg[-1] within 180 d, and remained relatively stable at 360 d. The growth curve of P. oxalicum SL2 and microbial community results indicated that γ-ray irradiation shortened the adaptation time of P. oxalicum SL2 and facilitated its colonization in soil. P. oxalicum SL2 colonization activated nZVI and its derivatives, and increased soil iron bioavailability. After restoration, the negative effect of Cr(VI) on soil microorganisms was markedly alleviated. Cr(VI), Fe(II), bioavailable Cr/Fe, Eh, EC and urease (SUE) were the key environmental factors of soil microbiota. Notably, Penicillium significantly stimulated the growth of urease-positive bacteria, Arthrobacter, Pseudarthrobacter, and Microvirga, synergistically reducing soil chromium availability. The combination of P. oxalicum SL2 and nZVI is expected to form a green, economical and long-lasting Cr(VI) reduction stabilization strategy.},
}

@article {pmid38507071,
year = {2024},
author = {Martin-Pozas, T and Nováková, A and Jurado, V and Cuezva, S and Fernandez-Cortes, A and Saiz-Jimenez, C and Sanchez-Moral, S},
title = {A Second Fungal Outbreak in Castañar Cave, Spain, Discloses the Fragility of Subsurface Ecosystems.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {53},
pmid = {38507071},
issn = {1432-184X},
support = {PID2019-110603RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-114978GB-I00//Ministerio de Ciencia e Innovación/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovación/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-114978GB-I00//Ministerio de Ciencia e Innovación/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovación/ ; },
abstract = {Castañar is a cave with strict visitor control measures since it was open to public visits in 2003. However, in recent years, the cave suffered two fungal outbreaks, the first in 2008 and controlled by cleaning the contaminated sediments and subsequent closure of the cave until 2014. The cave was reopened but limited to a maximum of 450 visitors/year. Despite these restrictions on visit, the cave experienced a second outbreak in 2021, originating from the installation of a steel grating walkway, aiming at protecting the ground sediments from the visitors' footsteps. Here, we conducted an analysis using Next-Generation Sequencing and culture-dependent techniques to investigate the fungal communities related to the second outbreak and compare with those present before the cave suffered the outbreak. The results show that the most abundant fungi involved in the 2021 outbreak were already detected in 2020, and even in 2008 and 2009, although the main species that originating both outbreaks were different, likely due to the different carbon sources introduced into the cave.},
}

@article {pmid38506907,
year = {2024},
author = {Sun, P and Wu, Y and Guo, M and Zhu, M and Zhang, L and Zhang, J and Li, Z},
title = {First Report of Powdery Mildew caused by Erysiphe astragali on Sphaerophysa salsula.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-02-24-0334-PDN},
pmid = {38506907},
issn = {0191-2917},
abstract = {Sphaerophysa salsula (Pall.) DC., also known as Yang Liao Pao, belongs to the Leguminosae family and is the only existing species in the Sphaerophysa genus. S. salsula is tolerance to cold, high salt, and alkaline soil, it is widely cultivated in China as a forage crop, and used as a Chinese folk medicine to treat hypertension (Ma et al., 2002). In 2023, signs and symptoms similar to powdery mildew were found on S. salsula planted in Tumd left (40.515°N, 110.424°E), Baotou City, Inner Mongolia Autonomous Region, China. The white powdery substance covered 90% of the leaf area, and the infected plants showed weak growth and senescence. More than 80% of plants (n=200) had these powdery mildew-like symptoms. Hyphal appressoria are solitary, conidiophores have few branches and septa. Conidia are cylindrical to clavate, 25-32 μm long and 8-15 μm wide (n=30), conidia form single subapical germ tubes, straight to curved-sinuous, with swollen apex or distinctly lobed conidial appressorium. Based on these morphological characteristics, the fungus was tentatively identified as an Erysiphe sp. (Schmidt and Braun 2020). Fungal structures were isolated from diseased leaves, and genomic DNA of the pathogen was extracted using the method described by Zhu et al. (2022). The internal transcribed spacer (ITS) region was amplified by PCR using the primers PMITS1/PMITS2 (Cunnington et al. 2003) and the amplicon sequenced by Invitrogen (Shanghai, China). The powdery mildew strain, named as KMD (GenBank accession no.: PP267067), showed an identity of 100% (645/645bp) with Erysiphe astragali, a powdery mildew reported on Astragalus glycyphyllos in Golestan, Iran (GenBank: OP806834) and identity of 99.6% (643/645bp) with Erysiphe astragali (GenBank: MW142495), a powdery mildew reported on A. scaberrimus in Inner Mongolia, China (Sun et al. 2023). Pathogenicity tests were conducted by brushing the conidia from infected S. salsula leaves onto leaves of four healthy plants, while four control plants were brushed in the same manner. All the treated plants were placed in separate growth chambers maintained at 19°C and 65% humidity, with a 16 h light/8 h dark photoperiod. Nine days after inoculation, the treated plants showed powdery mildew symptoms, while the control plants remained asymptomatic. The same results were obtained for two repeated pathogenicity experiments. The powdery mildew fungus was reisolated and identified as E. astragali based on morphological and molecular analysis, thereby fulfilling Koch's postulates. No report on the occurrence of powdery mildew on S. salsula plants has been found previously. The occurrence of this destructive powdery mildew may adversely affect the cultivation of S. salsula. Identifying the pathogen of powdery mildew will support future efforts to control and manage powdery mildew on S. salsula.},
}

@article {pmid38502221,
year = {2024},
author = {Saati-Santamaría, Z and Flores-Félix, JD and Igual, JM and Velázquez, E and García-Fraile, P and Martínez-Molina, E},
title = {Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {38502221},
issn = {1432-1432},
support = {SA293P18//Junta de Castilla y León/ ; },
abstract = {The bacterial strain SECRCQ15[T] was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15[T], we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15[T] genome. We also found that singletons of F. quinoae SECRCQ15[T] are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.},
}

@article {pmid38500703,
year = {2024},
author = {Dreyling, L and Penone, C and Schenk, NV and Schmitt, I and Dal Grande, F},
title = {Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae012},
pmid = {38500703},
issn = {2730-6151},
abstract = {Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.},
}

@article {pmid38499207,
year = {2024},
author = {Kodama, T and Takehara, T},
title = {Molecular genealogy of metabolic-associated hepatocellular carcinoma.},
journal = {Seminars in liver disease},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2289-2298},
pmid = {38499207},
issn = {1098-8971},
support = {JP23ama221410,JP23ck0106793,JP23fk0210131//Japan Agency for Medical Research and Development/ ; },
abstract = {This review examines the latest epidemiological and molecular pathogenic findings of metabolic-associated hepatocellular carcinoma (HCC). Its increasing prevalence is a significant concern and reflects the growing burden of obesity and metabolic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD), and type 2 diabetes. Metabolic-associated HCC has unique molecular abnormality and distinctive gene expression patterns implicating aberrations in bile acid, fatty acid metabolism, oxidative stress, and proinflammatory pathways. Furthermore, a notable frequency of single nucleotide polymorphisms (SNPs) in genes such as patatin-like phospholipase domain-containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), glucokinase regulator (GCKR), and membrane bound O-acyltransferase domain-containing 7 (MBOAT7) has been observed. The tumour immune microenvironment of metabolic-associated HCC is characterized by unique phenotypes of macrophages, neutrophils, and T lymphocytes. Additionally, the pathogenesis of metabolic-associated HCC is influenced by abnormal lipid metabolism, insulin resistance, and dysbiosis. In conclusion, deciphering the intricate interactions among metabolic processes, genetic predispositions, inflammatory responses, immune regulation, and microbial ecology is imperative for the development of novel therapeutic and preventative measures against metabolic-associated HCC.},
}

@article {pmid38498218,
year = {2024},
author = {Greipel, E and Nagy, K and Csákvári, E and Dér, L and Galajda, P and Kutasi, J},
title = {Chemotactic Interactions of Scenedesmus sp. and Azospirillum brasilense Investigated by Microfluidic Methods.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {52},
pmid = {38498218},
issn = {1432-184X},
mesh = {*Azospirillum brasilense ; *Scenedesmus/metabolism ; Microfluidics ; Oxaloacetic Acid/metabolism ; Plant Growth Regulators/metabolism ; Plants/metabolism ; },
abstract = {The use of algae for industrial, biotechnological, and agricultural purposes is spreading globally. Scenedesmus species can play an essential role in the food industry and agriculture due to their favorable nutrient content and plant-stimulating properties. Previous research and the development of Scenedesmus-based foliar fertilizers raised several questions about the effectiveness of large-scale algal cultivation and the potential effects of algae on associative rhizobacteria. In the microbiological practice applied in agriculture, bacteria from the genus Azospirillum are one of the most studied plant growth-promoting, associative, nitrogen-fixing bacteria. Co-cultivation with Azospirillum species may be a new way of optimizing Scenedesmus culturing, but the functioning of the co-culture system still needs to be fully understood. It is known that Azospirillum brasilense can produce indole-3-acetic acid, which could stimulate algae growth as a plant hormone. However, the effect of microalgae on Azospirillum bacteria is unclear. In this study, we investigated the behavior of Azospirillum brasilense bacteria in the vicinity of Scenedesmus sp. or its supernatant using a microfluidic device consisting of physically separated but chemically coupled microchambers. Following the spatial distribution of bacteria within the device, we detected a positive chemotactic response toward the microalgae culture. To identify the metabolites responsible for this behavior, we tested the chemoeffector potential of citric acid and oxaloacetic acid, which, according to our HPLC analysis, were present in the algae supernatant in 0.074 mg/ml and 0.116 mg/ml concentrations, respectively. We found that oxaloacetic acid acts as a chemoattractant for Azospirillum brasilense.},
}

*Azospirillum brasilense
*Scenedesmus/metabolism
Microfluidics
Oxaloacetic Acid/metabolism
Plant Growth Regulators/metabolism
Plants/metabolism

@article {pmid38497641,
year = {2024},
author = {Dean, CJ and Peña-Mosca, F and Ray, T and Wehri, TJ and Sharpe, K and Antunes, AM and Doster, E and Fernandes, L and Calles, VF and Bauman, C and Godden, S and Heins, B and Pinedo, P and Machado, VS and Caixeta, LS and Noyes, NR},
title = {Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0223423},
doi = {10.1128/aem.02234-23},
pmid = {38497641},
issn = {1098-5336},
abstract = {UNLABELLED: The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26).

IMPORTANCE: Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.},
}

@article {pmid38494494,
year = {2024},
author = {Liu, X and Salles, JF},
title = {Lose-lose consequences of bacterial community-driven invasions in soil.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {57},
pmid = {38494494},
issn = {2049-2618},
mesh = {*Soil ; Soil Microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; },
abstract = {BACKGROUND: Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities.

RESULTS: Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~ 5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community.

CONCLUSIONS: Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.},
}

*Soil
Soil Microbiology
Bacteria/genetics/metabolism
*Microbiota

@article {pmid38493536,
year = {2024},
author = {Mekonnen, YT and Savini, F and Indio, V and Seguino, A and Giacometti, F and Serraino, A and Candela, M and De Cesare, A},
title = {Systematic review on microbiome-related nutritional interventions interfering with the colonization of foodborne pathogens in broiler gut to prevent contamination of poultry meat.},
journal = {Poultry science},
volume = {103},
number = {5},
pages = {103607},
doi = {10.1016/j.psj.2024.103607},
pmid = {38493536},
issn = {1525-3171},
abstract = {This systematic review aimed to compile the available body of knowledge about microbiome-related nutritional interventions contributing to improve the chicken health and having an impact on the reduction of colonization by foodborne pathogens in the gut. Original research articles published between 2012 and 2022 were systematically searched in Scopus and PubMed. A total of 1,948 articles were retrieved and 140 fulfilled the inclusion criteria. Overall, 73 papers described 99 interventions against colonization by Escherichia coli and related organisms; 10 papers described 15 interventions against Campylobacter spp.; 36 papers described 54 interventions against Salmonella; 40 papers described 54 interventions against Clostridium perfringens. A total of 197 microbiome-related interventions were identified as effective against one or more of the listed pathogens and included probiotics (n = 80), prebiotics (n = 23), phytobiotics (n = 25), synbiotics (n = 12), organic acids (n = 12), enzymes (n = 4), essential oils (n = 14) and combination of these (n = 27). The identified interventions were mostly administered in the feed (173/197) or through oral gavage (11/197), in the drinking water (7/197), in ovo (2/197), intra amniotic (2/197), in fresh or reused litter (1/197) or both in the feed and water (1/197). The interventions enhanced the beneficial microbial communities in the broiler gut as Lactic acid bacteria, mostly Lactobacillus spp., or modulated multiple microbial populations. The mechanisms promoting the fighting against colonization by foodborne pathogens included competitive exclusion, production of short chain fatty acids, decrease of gut pH, restoration of the microbiome after dysbiosis events, promotion of a more stable microbial ecology, expression of genes improving the integrity of intestinal mucosa, enhancing of mucin production and improvement of host immune response. All the studies extracted from the literature described in vivo trials but performed on a limited number of animals under experimental settings. Moreover, they detailed the effect of the intervention on the chicken gut without details on further impact on poultry meat safety.},
}

@article {pmid38493186,
year = {2024},
author = {Wu, L and Wang, XW and Tao, Z and Wang, T and Zuo, W and Zeng, Y and Liu, YY and Dai, L},
title = {Data-driven prediction of colonization outcomes for complex microbial communities.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2406},
pmid = {38493186},
issn = {2041-1723},
support = {31971513//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Microbiota ; Feces/microbiology ; *Enterococcus faecium ; Microbial Interactions ; Enterococcus faecalis ; },
abstract = {Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.},
}

Humans
*Microbiota
Feces/microbiology
*Enterococcus faecium
Microbial Interactions
Enterococcus faecalis

@article {pmid38492828,
year = {2024},
author = {Malik, M and Das, S and Chakraborty, P and Paul, P and Roy, R and Das Gupta, A and Sarkar, S and Chatterjee, S and Maity, A and Dasgupta, M and Sarker, RK and Tribedi, P},
title = {Application of cuminaldehyde and ciprofloxacin for the effective control of biofilm assembly of Pseudomonas aeruginosa: A combinatorial study.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106624},
doi = {10.1016/j.micpath.2024.106624},
pmid = {38492828},
issn = {1096-1208},
abstract = {Pseudomonas aeruginosa is widely associated with biofilm-mediated antibiotic resistant chronic and acute infections which constitute a persistent healthcare challenges. Addressing this threat requires exploration of novel therapeutic strategies involving the combination of natural compounds and conventional antibiotics. Hence, our study has focused on two compounds; cuminaldehyde and ciprofloxacin, which were strategically combined to target the biofilm challenge of P. aeruginosa. The minimum inhibitory concentration (MIC) of cuminaldehyde and ciprofloxacin was found to be 400 μg/mL and 0.4 μg/mL, respectively. Moreover, the fractional inhibitory concentration index (FICI = 0.62) indicated an additive interaction prevailed between cuminaldehyde and ciprofloxacin. Subsequently, sub-MIC doses of cuminaldehyde (25 μg/mL) and ciprofloxacin (0.05 μg/mL) were selected for an array of antibiofilm assays which confirmed their biofilm inhibitory potential without exhibiting any antimicrobial activity. Furthermore, selected doses of the mentioned compounds could manage biofilm on catheter surface by inhibiting and disintegrating existing biofilm. Additionally, the test combination of the mentioned compounds reduced virulence factors secretion, accumulated reactive oxygen species and increased cell-membrane permeability. Thus, the combination of cuminaldehyde and ciprofloxacin demonstrates potential in combating biofilm-associated Pseudomonal threats.},
}

@article {pmid38492604,
year = {2024},
author = {Zhao, S and Zheng, Q and Wang, H and Fan, X},
title = {Nitrogen in landfills: Sources, environmental impacts and novel treatment approaches.},
journal = {The Science of the total environment},
volume = {924},
number = {},
pages = {171725},
doi = {10.1016/j.scitotenv.2024.171725},
pmid = {38492604},
issn = {1879-1026},
abstract = {Nitrogen (N) accumulation in landfills is a pressing environmental concern due to its diverse sources and significant environmental impacts. However, there is relatively limited attention and research focus on N in landfills as it is overshadowed by other more prominent pollutants. This study comprehensively examines the sources of N in landfills, including food waste contributing to 390 million tons of N annually, industrial discharges, and sewage treatment plant effluents. The environmental impacts of N in landfills are primarily manifested in N2O emissions and leachate with high N concentrations. To address these challenges, this study presents various mitigation and management strategies, including N2O reduction measures and novel NH4[+] removal techniques, such as electrochemical technologies, membrane separation processes, algae-based process, and other advanced oxidation processes. However, a more in-depth understanding of the complexities of N cycling in landfills is required, due to the lack of long-term monitoring data and the presence of intricate interactions and feedback mechanisms. To ultimately achieve optimized N management and minimized adverse environmental impacts in landfill settings, future prospects should emphasize advancements in monitoring and modeling technologies, enhanced understanding of microbial ecology, implementation of circular economy principles, application of innovative treatment technologies, and comprehensive landfill design and planning.},
}

@article {pmid38491554,
year = {2024},
author = {Xu, G and Zhao, S and Rogers, MJ and Chen, C and He, J},
title = {Global prevalence of organohalide-respiring bacteria dechlorinating polychlorinated biphenyls in sewage sludge.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {54},
pmid = {38491554},
issn = {2049-2618},
support = {R-302-000-198720//Ng Teng Fong Charitable Foundation (NTFCF)/ ; MOE-00003301//The Ministry of Education, Singapore/ ; },
abstract = {BACKGROUND: Massive amounts of sewage sludge are generated during biological sewage treatment and are commonly subjected to anaerobic digestion, land application, and landfill disposal. Concurrently, persistent organic pollutants (POPs) are frequently found in sludge treatment and disposal systems, posing significant risks to both human health and wildlife. Metabolically versatile microorganisms originating from sewage sludge are inevitably introduced to sludge treatment and disposal systems, potentially affecting the fate of POPs. However, there is currently a dearth of comprehensive assessments regarding the capability of sewage sludge microbiota from geographically disparate regions to attenuate POPs and the underpinning microbiomes.

RESULTS: Here we report the global prevalence of organohalide-respiring bacteria (OHRB) known for their capacity to attenuate POPs in sewage sludge, with an occurrence frequency of ~50% in the investigated samples (605 of 1186). Subsequent laboratory tests revealed microbial reductive dechlorination of polychlorinated biphenyls (PCBs), one of the most notorious categories of POPs, in 80 out of 84 sludge microcosms via various pathways. Most chlorines were removed from the para- and meta-positions of PCBs; nevertheless, ortho-dechlorination of PCBs also occurred widely, although to lower extents. Abundances of several well-characterized OHRB genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) and uncultivated Dehalococcoidia lineages increased during incubation and were positively correlated with PCB dechlorination, suggesting their involvement in dechlorinating PCBs. The previously identified PCB reductive dehalogenase (RDase) genes pcbA4 and pcbA5 tended to coexist in most sludge microcosms, but the low ratios of these RDase genes to OHRB abundance also indicated the existence of currently undescribed RDases in sewage sludge. Microbial community analyses revealed a positive correlation between biodiversity and PCB dechlorination activity although there was an apparent threshold of community co-occurrence network complexity beyond which dechlorination activity decreased.

CONCLUSIONS: Our findings that sludge microbiota exhibited nearly ubiquitous dechlorination of PCBs indicate widespread and nonnegligible impacts of sludge microbiota on the fate of POPs in sludge treatment and disposal systems. The existence of diverse OHRB also suggests sewage sludge as an alternative source to obtain POP-attenuating consortia and calls for further exploration of OHRB populations in sewage sludge. Video Abstract.},
}

@article {pmid38488929,
year = {2024},
author = {Dayang Najwa, AB and Elexson, N and Dalene, L and Teng, ST},
title = {Vibrio Species and Cyanobacteria: Understanding Their Association in Local Shrimp Farm Using Canonical Correspondence Analysis (CCA).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {51},
pmid = {38488929},
issn = {1432-184X},
abstract = {In aquatic environments, Vibrio and cyanobacteria establish varying relationships influenced by environmental factors. To investigate their association, this study spanned 5 months at a local shrimp farm, covering the shrimp larvae stocking cycle until harvesting. A total of 32 samples were collected from pond A (n = 6), pond B (n = 6), effluent (n = 10), and influent (n = 10). Vibrio species and cyanobacteria density were observed, and canonical correspondence analysis (CCA) assessed their correlation. CCA revealed a minor correlation (p = 0.847, 0.255, 0.288, and 0.304) between Vibrio and cyanobacteria in pond A, pond B, effluent, and influent water, respectively. Notably, Vibrio showed a stronger correlation with pH (6.14-7.64), while cyanobacteria correlated with pH, salinity (17.4-24 ppt), and temperature (30.8-31.5 °C), with salinity as the most influential factor. This suggests that factors beyond cyanobacteria influence Vibrio survival. Future research could explore species-specific relationships, regional dynamics, and multidimensional landscapes to better understand Vibrio-cyanobacteria connections. Managing water parameters may prove more efficient in controlling vibriosis in shrimp farms than targeting cyanobacterial populations.},
}

@article {pmid38488280,
year = {2024},
author = {Giacomini, JJ and Torres-Morales, J and Tang, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0401723},
doi = {10.1128/spectrum.04017-23},
pmid = {38488280},
issn = {2165-0497},
abstract = {UNLABELLED: Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility.

IMPORTANCE: Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.},
}

@article {pmid38485445,
year = {2024},
author = {Harris, TD and Reinl, KL and Azarderakhsh, M and Berger, SA and Berman, MC and Bizic, M and Bhattacharya, R and Burnet, SH and Cianci-Gaskill, JA and Domis, LNS and Elfferich, I and Ger, KA and Grossart, HF and Ibelings, BW and Ionescu, D and Kouhanestani, ZM and Mauch, J and McElarney, YR and Nava, V and North, RL and Ogashawara, I and Paule-Mercado, MCA and Soria-Píriz, S and Sun, X and Trout-Haney, JV and Weyhenmeyer, GA and Yokota, K and Zhan, Q},
title = {What makes a cyanobacterial bloom disappear? A review of the abiotic and biotic cyanobacterial bloom loss factors.},
journal = {Harmful algae},
volume = {133},
number = {},
pages = {102599},
doi = {10.1016/j.hal.2024.102599},
pmid = {38485445},
issn = {1878-1470},
abstract = {Cyanobacterial blooms present substantial challenges to managers and threaten ecological and public health. Although the majority of cyanobacterial bloom research and management focuses on factors that control bloom initiation, duration, toxicity, and geographical extent, relatively little research focuses on the role of loss processes in blooms and how these processes are regulated. Here, we define a loss process in terms of population dynamics as any process that removes cells from a population, thereby decelerating or reducing the development and extent of blooms. We review abiotic (e.g., hydraulic flushing and oxidative stress/UV light) and biotic factors (e.g., allelopathic compounds, infections, grazing, and resting cells/programmed cell death) known to govern bloom loss. We found that the dominant loss processes depend on several system specific factors including cyanobacterial genera-specific traits, in situ physicochemical conditions, and the microbial, phytoplankton, and consumer community composition. We also address loss processes in the context of bloom management and discuss perspectives and challenges in predicting how a changing climate may directly and indirectly affect loss processes on blooms. A deeper understanding of bloom loss processes and their underlying mechanisms may help to mitigate the negative consequences of cyanobacterial blooms and improve current management strategies.},
}

@article {pmid38485438,
year = {2024},
author = {Woodhouse, JN and Burford, MA and Neilan, BA and Jex, A and Tichkule, S and Sivonen, K and Fewer, DP and Grossart, HP and Willis, A},
title = {Long-term stability of the genome structure of the cyanobacterium, Dolichospermum in a deep German lake.},
journal = {Harmful algae},
volume = {133},
number = {},
pages = {102600},
doi = {10.1016/j.hal.2024.102600},
pmid = {38485438},
issn = {1878-1470},
abstract = {Dolichospermum is a cyanobacterial genus commonly associated with toxic blooms in lakes and brackish water bodies worldwide, and is a long-term resident of Lake Stechlin, northeastern Germany. In recent decades, shifts in the phosphorus loading and phytoplankton species composition have seen increased biomass of Dolichospermum during summer blooms from 1998, peaking around 2005, and declining after 2020. Cyanobacteria are known to rapidly adapt to new environments, facilitated by genome adaptation. To investigate the changes in genomic features that may have occurred in Lake Stechlin Dolichospermum during this time of increased phosphorus loading and higher biomass, whole genome sequence analysis was performed on samples of ten akinetes isolated from ten, 1 cm segments of a sediment core, representing a ∼45-year period from 1970 to 2017. Comparison of these genomes with genomes of extant isolates revealed a clade of Dolichospermum that clustered with the ADA-6 genus complex, with remarkable genome stability, without gene gain or loss events in response to recent environmental changes. The genome characteristics indicate that this species is suited to a deep-chlorophyll maximum, including additional light-harvesting and phosphorus scavenging genes. Population SNP analysis revealed two sub-populations that shifted in dominance as the lake transitioned between oligotrophic and eutrophic conditions. Overall, the results show little change within the population, despite diversity between extant populations from different geographic locations and the in-lake changes in phosphorus concentrations.},
}

@article {pmid38484962,
year = {2024},
author = {Fang, X and Colina Blanco, AE and Christl, I and Le Bars, M and Straub, D and Kleindienst, S and Planer-Friedrich, B and Zhao, FJ and Kappler, A and Kretzschmar, R},
title = {Simultaneously decreasing arsenic and cadmium in rice by soil sulfate and limestone amendment under intermittent flooding.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {123786},
doi = {10.1016/j.envpol.2024.123786},
pmid = {38484962},
issn = {1873-6424},
abstract = {Water management in paddy soils can effectively reduce the soil-to-rice grain transfer of either As or Cd, but not of both elements simultaneously due to the higher mobility of As under reducing and Cd under oxidizing soil conditions. Limestone amendment, the common form of liming, is well known for decreasing Cd accumulation in rice grown on acidic soils. Sulfate amendment was suggested to effectively decrease As accumulation in rice, especially under intermittent soil flooding. To study the unknown effects of combined sulfate and limestone amendment under intermittent flooding for simultaneously decreasing As and Cd in rice, we performed a pot experiment using an acidic sandy loam paddy soil. We also included a clay loam paddy soil to study the role of soil texture in low-As rice production under intermittent flooding. We found that liming not only decreased rice Cd concentrations but also greatly decreased dimethylarsenate (DMA) accumulation in rice. We hypothesize that this is due to suppressed sulfate reduction, As methylation, and As thiolation by liming in the sulfate-amended soil and a higher share of deprotonated DMA at higher pH which is taken up less readily than protonated DMA. Decreased gene abundance of potential soil sulfate-reducers by liming further supported our hypothesis. Combined sulfate and limestone amendment to the acidic sandy loam soil produced rice with 43% lower inorganic As, 72% lower DMA, and 68% lower Cd compared to the control soil without amendment. A tradeoff between soil aeration and water availability was observed for the clay loam soil, suggesting difficulties to decrease As in rice while avoiding plant water stress under intermittent flooding in fine-textured soils. Our results suggest that combining sulfate amendment, liming, and intermittent flooding can help to secure rice safety when the presence of both As and Cd in coarse-textured soils is of concern.},
}

@article {pmid38483479,
year = {2024},
author = {Mermans, F and De Baets, H and García-Timermans, C and Teughels, W and Boon, N},
title = {Unlocking the mechanism of action: a cost-effective flow cytometry approach for accelerating antimicrobial drug development.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0393123},
doi = {10.1128/spectrum.03931-23},
pmid = {38483479},
issn = {2165-0497},
abstract = {Antimicrobial resistance is one of the greatest challenges to global health. While the development of new antimicrobials can combat resistance, low profitability reduces the number of new compounds brought to market. Elucidating the mechanism of action is crucial for developing new antimicrobials. This can become expensive as there are no universally applicable pipelines. Phenotypic heterogeneity of microbial populations resulting from antimicrobial treatment can be captured through flow cytometric fingerprinting. Since antimicrobials are classified into limited groups, the mechanism of action of known compounds can be used for predictive modeling. We demonstrate a cost-effective flow cytometry approach for determining the mechanism of action of new compounds. Cultures of Actinomyces viscosus and Fusobacterium nucleatum were treated with different antimicrobials and measured by flow cytometry. A Gaussian mixture mask was applied over the data to construct phenotypic fingerprints. Fingerprints were used to assess statistical differences between mechanism of action groups and to train random forest classifiers. Classifiers were then used to predict the mechanism of action of cephalothin. Statistical differences were found among the different mechanisms of action groups. Pairwise comparison showed statistical differences for 35 out of 45 pairs for A. viscosus and for 32 out of 45 pairs for F. nucleatum after 3.5 h of treatment. The best-performing random forest classifier yielded a Matthews correlation coefficient of 0.92 and the mechanism of action of cephalothin could be successfully predicted. These findings suggest that flow cytometry can be a cheap and fast alternative for determining the mechanism of action of new antimicrobials.IMPORTANCEIn the context of the emerging threat of antimicrobial resistance, the development of novel antimicrobials is a commonly employed strategy to combat resistance. Elucidating the mechanism of action of novel compounds is crucial in this development but can become expensive, as no universally applicable pipelines currently exist. We present a novel flow cytometry-based approach capable of determining the mechanism of action swiftly and cost-effectively. The workflow aims to accelerate drug discovery and could help facilitate a more targeted approach for antimicrobial treatment of patients.},
}

@article {pmid38481338,
year = {2024},
author = {Sun, J and Zhao, J and Liu, M and Li, J and Cheng, J and Li, W and Yuan, M and Xiao, S and Xue, C},
title = {SreC-dependent adaption to host iron environments regulates the transition of trophic stages and developmental processes of Curvularia lunata.},
journal = {Molecular plant pathology},
volume = {25},
number = {3},
pages = {e13444},
doi = {10.1111/mpp.13444},
pmid = {38481338},
issn = {1364-3703},
support = {31271992//National Natural Science Foundation of China/ ; 2022JH2/101300168//Liaoning Provincial Applied Basic Program/ ; },
abstract = {Plant pathogens are challenged by host-derived iron starvation or excess during infection, but the mechanism of plant pathogens rapidly adapting to the dynamic host iron environments to assimilate iron for invasion and colonization remains largely unexplored. Here, we found that the GATA transcription factor SreC in Curvularia lunata is required for virulence and adaption to the host iron excess environment. SreC directly binds to the ATGWGATAW element in an iron-dependent manner to regulate the switch between different iron assimilation pathways, conferring adaption to host iron environments in different trophic stages of C. lunata. SreC also regulates the transition of trophic stages and developmental processes in C. lunata. SreC-dependent adaption to host iron environments is essential to the infectious growth and survival of C. lunata. We also demonstrate that CgSreA (a SreC orthologue) plays a similar role in Colletotrichum graminicola. We conclude that Sre mediates adaption to the host iron environment during infection, and the function is conserved in hemibiotrophic fungi.},
}

@article {pmid38477597,
year = {2024},
author = {Miliotis, G and Sengupta, P and Hameed, A and Chuvochina, M and McDonagh, F and Simpson, AC and Parker, CW and Singh, NK and Rekha, PD and Morris, D and Raman, K and Kyrpides, NC and Hugenholtz, P and Venkateswaran, K},
title = {Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.},
journal = {mBio},
volume = {},
number = {},
pages = {e0018124},
doi = {10.1128/mbio.00181-24},
pmid = {38477597},
issn = {2150-7511},
abstract = {UNLABELLED: A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HS[T], exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HS[T] is most closely related to Virgibacillus halophilus 5B73C[T], sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HS[T] is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HS[T] = DSM 115946[T] = NRRL B-65666[T]), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73C[T] = DSM 21623[T] = JCM 21758[T] = KCTC 13935[T]). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6[T] = DSM 22952[T] = CCM 7714[T]). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins.

IMPORTANCE: The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.},
}

@article {pmid38476936,
year = {2024},
author = {Dittoe, DK and Feye, KM and Ovall, C and Thompson, HA and Ricke, SC},
title = {Exploiting the microbiota of organic and inorganic acid-treated raw poultry products to improve shelf-life.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1348159},
pmid = {38476936},
issn = {1664-302X},
abstract = {INTRODUCTION: Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The current research determines the microbiota and spoilage indicator (total aerobes and lactic acid bacteria; LAB) response to inorganic and organic antimicrobial intervention use on the shelf-life of fresh, never-frozen, skin-on, bone-in chicken wings.

METHODS: Wings (n=200) were sourced from local processor and either not treated (NT) or treated with 15-s dips of tap water (TW), organic (peracetic acid; PAA), inorganic acids (sodium bisulfate; SBS), and their combination (SBS + PAA). Wings were stored (4°C) and rinsed in neutralizing Buffered Peptone Water (BPW) for 1 min on d 0, 7, 14, and 21 post-treatment. Spoilage indicators, aerobic mesophiles and LAB, were quantified from rinsates. Genomic DNA of d 14 and 21 rinsates were extracted, and V4 of 16S rRNA gene was sequenced. Sequences were analyzed using QIIME2.2019.7. APC and LAB counts were reported as Log10 CFU/g of chicken and analyzed in R Studio as a General Linear Model using ANOVA. Pairwise differences were determined using Tukey's HSD (P£0.05).

RESULTS: Spoilage was indicated for all products by day 21 according to APC counts (>7 Log10 CFU/g); however, wings treated with SBS and SBS + PAA demonstrated a 7-day extended shelf-life compared to those treated with NT, TW, or PAA. The interaction of treatment and time impacted the microbial diversity and composition (p < 0.05), with those treated with SBS having a lower richness and evenness compared to those treated with the controls (NT and TW; p < 0.05, Q < 0.05). On d 14, those treated with SBS and SBS + PAA had lower relative abundance of typical spoilage population while having a greater relative abundance of Bacillus spp. (~70 and 50% of population; ANCOM p < 0.05). By d 21, the Bacillus spp. populations decreased below 10% of the population among those treated with SBS and SBS + PAA.

DISCUSSION: Therefore, there are differential effects on the microbial community depending on the chemical intervention used with organic and inorganic acids, impacting the microbial ecology differently.},
}

@article {pmid38476935,
year = {2024},
author = {Indong, RA and Park, JM and Hong, JK and Lyou, ES and Han, T and Hong, JK and Lee, TK and Lee, JI},
title = {A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1347797},
pmid = {38476935},
issn = {1664-302X},
abstract = {The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.},
}

@article {pmid38475926,
year = {2024},
author = {Suarez, C and Rosenqvist, T and Dimitrova, I and Sedlacek, CJ and Modin, O and Paul, CJ and Hermansson, M and Persson, F},
title = {Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {51},
pmid = {38475926},
issn = {2049-2618},
support = {2018-01423//Svenska Forskningsrådet Formas/ ; 2019-00432//Svenska Forskningsrådet Formas/ ; 2019-00432//Svenska Forskningsrådet Formas/ ; 2018-01423//Svenska Forskningsrådet Formas/ ; 2020-01905//Svenska Forskningsrådet Formas/ ; ZK74//Austrian Science Fund/ ; },
mesh = {*Ammonia ; *Anaerobic Ammonia Oxidation ; Phylogeny ; Sewage/microbiology ; Bacteria ; Bioreactors/microbiology ; Nitrogen ; Biofilms ; Oxidation-Reduction ; },
abstract = {BACKGROUND: Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms.

RESULTS: We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers.

CONCLUSIONS: We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.},
}

*Ammonia
*Anaerobic Ammonia Oxidation
Phylogeny
Sewage/microbiology
Bacteria
Bioreactors/microbiology
Nitrogen
Biofilms
Oxidation-Reduction

@article {pmid38471203,
year = {2024},
author = {Malinowski, N and Morgan, MJ and Wylie, J and Walsh, T and Domingos, S and Metcalfe, S and Kaksonen, AH and Barnhart, EP and Mueller, R and Peyton, BM and Puzon, GJ},
title = {Prokaryotic microbial ecology as an ecosurveillance tool for eukaryotic pathogen colonisation: Meiothermus and Naegleria fowleri.},
journal = {Water research},
volume = {254},
number = {},
pages = {121426},
doi = {10.1016/j.watres.2024.121426},
pmid = {38471203},
issn = {1879-2448},
abstract = {Naegleria fowleri has been detected in drinking water distribution systems (DWDS) in Australia, Pakistan and the United States and is the causative agent of the highly fatal disease primary amoebic meningoencephalitis. Previous small scale field studies have shown that Meiothermus may be a potential biomarker for N. fowleri. However, correlations between predictive biomarkers in small sample sizes often breakdown when applied to larger more representative datasets. This study represents one of the largest and most rigorous temporal investigations of Naegleria fowleri colonisation in an operational DWDS in the world and measured the association of Meiothermus and N. fowleri over a significantly larger space and time in the DWDS. A total of 232 samples were collected from five sites over three-years (2016-2018), which contained 29 positive N. fowleri samples. Two specific operational taxonomic units assigned to M. chliarophilus and M. hypogaeus, were significantly associated with N. fowleri presence. Furthermore, inoculation experiments demonstrated that Meiothermus was required to support N. fowleri growth in field-collected biofilms. This validates Meiothermus as prospective biological tool to aid in the identification and surveillance of N. fowleri colonisable sites.},
}

@article {pmid38470030,
year = {2024},
author = {Tittes, C and Nijland, J and Schoentag, AMC and Hackl, T and Di Cianni, N and Marchfelder, A and Quax, TEF},
title = {Development of a genetic system for Haloferax gibbonsii LR2-5, model host for haloarchaeal viruses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0012924},
doi = {10.1128/aem.00129-24},
pmid = {38470030},
issn = {1098-5336},
abstract = {UNLABELLED: Archaeal viruses are among the most enigmatic members of the virosphere, and their diverse morphologies raise many questions about their infection mechanisms. The study of molecular mechanisms underlying virus-host interactions hinges upon robust model organisms with a system for gene expression and deletion. Currently, there are only a limited number of archaea that have associated viruses and have a well-developed genetic system. Here, we report the development of a genetic system for the euryarchaeon Haloferax gibbonsii LR2-5. This strain can be infected by multiple viruses and is a model for the study of virus-host interactions. We created a Hfx. gibbonsii LR2-5 ∆pyrE strain, resulting in uracil auxotrophy, which could be used as a selection marker. An expression plasmid carrying a pyrE gene from the well-established Haloferax volcanii system was tested for functionality. Expression of a GFP-MinD fusion under a tryptophan inducible promoter was fully functional and showed similar cellular localization as in Hfx. volcanii. Thus, the plasmids of the Hfx. volcanii system can be used directly for the Hfx. gibbonsii LR2-5 genetic system, facilitating the transfer of tools between the two. Finally, we tested for the functionality of gene deletions by knocking out two genes of the archaeal motility structure, the archaellum. These deletion mutants were as expected non-motile and the phenotype of one deletion could be rescued by the expression of the deleted archaellum gene from a plasmid. Thus, we developed a functional genetic toolbox for the euryarchaeal virus host Hfx. gibbonsii LR2-5, which will propel future studies on archaeal viruses.

IMPORTANCE: Species from all domains of life are infected by viruses. In some environments, viruses outnumber their microbial hosts by a factor of 10, and viruses are the most important predators of microorganisms. While much has been discovered about the infection mechanisms of bacterial and eukaryotic viruses, archaeal viruses remain understudied. Good model systems are needed to study their virus-host interactions in detail. The salt-loving archaeon Haloferax gibbonsii LR2-5 has been shown to be infected by a variety of different viruses and, thus, is an excellent model to study archaeal viruses. By establishing a genetic system, we have significantly expanded the toolbox for this model organism, which will fuel our understanding of infection strategies of the underexplored archaeal viruses.},
}

@article {pmid38467467,
year = {2024},
author = {Powell, ME and McCoy, SJ},
title = {Divide and conquer: Spatial and temporal resource partitioning structures benthic cyanobacterial mats.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.13443},
pmid = {38467467},
issn = {1529-8817},
support = {DGE-2040435//National Science Foundation/ ; OCE-2239425//National Science Foundation/ ; },
abstract = {Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions.},
}