FLASH: fast length adjustment of short reads to improve genome assemblies

A modelling framework to characterize the impact of antibiotics on the gut microbiota diversity

Metagenomic sequencing deepened our knowledge about the role of the intestinal microbiota in human health, and several studies with various methodologies explored its dynamics during antibiotic treatments. We compared the impact of four widely used antibiotics on the gut bacterial diversity. We used plasma and fecal samples collected during and after treatment from healthy volunteers assigned to a 5-day treatment either by ceftriaxone (1 g every 24 h through IV route), ceftazidime/avibactam (2 g/500 mg every 8 h through IV route), piperacillin/tazobactam (1 g/500 mg every 8 h through IV route) or moxifloxacin (400 mg every 24 h through oral route). Antibiotic concentrations were measured in plasma and feces, and bacterial diversity was assessed by the Shannon index from 16S rRNA gene profiling. The relationship between the evolutions of antibiotic fecal exposure and bacterial diversity was modeled using non-linear mixed effects models. We compared the impact of antibiotics on gut microbiota diversity by simulation, using various reconstructed pharmacodynamic indices. Piperacillin/tazobactam was characterized by the highest impact in terms of intensity of perturbation (maximal [IQR] loss of diversity of 27.3% [1.9; 40.0]), while moxifloxacin had the longest duration of perturbation, with a time to return to 95% of baseline value after the last administration of 13.2 d [8.3; 19.1]. Overall, moxifloxacin exhibited the highest global impact, followed by piperacillin/tazobactam, ceftazidime/avibactam and ceftriaxone. Their AUC between day 0 and day 42 of the change of diversity indices from day 0 were, respectively, -13.2 Shannon unit.day [-20.4; -7.9], -10.9 Shannon unit.day [-20.4; -0.6] and -10.1 Shannon unit.day [-18.3; -4.6]. We conclude that antibiotics alter the intestinal diversity to varying degrees, both within and between antibiotics families. Such studies are needed to help antibiotic stewardship in using the antibiotics with the lowest impact on the intestinal microbiota.

Engineered ipilimumab variants that bind human and mouse CTLA-4

Testing of candidate monoclonal antibody therapeutics in preclinical models is an essential step in drug development. Identification of antibody therapeutic candidates that bind their human targets and cross-react to mouse orthologs is often challenging, especially for targets with low sequence homology. In such cases, surrogate antibodies that bind mouse orthologs must be used. The antibody 9D9, which binds mouse CTLA-4, is a commonly used surrogate for CTLA-4 checkpoint blockade studies in mouse cancer models. In this work, we reveal that 9D9 has significant biophysical dissimilarities to therapeutic CTLA-4 antibodies. The 9D9-mCTLA4 complex crystal structure was determined and shows that the surrogate antibody binds an epitope distinct from ipilimumab and tremelimumab. In addition, while ipilimumab has pH-independent binding to hCTLA-4, 9D9 loses binding to mCTLA-4 at physiologically relevant acidic pH ranges. We used phage and yeast display to engineer ipilimumab to bind mouse CTLA-4 with single-digit nM affinity from an initial state with no apparent binding. The engineered variants showed pH-independent and cross-reactive binding to both mouse and human CTLA-4. Crystal structures of a variant in complex with both mouse and human CTLA-4 confirmed that it targets an equivalent epitope as ipilimumab. These cross-reactive ipilimumab variants may facilitate improved translatability and future mechanism-of-action studies for anti-CTLA-4 targeting in murine models.

Influence of aquaculture practices on microbiota composition and pathogen abundance in pond ecosystems in South China

Pond microbiota play a crucial role in maintaining water quality and the health of aquaculture species. This study aimed to explore the relationship between pond water and sediment microbiota (especially potential pathogens) and physicochemical parameters under different aquaculture conditions. Samples of pond water and sediment were collected from 21 monitoring sites across eastern, western, and northern Guangdong, and the Pearl River Delta in November 2021, March 2022, and July 2022. Microbial structures were analyzed using high-throughput sequencing of the 16S rRNA gene. The results indicated that sediment microbiota distribution was more uniform than that of water microbiota. Additionally, sampling time significantly influenced the uniformity of water microbiota distribution more than that sediment microbiota. Factors such as aquaculture species, culture pattern, NH4 +-N, longitude, latitude, total nitrogen (TN), NO3 --N, NO2 --N, and total phosphorus (TP) were significantly correlated with water microbiota structure, and TN, TP, and organic carbon were significantly correlated with sediment microbiota structure. Furthermore, an increase in the NH4 +-N concentration in the pond water significantly increased the variety of pathogenic bacteria. Higher nitrogen levels also increased the relative abundance of Mycobacterium in pond water, whereas the culture pattern (freshwater, seawater, brackish, modern captive culture, freshwater factory container aquaculture, or seawater factory culture) and species significantly influenced the relative abundances of Vibrio, Tenacibaculum, Pseudoalteromonas, and Francisella. Additionally, the relative abundance of pathogenic bacteria in the sediment microbiota was significantly higher than that in the water microbiota. Our results suggest that the culture patterns, species, and nitrogen concentrations should be considered when preventing pathogenic bacteria growth in aquaculture waters.

Effect of intestinal microbiota on adaptation to overcrowding stress in grouper (Epinephelus fuscoguttatus♀×E. lanceolatus♂)

Density is an important aquaculture parameter. When the pearl gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) is farmed intensively, it could lead to a degradation in genetic resources and an increase in disease outbreaks. The composition of the intestinal microbiota plays a key role in creating a specific intestinal microecosystem, which is essential for the survival, growth, and immune response of the host under environmental stress like overcrowding. This study utilized 16S rRNA sequencing and metabolomics analysis techniques to investigate the differences in intestinal microbial community stability of grouper under different stocking time and density pressure conditions. The research results showed that compared to the low-density group, the high-density group of groupers experienced an increase in mortality rate and feed coefficient in the early stages of culture, while the weight gain rate decreased. Differential analysis of intestinal microbial communities revealed significant differences in the gut microbiota of grouper between different density groups after 10 days of culture, but no significant differences were observed after 20 days of culture. At the same time, intestinal histopathology showed that the high-density group of groupers exhibited a reduction in intestinal villi length and thickness of the intestinal wall after 10 days of culture. However, the intergroup differences had reduced after 20 days of culture. Furthermore, high density cultivation upregulated the expression of inflammatory factors like IL-1β, TNF-α, IL-8, and IL-6 in the intestinal tract of groupers after 10 days of culture. However, after 20 days of culture, the expression levels of intestinal inflammatory factors in both the high-density and low-density groups of groupers were significantly reduced, and the differences between the intergroup diminished. Through correlation analysis of differential metabolites and species in the intestine, multiple metabolites significantly upregulated and associated with the upregulation of the Staphylococcus genus were identified in the intestinal tract of groupers after 20 days of high-density cultivation. The selected four associated metabolites (including creatine, fosinopril, 4-aminobutyric acid, and guanidinopropanoic acid) were validated to significantly reduce the expression of cellular inflammatory factors using the self-established grouper head kidney (HK) cell line. In conclusion, density pressure in the early culture period could affect the stability of the intestinal microbial environment of grouper. As aquaculture time increases, the intestinal microbial community of grouper drives the body's anti-inflammatory response and enhanced its adaptation to density pressure by regulating own structure and secretion of metabolites.

The Cry2Aa protein is not enough to pose a threat to Pardosa astrigera

The widespread commercialization of genetically modified (GM) crops makes it important to assess the potential impact of Bacillus thuringiensis (Bt) on non-target organisms. Pardosa astrigera is an important predator in agroforestry ecosystems, and female and male spiders may react differently to Bt toxins due to their different activity habits and nutritional requirements. In this study, we found that exposure to Cry2Aa protein did not affect the survival and body weight of P. astrigera during growth and development. However, according to 16S rRNA sequencing results of the P. astrigera adults, Cry2Aa protein not only changed the diversity of symbiont bacteria, but also changed its symbiont composition. During feeding on prey without Bt artificial feed, the dominant communities in female and male adults were Actinobacteria and Corynebacterium-1, respectively. Feeding on prey containing Cry2Aa protein, Firmicutes were the dominant phyla. At the genus level, Cry2Aa protein significantly increased the relative abundance of Enterococcus and became the dominant genus in females only. In addition, Bacillus, Weissella and other symbiotic bacteria had significant changes in females. In terms of species composition, sex differences resulted in the absence of different types of symbiotic bacteria. Functional analysis of enrichment pathways showed significant changes in various metabolic pathways such as "Carbohydrate metabolism" and "Nucleotide metabolism", and there are differences between the sexes. These findings provide new data information and support for revealing the different strategies of spiders to cope with Cry2Aa protein based on sex differences, and also provide new data information and support for environmental safety assessment of GM crops.

dsDAP: An efficient method for high-abundance DNA-encoded library construction in mammalian cells

DNA-encoded libraries are invaluable tools for high-throughput screening and functional genomics studies. However, constructing high-abundance libraries in mammalian cells remains challenging. Here, we present dsDNA-assembly-PCR (dsDAP), a novel Gibson-assembly-PCR strategy for creating DNA-encoded libraries, offering improved flexibility and efficiency over previous methods. We demonstrated this approach by investigating the impact of translation initiation sequences (TIS) on protein expression in HEK293T cells. Both CRISPR-Cas9 and piggyBac systems were employed for genomic integration, allowing comparison of different integration methods. Our results confirmed the importance of specific nucleotides in the TIS region, particularly the preference for adenine at the -3 position in high-expression sequences. We also explored the effects of library dilution on genotype-phenotype correlations. This Gibson-assembly-PCR strategy overcomes limitations of existing methods, such as restriction enzyme dependencies, and provides a versatile tool for constructing high-abundance libraries in mammalian cells. Our approach has broad applications in functional genomics, drug discovery, and the study of gene regulation.

Bacterial and fungal diversity and species interactions inversely affect ecosystem functions under drought in a semi-arid grassland

Extreme climatic events, such as drought, can significantly alter belowground microbial diversity and species interactions, leading to unknown consequences for ecosystem functioning. Here, we simulated a drought gradient by removing 30 %, 50 %, and 70 % of precipitation in a semi-arid grassland over five years. We assessed the effects of drought on bacterial and fungal diversity, as well as on their species interactions. We also evaluated the impact of drought on ecosystem individual functions (e.g., plant biomass and microbial activity), and on multifunctionality (EMF). Finally, we linked the drought-induced changes in microbial communities with the variations in EMF. Drought significantly increased fungal diversity and intensified species interactions, but it decreased bacterial diversity and species interactions. Both plant and microbial biomass significantly decreased with increasing drought severity, while microbial activity showed the opposite trend. Only the -50 % rainfall treatment notably reduced EMF. Bacterial diversity and species interactions positively correlated with most ecosystem functions. However, fungal parameters were negatively associated with these functions. Structural equation modeling indicated that bacterial diversity had a strong direct positive effect on EMF (standardized path coefficient: 0.52), and that bacterial diversity was indirectly suppressed by drought through decreasing soil water content and bacterial phospholipid fatty acids (PLFAs). In contrast, fungal species interactions had a significant direct negative effect on EMF with the highest standardized path coefficient (-0.6) and were directly enhanced by fungal diversity. Drought had indirect positive effects on fungal diversity by decreasing soil water content and stimulating fungal PLFAs. Our results highlight the importance of considering soil microbial species interactions when evaluating the ecological impacts of drought. Furthermore, the divergent regulatory pathways of bacterial and fungal communities to EMF suggest that improving ecosystem functionality may be achieved by enhancing bacterial diversity while mitigating fungal species interactions through reducing fungal diversity.

High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China

The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.

Porous polyurethane biocarriers could enhance system nitrification resilience under high organic loading by retaining key functional bacteria

Resilience to increasing organic loading rates (OLRs) is the key to maintaining stable performance in treating industrial wastewater. First, this study compared the stability, particularly the nitrification performance, of two lab-scale moving bed biofilm reactors (MBBRs) filled with porous polyurethane biocarriers with two conventional activated sludge reactors (ASRs) in the treatment of synthetic coking wastewater under OLRs increasing from 0.3 kg to 1.5 kg COD m-3 day-1. In comparison with the ASRs, which could only achieve complete nitrification (99.31 % ± 0.43 %) at an OLR of 0.7 kg COD m-3 day-1, the MBBRs could achieve efficient NH4+-N removal (99.45 % ± 0.21 %) at an OLR as high as 1.3 kg COD m-3 day-1. Even at an OLR of 1.5 kg COD m-3 day-1 where nitrification was inhibited, the porous polyurethane biocarriers in the MBBRs still maintained a highly diversified bacterial community (Shannon index, 4.34 ± 0.31) by retaining the slow-growing nitrifying bacteria and phenol-degrading bacteria, including Methyloversatilis and Acinetobacter, whose phenol degradation functions were confirmed by metagenome-assembled genome extraction and analysis, while the ASRs lost diversity (Shannon index, 1.41 ± 0.45) due to the sequential occurrence of filamentous and viscous sludge bulking. The advantage of the MBBR was further verified in a full-scale coking wastewater treatment system, where a reactor series filled with 4.35 % porous polyurethane biocarriers exhibited better NH4+-N removal of 99.57 % ± 0.34 % compared to 96.85 % ± 2.56 % for a conventional one under an OLR of 0.54 ± 0.12 kg COD m-3 day-1. The results could contribute to the development of more effective and resilient treatment systems for industrial wastewater.

Insight into how fermentation might contribute to the distinctiveness of Australian coffee

With a view to modulating the flavour profiles of Australian coffee, this investigation focused on three estates in New South Wales. Coffee cherries were processed into beans with wet fermented and non-fermented methods to evaluate the effects of fermentation and terroir on microbial population dynamics, volatile composition, and sensory properties. Thirty-three volatiles were quantified in green and roasted coffee beans - 12 esters, 9 alcohols, 6 acids, 3 monoterpenes, 2 norisoprenoids, 1 aldehyde - and 5 thiols were quantified in roasted coffee brews. Sensory descriptive analysis defined appearance, aroma, and flavour attributes to describe the coffee brews. Fermented coffees were characterised by increased intensity of 'black tea leaves' and 'dark chocolate' aromas and 'burnt toast' flavour. Results suggested that wet fermentation of Australian coffee cherries could enhance the content of some volatile compounds known to convey "floral" and "fruity" aromas commonly ascribed to premium coffees from traditional producing regions.

18S rRNA Metagenomic Analysis of Nodular Gill Disease in Swiss Rainbow Trout (Oncorhynchus mykiss)

Nodular gill disease (NGD) is a serious proliferative gill condition that affects farmed salmonids, particularly in Europe. While the cause of NGD remains unknown (and maybe multifactorial), various amoebae are often isolated from the gills of affected fish and can in some cases be seen associated with lesions by histopathology. The present study aimed to quantify the abundance of different amoeba species directly from the gills of rainbow trout affected by NGD and healthy controls. An 18S rRNA amplicon metagenomic approach was employed to profile the diversity and abundance of micro-eukaryotes (including amoebae) while suppressing the amplification of host DNA using a salmonid-specific C3 spacer blocking primer. The 18S rRNA metagenomics approach identified a diversity of micro-eukaryotes on the gills of rainbow trout, including the phylum's Amoebozoa, Diatomea, Platyhelminthes and Ciliophora. Rainbow trout clinically affected by NGD had a significantly higher abundance of a specific sequence (zOTU2) classified as Vannella sp. compared to healthy controls. A quantitative PCR assay was then developed and validated which accurately quantified the abundance of this Vannella sp. sequence from a NGD outbreak in a Swiss rainbow trout farm. Additional PCR and Sanger sequencing analysis of the zOTU2 sequence demonstrated that this sequence is most likely derived from Vannella mustalahtiana. Our study highlights the potential role of Vannella mustalahtiana in NGD in Switzerland and further describes a specific and validated diagnostic PCR assay for accurate detection of this Vannella species.

Response mechanisms of eukaryotic plankton community structure to complex environmental conditions in semi-arid river basins, China

Semi-arid regions, such as the Yellow River Basin in China, are highly sensitive to environmental changes due to their scarce water resources and fragile ecosystems. This study explores the response mechanisms of eukaryotic plankton community structure to environmental conditions in the Dahei River Basin, a representative semi-arid region in central-western Inner Mongolia, across different seasons (spring, summer, autumn) and regions (hills, plain, urban). Our results reveal significant temporal and spatial variability in water resources and quality factors, which in turn affect eukaryotic plankton community structure. Using distance decay relationship (DDR) modeling and random forest analysis, we demonstrate that water quality factors, especially water temperature, are the primary factors influencing community composition in urban regions, where human activities such as industrial thermal discharges and urban heat island effects elevate water temperatures. In summer, increased water volume and flow velocity enhanced river connectivity, promoting greater community structure similarity across the basin, while in autumn, reduced flow and connectivity led to spatial heterogeneity and increased growth of the pollutant-tolerant species like Desmodesmus and Stephanocyclus. The synergistic effects of low flow rates and deteriorating water quality during the dry period intensified the influence of environmental factors on phytoplankton, decreasing community stability and increasing deterministic processes in community assembly. This shift towards determinism, especially in urban regions heavily impacted by human activities, highlights the sensitivity of semi-arid aquatic ecosystems. Co-occurrence network analysis further reveals that urban regions exhibit lower network complexity and stability, underscoring the heightened ecological sensitivity in these regions. In conclusion, the study highlights the critical role of water volume and quality in shaping eukaryotic plankton communities and elucidates how environmental changes, exacerbated by human activities and climate change, disrupt ecosystem stability. These findings offer essential insights for managing and conserving aquatic ecosystems in semi-arid regions facing dual pressures of climate change and human activity.

Growth Stage-Dependent Variation in Soil Quality and Microbial Diversity of Ancient Gleditsia sinensis

The environment monitoring of forest is vital for the ecosystem sustainable management, especially soil quality. Ancient Gleditsia sinensis is one of the most distributed ancient trees in Shaanxi. Comprehensive soil evaluate is important for the ancient tree protection. In this study, we selected the most distributed ancient tree Gleditsia sinensis and immature tree to compare the effect of growth stage to soil quality and soil bacteria. Most ancient tree soil nutrients were in good condition compared with immature tree. The bacterial community were composed with Proteobacteria (27.55%), Acidobacteriota (16.82%), Actinobacteriota (15.77%), Gemmatimonadota (6.82%), Crenarchaeota (4.61%), Bacteroidota (4.41%), Firmicutes (4.32%), Chloroflexi (4.28%), Planctomycetota (3.24%) and Verrucomicrobiota (3.04%). The level 2 ancient tree (300-400 years old) was different in bacterial community diversity. SOC and STN were important to level 2 (300-400 years old Gleditsia sinensis), and other levels were opposite. Our results suggested that the ancient tree management should not be lumped together.

Assemblage of root-associated microbiome contributes to disparate performance of two rice genotypes under aluminum stress

Aluminum (Al) toxicity severely inhibits rice growth under acidic soils, posing a significant threat to food security. The assemblies of root-associated microbiomes throughout the lifecycle of rice are hypothesized to furnish a resilient reservoir of ecological functions for rice growth performance under Al stresses. However, the mechanisms that drive the assembly of root-associated microbiomes of rice are largely unknown. In this study, we chose two rice genotypes (including aluminum-tolerant (Al-T) and aluminum-sensitive (Al-S)) as model plants to investigate the microbial assemblage of root-associated microbiome and their potential roles on the plant growth performance under Al stress. The microbial community diversity (Shannon) and evenness (Chao1) in the endosphere of the Al-T genotype gradually decreased, converging towards levels observed in the Al-S genotype. In addition, the rhizosphere and endosphere microbiomes of Al-T genotype are primarily influenced by deterministic processes, while those of Al-S genotype are more influenced by stochastic processes. Compared to Al-S genotype, Al-T genotype exhibited higher complexity and stability in its rhizosphere and endosphere microbiomes, while the rhizoplane microbiome showed the opposite trend. In the rhizosphere microbiome of the Al-T genotype, we identified Gallionellales, Rhodobacterales, and Rhizobiales as keystone taxa. Their abundance was closely associated with microbial functions, including indole-3-acetic acid (IAA) synthesis, phosphorus solubilization, glutathione (GSH) metabolism, and 1-aminocyclopropane-1-carboxylate (ACC) metabolism. In the Al-S genotype, the keystone taxa included Actinomycetales and Burkholderiales. This study offers new insights into plant adaptation to abiotic stress and underscores the significance of the assemblage of root-associated microbiome in this process.

Phage cocktail against Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei: Genomic, biological, and pathological characterization

Phages vB_Pd_PDCC-1, vB_Vc_SrVc9, and vB_Vp_PvVp11 were found to be lytic against Vibrio parahaemolyticus acute hepatopancreatic necrosis disease (AHPND) and other pathogenic vibrios. The complete genomic and biological characterization of phage vB_Vp_PvVp1 was conducted, and a cocktail of these three phages was applied to juvenile Penaeus vannamei infected with V. parahaemolyticus AHPND. Water samples collected during the challenges were analyzed using metagenomics. At the end of the experimental infection, the phage cocktail did not improve shrimp survival compared to the positive control group (infected only with bacteria). This suggests the emergence of phage-resistant V. parahaemolyticus strains. However, a significantly lower mortality rate was observed 12 h post-infection, along with a shortening of the disease course in the phage therapy treatment. A phage-resistant strain of V. parahaemolyticus AHPND was in vitro isolated. For the first time, we report the identification of nucleotide variants in the glycosyltransferase gene of this mutant strain through genome sequencing. Although the phage cocktail was ineffective in controlling AHPND, some protective benefits of phage therapy were noted in P. vannamei during the acute phase-the most critical stage-compared to the positive control. Phage therapy decreased alpha diversity and altered the microbiota composition during the challenge, increasing V. parahaemolyticus. The Vibrio AHPND pathogen produces a potent PirAB toxin, making this disease difficult to manage. Further studies are needed to explore synergistic approaches as effective therapeutic tools.

Effects of transient change in temperature by daki warm treatment on the growth of bacteria during kimoto-style seed mash preparation

Daki warm treatment (daki-ire) is performed during the process of seed mash preparation in the brewing of Japanese sake in order to promote the saccharification of rice by koji enzyme and to enhance the growth of Saccharomyces cerevisiae. Although it is important to control the growth of lactic acid bacteria in the preparation of kimoto-style seed mash (traditional sake-brewing method), it has not been known whether the transient increase in the temperature and/or appropriate temperature zone produced by daki-ire influences the growth of bacteria. A temperature increase generally helps bacterial growth, but we have found no published investigation of the influence of temperature changes in daki-ire on bacterial growth during the kimoto-style seed mash preparation process. In this first comprehensive evaluation of the effects of the temperature change by daki-ire on bacterial communities, we investigated the bacterial community in three batches that were brewed by the same brewery using identical ingredients. The results demonstrated that the bacterial community or its transition during lactic acid fermentation was diverse despite the use of the same brewing conditions. We observed that (i) some lactic acid bacteria were carried over to the subsequent batches, and (ii) the increase in the initial amount of lactic acid bacteria plays an important role in the formation of the bacterial community. Our analysis of the bacterial growth activity before and after daki-ire indicated that the transient increase in temperature and/or local appropriate temperature by daki-ire, in and of itself, has relatively little direct impact on bacterial growth.

Spatial mapping of dextran sodium sulphate-induced intestinal inflammation and its systemic effects

Inflammatory bowel disease (IBD) is a multifactorial disease, and patients frequently experience extraintestinal manifestations affecting multiple sites. Causes of systemic inflammation remain poorly understood, but molecules originating from the intestine likely play a role, with microbial and host small molecules polarizing host immune cells towards a pro- or anti-inflammatory phenotype. Using the dextran sodium sulfate (DSS) mouse model, which mimics the disrupted barrier function, microbial dysbiosis, and immune cell dysregulation of IBD, we investigated metabolomic and phenotypic changes at intestinal and systemic sites. Using spatial biology approaches, we mapped the distribution and relative abundance of molecules and cell types across a range of tissues, revealing significant changes in DSS-treated mice. Molecules identified as contributing to the statistical separation of treated from control mice were spatially localized within organs to determine their effects on cellular phenotypes through imaging mass cytometry. This spatial approach identified both intestinal and systemic molecular drivers of inflammation, including several not previously implicated in inflammation linked to IBD or the systemic effects of intestinal inflammation. Metabolic and inflammatory pathway interplay underpins systemic disease, and determining drivers at the molecular level may aid the development of new targeted therapies.

Gut Microbiota-Butyrate-PPARγ Axis Modulates Adipose Regulatory T Cell Population

Gut microbiota is essential for the function of peripherally-induced regulatory T (pTreg) cells. However, how commensal bacteria affect thymically derived fat-resident Treg cells that harbor a unique expression of peroxisome proliferator-activated receptor (PPAR)-γ and suppress inflammation in visceral adipose tissue (VAT), is not well defined. Here it is revealed that microbiota depletion causes a drastic decline in Treg cell population in VAT, particularly those expressing ST2 (ST2+ Treg), which are largely restored after gut microbiome reconstruction. Mechanistically, gut microbiota-derived butyrate increases VAT ST2+ Treg cells through binding PPARγ. Butyrate supplementation and high fiber diet increase VAT ST2+ Treg population in obese mice, and ameliorated glucose tolerance and visceral inflammation. Furthermore, human omental adipose Treg cells show positive correlation with fecal butyrate and certain butyrate-producing microbes. This study identifies the critical role of gut microbiota-butyrate-PPARγ axis in maintaining VAT Treg population, pinpointing a potential approach to augment VAT Treg population and ameliorate inflammation.

SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx

The gastrointestinal (GI) tract is a site of replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and GI symptoms are often reported by patients. SARS-CoV-2 cell entry depends upon heparan sulfate (HS) proteoglycans, which commensal bacteria that bathe the human mucosa are known to modify. To explore human gut HS-modifying bacterial abundances and how their presence may impact SARS-CoV-2 infection, we developed a task-based analysis of proteoglycan degradation on large-scale shotgun metagenomic data. We observed that gut bacteria with high predicted catabolic capacity for HS differ by age and sex, factors associated with coronavirus disease 2019 (COVID-19) severity, and directly by disease severity during/after infection, but do not vary between subjects with COVID-19 comorbidities or by diet. Gut commensal bacterial HS-modifying enzymes reduce spike protein binding and infection of authentic SARS-CoV-2, suggesting that bacterial grooming of the GI mucosa may impact viral susceptibility.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019, can infect the gastrointestinal (GI) tract, and individuals who exhibit GI symptoms often have more severe disease. The GI tract's glycocalyx, a component of the mucosa covering the large intestine, plays a key role in viral entry by binding SARS-CoV-2's spike protein via heparan sulfate (HS). Here, using metabolic task analysis of multiple large microbiome sequencing data sets of the human gut microbiome, we identify a key commensal human intestinal bacteria capable of grooming glycocalyx HS and modulating SARS-CoV-2 infectivity in vitro. Moreover, we engineered the common probiotic Escherichia coli Nissle 1917 (EcN) to effectively block SARS-CoV-2 binding and infection of human cell cultures. Understanding these microbial interactions could lead to better risk assessments and novel therapies targeting viral entry mechanisms.

Influence of biochar-based microbial agents on post-consumption food waste composting

Recycling nutrients by post-consumption food waste (PCFW) composting is impeded by the slow composting process because of the high perishability and moisture content of PCFW. Concerning this issue, a biochar-based microbial agent with trehalose as a protectant was developed, and was evaluated as inoculum in PCFW composting. Inoculation effectively ameliorated acidic conditions, accelerated organics degradation resulting in quick temperature rising, shortened maturation from 28 to 14 days, and altered the succession of the bacterial community structure. The combination of microbial consortium and biochar effectively inhibited the acid-producing bacteria Weissella and increased Bacillus, which contributed to a better condition for indigenous microbes by ameliorating the acidic condition of PCFW. This further expedited temperature rising that selectively enriched Firmicutes (Bacillus, Compostibacillus, Novibacillus) and Actinobacteria (Pseudonocardia) at the thermophilic stage. Moreover, carbon cycle was strengthened by chemoheterotrophy and aerobic chemoheterotrophy, while fermentation was inhibited, which was in favor of organic material degradation. The addition of 5% trehalose further enhanced the effect, and increased germination index to 152% at day 14. This study suggested that a biochar-based microbial agent was an efficient inoculant specifically for PCFW composting.

Developmental validation of an mRNA-cSNP profiling panel for body fluids identification and individualization

Forensic analysis of body fluid stains is extremely important, which helps reconstruct crime scenes. It involves two main challenges: body fluid identification (BFID) and individualization. The former aims to ascertain the type/origin of the body fluid stain, while the latter tries to assign the stain to a specific donor. Generally, they are addressed through RNA and DNA analyses, respectively, but this can be time-consuming, laborious, and sometimes yield suboptimal results, especially mixed body fluid stains. To overcome these limitations, we developed an innovative mRNA-based sequencing panel with a dual function. This system comprises 34 body fluid-specific mRNA genes and 39 cSNP markers (amplicon length: 50 ~ 90 bp), enabling a direct link between specific body fluids and their donors. We thoroughly validated the integrated system according to the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM) on the MGI massively parallel sequencing (MPS) platform. As a result, this panel showed robust identification efficiency for body fluids at 20 ng RNA input, and the range of cumulative discrimination power (CDP) value was 0.802445047 ~ 0.999310789 in five types of body fluid. Furthermore, it had been employed in actual cases and provided the guidance. In conclusion, this system can efficiently, rapidly, and accurately perform body fluid identification and individualization for single-source and mixed samples, meeting the daily investigative demands in forensic genetics.

Harnessing Non-standard Nucleic Acids for Highly Sensitive Icosaplex (20-Plex) Detection of Microbial Threats for Environmental Surveillance

Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. Using parallelized multitarget TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay on wastewater, soil, and human stool samples, we found 90% agreement on positive calls and 89% agreement on negative calls. Additionally, we show how long-read and short-read sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish subspecies. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.

Sex-specific effects of gastrointestinal microbiome disruptions on Helicobacter pylori-induced gastric carcinogenesis in INS-GAS mice

BACKGROUND

Accumulating evidence indicates that the dysbiosis of gastrointestinal microbiota is associated with the development of gastric carcinogenesis. However, the sex-specific traits of gastrointestinal microbiota and their correlation with the sexually dimorphic response to gastric cancer remain poorly understood.

METHODS

Male and female transgenic FVB/N insulin-gastrin (INS-GAS) mice as a model of gastric cancer were randomly administered Brucella Broth or Helicobacter pylori (H. pylori). Stomachs were evaluated by histopathology. The gastric inflammation was examined by immunohistochemical and immunofluorescence staining. Gastric mucosal and fecal samples were collected for microbiota analysis using 16S rRNA gene sequencing.

RESULTS

Following H. pylori infection, male mice showed heightened inflammatory infiltration and notably greater intestinal metaplasia compared to female mice. The structure of gastrointestinal microbiota was different between male and female mice, with relative higher diversity in females than males. Notably, we found gender disparities in the alterations of gastric and intestinal microbiota in mice post H. pylori infection. While the enrichment of Bifidobacterium and Lachnospiraceae was observed in female mice, Escherichia_Shigella and Akkermansia were more abundant in males. Furthermore, the microbial profile was distinct in estrogen-deficient ovariectomized (OVX) mice, including the overgrowth of Akkermansia and the loss of Butyricicoccus. Infected OVX females developed significantly more severe gastric lesions, which was normalized through co-housing with intact females.

CONCLUSIONS

We have identified a novel microbiome-based mechanism that provides insight into the sexual dimorphism in the development of H. pylori-associated gastric cancer.

Influence of different diet categories on gut bacterial diversity in Frankliniella occidentalis

The microbial composition of insect guts is typically influenced by the type of food consumed, and conversely, these microbes influence the food habits of insects. Western flower thrips (WFT; Frankliniella occidentalis) is an invasive pest with a wide range of hosts, including vegetables and horticultural crops. To elucidate variations in gut bacteria among WFT feeding on rose (Rosa rugosa) flowers (FF), kidney bean (Phaseolus vulgaris) pods (PF), and kidney bean leaves (LF), we collected adult guts and extracted DNA for 16S ribosomal RNA gene sequencing of microbial communities. The results revealed that the FF population had the highest number of annotations. Alpha diversity analysis revealed that the Chao and Ace indexes were the greatest in the PF population, indicating a higher abundance of gut bacteria. Moreover, the Simpson index was the highest in the FF population, indicating that gut bacterial diversity was the highest in the FF population. Comparison of species composition demonstrated that Proteobacteria dominated all 3 populations at the phylum level, with Actinobacteria being the subdominant phylum. At the genus level, Stenotrophomonas was the dominant bacteria in the PF and LF populations, whereas Rosenbergiella was dominant in the FF population. KEGG pathway annotation predicted that the gut bacteria of adult WFT were mainly involved in carbohydrate and amino acid metabolism. Our results revealed that the diversity and composition of WFT gut microbiota are influenced by diet, offering evidence for future studies on the ecological adaptability of WFT and the mechanisms underlying the interaction between gut microbiota and host.

Environmental DNA is more effective than hand sorting in evaluating earthworm biodiversity recovery under regenerative agriculture

Regenerating soil biodiversity can help to reverse declines in soil health caused by cultivation and continuous arable cropping, and support sustainable food production and agro-ecosystem services. Earthworms are key functional components of soil biodiversity, with different ecological categories and species delivering specific beneficial soil functions. Conventional monitoring by hand-sorting from soil pits is highly labour intensive, can reliably identify only adults to species, and may under-record anecics (deep-burrowers). Here, we compare soil environmental DNA (eDNA) metabarcoding using two different primer sets and next-generation sequencing, with earthworm hand-sorting from standard soil-pits, in four conventionally managed arable fields into which strips of grass-clover ley had been introduced three years earlier. Earthworm populations had been recorded by hand-sorting in the previous three years and our goal was to assess the effects of the three-year leys compared to arable cropping using both hand-sorting and eDNA. The eDNA method found the same eight earthworm species as hand-sorting, but had greater power for detecting anecic earthworms and quantifying local species richness. Earthworm abundance increased by over 55% into the third year of the leys, surpassing abundances in adjacent permanent grasslands, helping to explain the observed soil health regeneration. Both overall relative read abundances and site occupancy proportions of earthworm eDNA were found to have potential as proxies for abundance, and the performance of each of these measures and the implications for further work are discussed. We show that eDNA can improve earthworm diversity monitoring and recommend its wider use both to better understand soil management effects on earthworm populations, and to guide agricultural policy and practice decisions affecting soil health.

Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota

Suppression of chronic Arabidopsis immune responses is a widespread but typically strain-specific trait across the major bacterial lineages of the plant microbiota. We show by phylogenetic analysis and in planta associations with representative strains that immunomodulation is a highly conserved, ancestral trait across Xanthomonadales, and preceded specialization of some of these bacteria as host-adapted pathogens. Rhodanobacter R179 activates immune responses, yet root transcriptomics suggest this commensal evades host immune perception upon prolonged association. R179 camouflage likely results from combined activities of two transporter complexes (dssAB) and the selective elimination of immunogenic peptides derived from all partners. The ability of R179 to mask itself and other commensals from the plant immune system is consistent with a convergence of distinct root transcriptomes triggered by immunosuppressive or non-suppressive synthetic microbiota upon R179 co-inoculation. Immunomodulation through dssAB provided R179 with a competitive advantage in synthetic communities in the root compartment. We propose that extensive immunomodulation by Xanthomonadales is related to their adaptation to terrestrial habitats and might have contributed to variation in strain-specific root association, which together accounts for their prominent role in plant microbiota establishment.

Diversity and dynamics of multiple symbionts contribute to early development of broadcast spawning reef-building coral Dipsastraea veroni

Sexual reproduction and recruitment enhance the genetic diversity and evolution of reef-building corals for population recovery and coral reef conservation under climate change. However, new recruits are vulnerable to physical changes and the mechanisms of symbiosis establishment remain poorly understood. Here, Dipsastraea veroni, a broadcast spawning hermaphrodite reef-building coral, was subjected to settlement and juvenile growth in flow-through in situ seawater at 27.93 ± 0.96°C. Symbiosis of Symbiodiniaceae, bacteria, and/or archaea by horizontal acquisition and/or hypothetical vertical transmission through the mucus with symbionts from the parent appears to be a heritable process of selection and adaptation in D. veroni at the egg, larva, juvenile (5 days post settlement, d p.s. and 32 d p.s.) stages. Symbiodiniaceae was dominated by the genera Cladocopium, Durusdinium, Symbiodinium, with increasing relative abundance of Durusdinium at 5 d p.s. and Symbiodinium at 32 d p.s. Mixed acquisition of the dominant phyla Pseudomonadota, Bacteroidota, Cyanobacteriota, Bacillota, Planctomycetota, and Actinomycetota in egg, larva, and/or juvenile showed a winnowing and regulated bacterial diversity and dynamics, resulting in stage-abundant orders Pseudomonadales and Bacillales in egg and Rhodobacterales, Rhodospirillales, Cyanobacteria, and Cyanobacteriales in larva and/or juvenile. The photoautotrophic Chloroflexales, Cyanobacteriales, and Chlorobiales were abundant in adults. The stable archaeal community contained predominant Crenarchaeota, Halobacterota, Nanoarchaeia Thermoplasmatota, and eight rare phyla, with increased relative abundance of the genera Bathyarchaeota, Candidatus_Nitrosopumilus, Candidatus_Nitrocosmicus, Nitrosarchaeum, Candidatus_Nitrosotenuis, Candidatus_Nitrosopelagicus, Cenarchaeum, Haladaptatus, Halogranum, Halolamina, and Woesearchaeales and GW2011-AR15 in juveniles. All results revealed flexible symbiotic mechanisms in D. veroni during early ontogeny for coral survival and evolution.IMPORTANCEFlexible symbioses of Symbiodiniaceae, bacteria, and archaea appear to be a heritable process of selection and adaptation in Dipsastraea veroni in the field, benefiting early coral development and facilitating coral population recovery and reef conversation.

Bacterial Community Structures in Raw Pork from Supermarkets and Farmers' Markets Determined by High-Throughput Sequencing Analysis

Pork contaminated with bacteria can shorten the shelf life and cause foodborne diseases. Bacterial community analysis of raw pork in sale process can help identify bacteria associated with food quality and safety. In this study, 52 pork samples were collected from various supermarkets and farmers' markets in Qingdao, China. And the bacterial community structures in pork were analyzed by high-throughput sequencing of 16S rDNA. Both the α-diversity and β-diversity of bacterial communities in pork samples from farmers' market were higher than those from supermarkets (ANOSIM test, R2 = 0.049, p = 0.016). Proteobacteria (88.8%) was the most dominant phylum, and Photobacterium (44.5%) and Acinetobacter (23.9%) were the top two dominant genera in all pork samples. The abundance of most dominant bacterial genera was higher in pork samples from farmers' markets than those from supermarkets, But Photobacterium (ranking first) was just the opposite (p = 0.003). The bacterial communities in pork hadn't obvious clustering characteristics between the two sale locations, while Photobacterium was considered as the biomarker in pork samples from supermarkets according to LefSe analysis (linear discriminant analysis score >4.0). A strong correlation was observed between some samples (R >0.7) collected from different stalls within the same sampling location, indicating cross-contamination possibility in sale process. The findings may have implications for the quality and safety control of pork, particularly for microbial prevention and control during selling and consumption.

Self-reactive B cells are increased in all major stages of peripheral development in Sjögren's disease

Sjögren's disease (SjD) is a chronic autoimmune disorder characterized by increased circulating self-reactive B cells. While many of these self-reactive B cells emerge from the bone marrow, it is not known whether they are excluded from or enriched in specific developmental stages in the periphery. The aim of this study was to determine the immunophenotype of circulating self-reactive B cells in SjD to inform more precise therapeutic targeting. Five major B cell populations: transitional, mature naïve, switched memory, double negative and plasmablasts were single-cell sorted and cultured to produce IgG. Self-reactive IgG was identified by ELISA, flow cytometry of permeabilized HEK293 cells and HEp-2 indirect immunofluorescence. Immunoglobulin heavy chains were sequenced by Sanger and next-generation sequencing. Compared with healthy donor controls (HCs), SjD patients had higher frequencies of naïve and CD21low atypical memory B cell subsets, while antigen-experienced B cells expressed more Ki67 and CD86. B cells recognizing intracellular self-antigens were identified in all stages of peripheral B cell development for SjD and HCs, but frequencies of autoreactive B cells were up to 10-fold higher in SjD. Self-reactive transitional B cells expressed higher surface CD38 and lower surface IgM. An increase in self-reactive B cells throughout peripheral development in SjD compared with HCs suggests that counterselection of autoantibody-bearing B cells during central and peripheral tolerance checkpoints are reduced in SjD. Therapeutic strategies focused on depleting B cells based on B cell receptor specificity rather than the developmental stage would be more efficient to target self-reactive B cells in SjD.

Nitrogen utilization dynamics in a tropical estuary: Interplay of temperature and phytoplankton communities

Nitrogenous nutrients-such as nitrate (NO3-), nitrite (NO2-), ammonium (NH4+), and urea-are key drivers of phytoplankton productivity and biogeochemical cycles in marine ecosystems, often entering coastal zones through estuarine discharge. Estuaries, particularly tropical ones, play a vital role in regulating the composition and export of nitrogen (N) species to downstream coastal waters. Despite their ecological significance, the factors influencing N utilization in tropical estuaries remain poorly understood. In this study, we used 15N isotope tracer incubation techniques to explore the seasonal variations in the uptake rates of NO3-, NO2-, NH4+, and urea in the Dongzhai Harbor estuary, a tropical system in China. We found that while NO3- was the most abundant reactive N species in both seasons, NH4+ was preferentially taken up by phytoplankton during the warm season. Conversely, urea uptake increased unexpectedly during the cold season, likely due to shifts in phytoplankton community composition favoring urea-preferred taxa like Peridiniopsis. Seasonal variations in N uptake rates were primarily governed by temperature and phytoplankton community structure. Enhanced inorganic N uptake during the warm season reduced the export of reactive inorganic N, whereas higher organic N uptake in the cold season facilitated the inorganic N exported to coastal waters. These findings highlight the interplay between environmental drivers and community dynamics in shaping nitrogen cycling in tropical estuaries. They underscore the importance of managing nutrient inputs to potentially safeguard sensitive downstream ecosystems, such as coral reefs, from eutrophication and degradation.

Profiles of gut microbiota and metabolites for high risk of transgenerational depression-like behavior by paternal methamphetamine exposure

Parental substance abuse increases the risk of neurological and psychiatric disorders in offsprings. However, its underlying mechanism remains elusive. Our previous study demonstrated that long-term exposure to methamphetamine (Meth), a psychostimulant drug with high addiction potential, remarkably alters the gut microbiome and metabolites in male mice, which contribute to Meth-induced anxiety-like behaviors. The current study aimed to investigate whether gut microbiota and metabolism serve as potential peripheral targets for transgenerational mental problems by paternal Meth exposure. We found that paternal Meth exposure induced depression-like behaviors both in the first (F1) and the second (F2) generations of male mice. Further, the depletion of gut bacteria through antibiotic treatments normalized the depression-like behaviors to normal levels in both F1 and F2 male mice. Then, alterations in gut bacterial composition were observed in both F1 and F2 male mice. Specifically, Eubacterium_ruminantium_group, Enterorhabdus, Alloprevotella, and Parabacteroides were the commonly affected bacterial taxa in F1 and F2 male mice. In addition, the results of alterations in gut metabolism showed that LPC 14:1-SN1 emerged as the consistently altered metabolite in the colons of F1 and F2 male mice. Taken together, our findings provide the first evidence that paternal Meth exposure enhances depression-like behaviors in F1 and F2 male mice, potentially mediated by the gut microbiome and metabolism.

Tongue coating microbial communities vary in children with Henoch-Schönlein purpura

Previous research has shown that microbes play a role in immune-related diseases. Our study reveals that children with Henoch-Schönlein purpura nephritis have distinct and altered tongue coating microbiota, characterized by significant changes in species richness, diversity, and specific microbial compositions compared with healthy controls. Nevertheless, the particular involvement of tongue coating microbiota in Henoch-Schönlein Purpura remains unclear. A total of 26 children were enrolled, including 13 patients with HSP and 13 healthy children. Tongue coating samples were collected for DNA extraction and 16S rRNA gene sequencing. Alpha diversity indices, including ACE, Chao1, Shannon, and Simpson indices, revealed significantly lower richness and diversity of tongue coating microbiota in children with Henoch-Schönlein purpura compared to healthy controls. Beta diversity analysis demonstrated distinct clustering of microbial communities between HSP and healthy children, with significant compositional differences. 16S rRNA gene sequencing showed that the relative abundance of key genera, such as Veillonella and Prevotella, differed between the two groups. A random forest algorithm identified five genera as potential diagnostic biomarkers for HSP. Co-occurrence analysis revealed different hub microbes in HSP and healthy children. BugBase predicted an increased proportion of stress-tolerant bacteria in the HSP group compared to the healthy controls group. PICRUSt analysis indicated alterations in metabolic functions of tongue coating microbiota between HSP and healthy children, with 25 KEGG pathways exhibiting significant differences. Children with HSP exhibit marked differences in their tongue coating microbiota when contrasted with their healthy counterparts.

Evaluation of Cas13d as a tool for genetic interaction mapping

Mapping genetic interactions (GIs) is crucial for understanding genetic network complexity. In this study, we investigate the utility of Cas13d, a CRISPR system targeting RNA, for GI mapping and compare it to Cas9 and Cas12a, two DNA nucleases commonly used for GI mapping. We find that Cas13d induces faster target gene perturbation and generates more uniform cell populations with double perturbations than Cas9 or Cas12a. We then encounter Cas13d gRNA-gRNA interference when concatenating gRNAs targeting different genes into one gRNA array, which we overcome by a dual promoter gRNA expression strategy. Moreover, by concatenating three gRNAs targeting the same gene into one array, we are able to maximize the Cas13d-mediated knockdown effects. Combining these strategies enhances proliferation phenotypes while reducing library size and facilitates reproducible quantification of GIs in oncogenic signaling pathways. Our study highlights the potential of Cas13d for GI mapping, promising advancements in understanding therapeutically relevant drug response pathways.

Structure and diversity of intestinal methanogens in black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella) and water samples

The present research investigation aims to examine the community features of methanogens in the intestinal tract of black and grass carp, as well as their association with methanogens in water samples. Samples of black carp, grass carp and water in a pond were gathered in Spring 2021. Using the Illumina HiSeq 2500 high-throughput sequencing platform, the metagenomic mcrA gene sequences of black carp, grass carp and cultured water specimens were determined and analyzed. The outcomes indicate that the richness and diversity of methanogens in the intestinal tract of black and carp grass carp were highly correlated with the cultured water. Five bacterial genera were found in the three sets of samples, Methanosarcina, Methanocorpusculum, Methanospirillum, Methanobacterium and Methanofollis, in which Methanosarcina and Methanocorpusculum were the dominant genera. In addition, Methanosarcina had the greatest amount in grass carp and Methanocorpusculum had the greatest quantity in black carp. In conclusion, Methanosarcina and Methanocorpusculum were the main methanogens in the digestive tract of black and grass carp and culture water, and hydrolytic fermentative bacteria were its main metabolic substrate, hydrotrophic was its main metabolic pathway. The results will provide a reference for the relationship between intestinal methanogens and aquaculture and the greenhouse effect.

Oligonucleotide subsets selection by single nucleotide resolution barcode identification

Effective subset selection from complex oligonucleotide libraries is crucial for genomics, synthetic biology, and DNA data storage. The polymerase chain reaction, foundational for amplifying target subsets is limited by primer design and length for specificity, which constrains the scalability of oligo libraries and increases the synthesis burden for primers. We introduce an oligo subset selection methodology that utilizes sequence-specific cyclic nucleotide synthesis and blocking of the template oligos. This approach eliminates the need for primers for selective hybridization and enables the encoding and selection of hundreds of subsets with barcode lengths of fewer than five nucleotides. Moreover, cyclic selection enables a hierarchical data structure in the oligo library, enhancing the programmability. This advancement offers a scalable and cost-effective solution for handling complex oligo libraries.

Multi-Omic Analysis of the Differences in Growth and Metabolic Mechanisms Between Chinese Domestic Cattle and Simmental Crossbred Cattle

In livestock production, deeply understanding the molecular mechanisms of growth and metabolic differences in different breeds of cattle is of great significance for optimizing breeding strategies, improving meat quality, and promoting sustainable development. This study aims to comprehensively reveal the molecular-level differences between Chinese domestic cattle and Simmental crossbred cattle through multi-omics analysis, and further provide a theoretical basis for the efficient development of the beef cattle industry. The domestic cattle in China are a unique genetic breed resource. They have characteristics like small size, strong adaptability, and distinctive meat quality. There are significant differences in the growth rate and meat production between these domestic cattle and Simmental hybrid cattle. However, the specific molecular-level differences between them are still unclear. This study conducted a comprehensive comparison between the domestic cattle in China and Simmental crossbred cattle, focusing on microbiology, short-chain fatty acids, blood metabolome, and transcriptome. The results revealed notable differences in the microbial Simpson index between the domestic and Simmental crossbred cattle. The differential strain Akkermansia was found to be highly negatively correlated with the differential short-chain fatty acid isocaproic acid, suggesting that Akkermansia may play a key role in the differences observed in isocaproic acid levels or phenotypes. Furthermore, the transcriptional metabolomics analysis indicated that the differentially expressed genes and metabolites were co-enriched in pathways related to insulin secretion, thyroid hormone synthesis, bile secretion, aldosterone synthesis and secretion, and Cyclic Adenosine Monophosphate (cAMP) signaling pathways. Key genes such as ADCY8 and 1-oleoyl-sn-glycero-3-phosphocholine emerged as crucial regulators of growth and metabolism in beef cattle.

Population-scale cellular GUIDE-seq-2 and biochemical CHANGE-seq-R profiles reveal human genetic variation frequently affects Cas9 off-target activity

Genome editing enzymes can introduce targeted changes to the DNA in living cells 1-4 , transforming biological research and enabling the first approved gene editing therapy for sickle cell disease 5 . However, their genome-wide activity can be altered by genetic variation at on- or off-target sites 6-8 , potentially impacting both their precision and therapeutic safety. Due to a lack of scalable methods to measure genome-wide editing activity in cells from large populations and diverse target libraries, the frequency and extent of these variant effects on editing remains unknown. Here, we present the first population-scale study of how genetic variation affects the cellular genome-wide activity of CRISPR-Cas9, enabled by a novel, sensitive, and unbiased cellular assay, GUIDE-seq-2 with improved scalability and accuracy compared to the original broadly adopted method 9 . Analyzing Cas9 genome-wide activity at 1,115 on- and off-target sites across six guide RNAs in cells from 95 individuals spanning four genetically diverse populations, we found that variants frequently overlap off-target sites, with 13% significantly altering Cas9 editing activity by up to 33% indels. To understand common features of high-impact variants, we developed a new massively parallel biochemical assay, CHANGE-seq-R, to measure Cas9 activity across millions of mismatched target sites, and trained a deep neural network model, CHANGE-net, to accurately predict and interpret the effects of single-nucleotide variants on off-targets with up to six mismatches. Taken together, our findings illuminate a path to account for genetic variation when designing genome editing strategies for research and therapeutics.

The occurrence of wheat crown rot correlates with the microbial community and function in rhizosphere soil

Wheat crown rot (WCR) is a significant soil-borne disease affecting wheat production worldwide. Understanding the impact of wheat crown rot on the structure and function of microbial communities in the wheat rhizosphere soil can provide a theoretical basis for the mining biological control resources against WCR. In this study, rhizosphere soils with varying WCR severities (light, moderate, severe) were analyzed for chemical properties, microbial community composition and functions using high-throughput sequencing. The results revealed that WCR decreased rhizosphere soil pH, the content of available nitrogen and phosphorus, and the abundance of beneficial taxa such as Bacillus and Streptomyces. Additionally, functional predictions showed that microbial communities adapted to WCR by enhancing signaling pathways and reducing their anabolic activity. From soil with light WCR occurrence, we isolated Bacillus velezensis BF-237, whose abundance was reduced by WCR. Greenhouse experiments demonstrated that BF-237 achieved a control efficiency of 56.61% against WCR in artificially inoculated sterilized soil and 53.32% in natural soil. This study clarifies the impact of wheat crown rot on the community structure, and function of rhizosphere soil microorganisms, alongside identifying a promising biocontrol agent. These findings contribute to understanding WCR pathogenesis and offer practical resources for its management.

Complete genome sequence of Schlesneria sp. strain DSM 10557, isolated from the leachate of an industrial compost heap

We present the complete genome of Schlesneria sp. DSM 10557, isolated from compost heap leakage (leachate). The genome consists of a single chromosome (7,067,087 bp) with a GC content of 56.48%. Genome-based phylogenetic analysis revealed that strain DSM 10557 is most closely related to members of the genus Schlesneria.

Draft genome sequences of Kluyveromyces marxianus strain U848 isolated from Agave sisalana

Kluyveromyces marxianus is a yeast widely used in the dairy industry and frequently isolated from vineyards and wineries. Its capacity to metabolize diverse sugars makes it highly promising for winemaking applications. We report the draft genome sequence of the K. marxianus strain U848.

Effect of Hemp Seed Oil on Milk Performance, Blood Parameters, Milk Fatty Acid Profile, and Rumen Microbial Population in Milk-Producing Buffalo: Preliminary Study

Vegetable oils rich in unsaturated fatty acids have been shown to improve animal health and enrich milk with functional fatty acids in various studies. This study investigates the effects of dietary supplementation with hemp seed oil (HSO), a native vegetable oil from the "longevity village" of Bama (Guangxi, China), on the milk performance, milk fatty acid composition, blood indicators, and rumen bacterial community of milk-producing buffalo. Seventeen healthy, four-year-old, crossbred, milk-producing buffaloes with the same parity (three), as well as similar body weights (BW = 580 ± 25 kg), number of days producing milk (DIM, 153 ± 10 d), and milk yields (8.56 ± 0.89 kg/d) were divided into three groups (n = 6, 5, and 6) and assigned to the following diets: (1) no HSO supplement (H0, n = 6), (2) a supplement of 100 g/d of HSO (H1, n = 5), and (3) a supplement of 200 g/d of HSO (H2, n = 6). The total experimental period was 42 days (including a 14-day adaptation period and a 28-day treatment period). The data were statistically analyzed by repeated measures analysis of variance. The results showed that compared to that of no HSO supplement group, the dry matter intake (DMI) showed a decreasing tendency (p = 0.06), while feed efficiency and rumen fermentation remained similar across all the groups (p > 0.05) with dietary HSO supplementation. Moreover, with dietary HSO supplementation, the total antioxidant capacity (T-AOC) (p = 0.05) and catalase (CAT) (p < 0.01) and glutathione peroxidase (GSH-Px) (p = 0.02) contents in the serum were greatly increased, with the highest levels observed in the H2 group (increased by 1.16 U/mL, 1.15 U/mL, and 134.51 U/mL, respectively). In contrast, the malondialdehyde (MDA) content was significantly decreased with dietary HSO supplementation (p = 0.02) and was the lowest in the H1 group (decreased by 0.72 nmol/mL). The high-density lipoprotein cholesterol (HDL-C) content in the blood showed an increasing tendency with dietary HSO supplementation (p = 0.09). Moreover, with dietary HSO supplementation, the proportions of C18:0 (p = 0.02), C18:1n9t (p = 0.02), C18:2n6c (p = 0.02), C18:3n3 (p < 0.01), C18:2n9c (p = 0.04), omega-3 (p = 0.02), and omega-6 (p = 0.02) were significantly increased, with the highest levels observed in the H2 group (increased by 5.29 g/100 g FA, 1.81 g/100 g FA, 0.55 g/100 g FA, 0.14 g/100 g FA, 0.75 g/100 g FA, 0.17 g/100 g FA, and 0.56 g/100 g FA, respectively). Additionally, rumen Acetobacter abundance was significantly affected by HSO addition (p = 0.03), with rumen Acetobacter abundance decreasing in the H1 group (by 0.55%) and increasing in the H2 group (by 0.73%). These results suggest that adding HSO to milk-producing buffalo diets does not affect feed efficiency or rumen fermentation, although it decreases the DMI. Meanwhile, it can improve the nutritional quality of milk, enhance the antioxidant status, and regulate blood lipid metabolism in milk-producing buffaloes.

Functionality of bacterial communities in constructed wetlands used for water purification: influence of root components and seasonality

Introduction

Constructed wetlands have become crucial ecosystems for the purification of industrial and agricultural water. The health of wetland plants and the efficacy of water purification are strongly influenced by root-associated bacteria. However, our understanding of the functions of bacterial communities in the plant different root components (i.e., rhizosphere, rhizoplane, and endosphere) and their impact on water purification is still limited.

Methods

To address this knowledge gap, we employed high-resolution 16S rRNA deep amplicon sequencing to explore the bacterial community structure and assembly within the root components of three plant species (i.e. Iris ensata, Canna indica, and Hymenocallis littoralis) found in constructed wetlands.

Results

Our findings revealed that the pollutant removal efficiency was higher in the wet season than in the dry season. The specific root compartment, plant species, environmental factors, and seasonality significantly influenced the bacterial composition, diversity and abundance. Across all three plant species, Proteobacteria emerged as the dominant bacterial groups in all root components. The abundance and diversity of bacterial communities exhibited a decline from the rhizosphere to the endosphere, accompanied by an increase in the number of distinctive biomarkers from the rhizosphere to the endosphere. The bacterial composition exhibited significant similarity in the rhizosphere in the dry season and the endosphere in the wet season. Bacterial genes in the rhizosphere-rhizoplane were associated with environmental information processing, transportation and metabolism, while those in the rhizoplane-endosphere primarily handle metabolic processes. The bacterial community positively correlated with total nitrogen content, chemical oxygen demand, and NO4 +-N in the dry season, while associated with total phosphorus, total organic carbon, and NO3 +-N content in the wet season.

Discussion

The structure and function of the bacterial community within the root rhizoplane-endosphere can serve as indicators of the water purification efficacy of constructed wetlands.

Micro-/nanobubble oxygenation irrigation enhances soil phosphorus availability and yield by altering soil bacterial community abundance and core microbial populations

Micro-/nanobubble oxygenation irrigation, as a novel irrigation technique, has been widely utilized to enhance soil phosphorus availability and maize yield. Nevertheless, currently, most of the studies remain unclear about the precise mechanism through which micro-/nanobubble oxygenation improves soil phosphorus availability and maize yield. Therefore, we established two irrigation methods, conventional irrigation (CF) and micro-/nanobubble oxygenation irrigation (MB), to investigate the combined effects on enzyme activity, microbial communities, and soil phosphorus availability in the rhizosphere soil of maize.The results showed that compared to the CF treatment, the MB treatment significantly increased available phosphorus content and alkaline phosphatase activity in maize rhizosphere soil by 21.3% and 15.4%, respectively. Furthermore, MB significantly influenced bacterial diversity in the maize rhizosphere soil but did not considerably affect fungal diversity. Specifically, MB regulated the microbial community structure in the maize rhizosphere by altering the relative abundances of the bacterial phylum Firmicutes and the fungal phyla Mucoromycota, Chytridiomycota, and Basidiomycota. In addition, MB reduced the complexity of the bacterial network while increasing the interaction density among bacterial species. Meanwhile, MB enhanced the complexity of the fungal network. Structural equation modeling indicated that MB primarily promoted soil alkaline phosphatase activity by regulating bacterial community diversity, thereby enhancing soil phosphorus availability. In conclusion, the application of micro-/nanobubble oxygenation irrigation enhances the activity of alkaline phosphatasein the soil by modulating the microbial community within the rhizosphere, thereby facilitating increased phosphorus availability in the rhizosphere of maize.

Three local plants adapt to ecological restoration of abandoned lead-zinc mines through assembly of rhizosphere bacterial communities

Introduction

The plant restoration and ecological restoration of lead-zinc mines are very important.

Methods

In this study, we used three local plants to carry out ecological restoration of abandoned lead-zinc mining areas and detected the adaptive mechanisms of soil bacterial diversity and function during the ecological restoration of lead-zinc mines through 16S rRNA sequencing.

Results

The results revealed that lead-zinc mining significantly reduced the soil bacterial diversity, including the Shannon, Simpson, and observed species indices, whereas the planting of the three ecological restoration plants restored the soil microbial diversity to a certain extent, leading to increases in the Shannon index and Observed species indices. Mining activities significantly reduced the abundances of RB41 and Bryobacter in the bulk soil compared with those in the nonmining areas, whereas the three ecological restoration plants increased the abundances of RB41 and Bryobacter in the rhizosphere soil compared with those in the bulk soil in the mining areas. Following the planting of the three types of ecologically restored plants, the soil bacterial community structure partially recovered. In addition, different plants have been found to have different functions in the lead-zinc ecological restoration process, including iron complex transport system-permitting proteins and ATP binding cassettes.

Discussion

This study confirms for the first time that plants adapt to the remediation process of abandoned lead-zinc mines by non-randomly assembling rhizosphere bacterial communities and functions, providing a reference for screening microbial remediation bacterial resources and plant microbe joint bioremediation strategies for lead-zinc mines.

Study on the synergistic mechanisms of fungal biodiversity and ecosystem multifunctionality across vegetation diversity gradients

Ecosystem multifunctionality denotes the capacity of an ecosystem to deliver various functions and services concurrently, emphasizing the overall effectiveness of these functions. Although biodiversity is intrinsically linked to ecosystem multifunctionality, research on the determinants of changes in this relationship remains limited. This study focused on 147 research plots across various ecosystems in the Lüliang region. Through high-throughput sequencing and data modeling, it was revealed that there exists a significant positive correlation between soil fungal biodiversity and ecosystem multifunctionality (P < 0.05). Notably, this correlation was found to be influenced by specialists and vegetation diversity. The specific results supporting this finding are presented as follows: 1) By means of linear regression and the establishment of various models, it was indicated that specialists exert a more substantial influence on the fungal biodiversity-ecosystem multifunctionality (BEF) relationship compared to generalists. 2) Moving window analysis demonstrated that changes in vegetation diversity affected BEF relationships within fungal communities, leading to synergistic shifts. As vegetation diversity increased, co-occurrence networks generally simplified, and the positive fungal BEF correlation was somewhat decreased. This study enhances the comprehension of fungal BEF relationships in natural ecosystems and provides a foundation for the development of effective management and conservation strategies in response to global changes.

Dynamic interplay of cNHEJ and MMEJ pathways of DNA double-strand break repair during embryonic development in zebrafish

Double strand breaks (DSBs) are the most deleterious DNA lesions as they frequently result in mutations when repaired by canonical non homologous end-joining (cNHEJ) and microhomology-mediated end-joining (MMEJ). Here, we investigated the relative importance of cNHEJ and MMEJ pathways during zebrafish embryonic development. We have analyzed the expression of cNHEJ and MMEJ related genes and found that it was dynamic during development and often become increased in specific tissues. We showed that inactivation of nuclear DNA ligase 3 (nLig3) or DNA polymerase theta (Polθ), two key MMEJ factors, did not affect zebrafish development but sensitized embryos to ionizing radiations and that deficiency of Polθ, but not nLig3, profoundly alters the mutation spectrum induced during repair of Cas9-mediated DSBs. By contrast, inactivation of DNA ligase 4, required for cNHEJ, did not seem to sensitize embryos to ionizing radiations nor to affect repair of Cas9-mediated DSBs but resulted in important larval growth defects. Our study underscores the dynamic and context-dependent roles of cNHEJ and MMEJ pathways during zebrafish development, highlighting their differential requirements across developmental stages and in response to genotoxic stress.

Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq

Eukaryotic genomes are extensively transcribed into various types of RNAs, many of which are physically associated with chromatin in cis at their transcription sites or in trans to other genomic loci. Emerging roles have been uncovered for these chromatin-associated RNAs (caRNAs) in gene regulation and genome organization, yet they remain challenging to interrogate. Here, we present TaDRIM-seq, a technique employing Protein G (PG)-Tn5-targeted DNA elements and in situ proximity ligation to concurrently probe caRNAs across diverse genomic regions as well as global RNA-RNA interactions within intact nuclei. Notably, this approach diminishes required cell inputs, minimizes hands-on time compared to established methodologies, and is compatible in both mammalian cells and plants. Using this technique, we identify extensive caRNAs at DNA anchor regions associated with chromatin loops and reveal diurnal variation in RNA-DNA and RNA-RNA connectivity networks within rice.

Microbiome Analysis of Area in Proximity to White Spot Lesions Reveals More Harmful Plant Pathogens in Maize

Plant microbiomes play a major role in plant health, growth, and development, enhancing resistance to pathogen invasion. However, despite the extensive research on the phyllosphere microbiome, it remains unclear how the microbiome of leaves in proximity to diseased leaves responds to pathogen invasion. We investigate the response of the maize phyllosphere microbiome to maize white spot by assessing the microbiome dynamics associated with the white spot portion and the area in proximity using 16S and ITS high-throughput sequencing analysis. Our results showed that the bacterial diversities were higher in the diseased portion and area in proximity to the spot than those in healthy plants. At the same time, lower fungal diversity was recorded in the diseased portion compared to portions in proximity to it and healthy leaves. The spot portion had a significant influence on the microbial composition. The diseased portion, the area in proximity to it, and the healthy leaves were dominated by the bacterial genera Sphingomonas, Delftia, Chryseobacterium, Stenotrophomonas, Methylobacterium-methylorubrum, and Bacteroides. Still, the abundance of Sphingomonas decreased in the healthy leaves with a corresponding increase in Stenotrophomonas. Conversely, the fungal genus Setophoma dominated the diseased portion, while the fungal pathogens Cladosporium, Alternaria, and Exserohilum were highly abundant in the samples from the area in proximity to it. In addition, a co-occurrence network analysis revealed a complex fungal network in healthy leaves and those in proximity to leaves infected with white spot compared to the diseased portion. This study suggests that the area in proximity to the maize leaf infected with white spot disease is colonized by more harmful plant pathogenic fungi for disease progression.

Comparative Analysis of Health, Inflammatory Markers, and Rumen Microbiota Between Mildly Lame and Healthy Cows

Bovine lameness leads to significant economic losses in the dairy industry. This study investigated the relationship between rumen microbiota and lameness in Holstein cows. Rumen fluid and blood samples were collected from 11 cows with mild lameness and 10 healthy cows before morning feeding. Using high-throughput sequencing and ELISA kits, we found that cows with lameness exhibited decreased rumen pH and increased lameness scores compared to healthy cows. Additionally, cows with lameness had higher blood concentrations of LPS, IL-1, IL-8, and TNF-α. Although there were no significant differences in microbial alpha diversity, principal coordinate analysis (PCoA) revealed significant differences in the rumen microbial structure between the two groups. Further analysis showed that the relative abundances of ruminal Clostridium_IV, Streptococcus, Bacillus, Acinetobacter, Desulfobulbus, Methanobrevibacter, and Mogibacterium were significantly higher in the lameness group, whereas Succinivibrio, Lachnobacterium, Elusimicrobium, Succiniclasticum, and Prevotella were significantly more abundant in the rumen of healthy cows. Importantly, the microbial interaction network in the rumen of cows with lameness was more complex, with key bacteria such as Mogibacterium dominating the microbial interaction network. This study highlights the relationship between rumen microbiota and lameness, providing insights into the prevention and treatment of bovine lameness.

Roles of core nosZ denitrifiers in enhancing denitrification activity under long-term rice straw retention

The denitrification process is known to contribute to soil nitrogen (N) loss, which is strongly affected by fertilization strategies; however, the effects of distinct straw retention modes on soil denitrification activity have rarely been discriminated and the underlying mechanisms remain unclear. This study coupled field and incubation experiments to explore the characteristics of soil denitrification activity, soil and standing water physicochemical properties, and the abundance, community diversity, and co-occurrence network of nosZ denitrifiers, based on a paddy field implementing 10-year straw retention under a rice-wheat rotation system. Four straw retention treatments with equivalent chemical fertilizers were applied, namely no straw (NS), wheat straw only (WS), rice straw only (RS), and wheat and rice straw (WRS). Results indicated a significant increase (by 41.93-45.80% when compared to that with NS) in the soil denitrification activity with RS and WRS. Correspondingly, treatments with rice straw retention resulted in the development of a similar community composition (P < 0.05), structure (P = 0.001), and more positively interconnected network, as well as similar specific keystone taxa of nosZ denitrifiers, relative to those in non-rice straw mode. Under long-term rice straw retention conditions, the core nosZ-denitrifying phylogroups shifted (r = 0.83, P < 0.001), with the recruitment of keystone taxa from the phyla Bacteroidetes and Euryarchaeota playing a key role in enhancing denitrification activity and stimulating N loss. Accordingly, in a rice-wheat rotation field, the practice of wheat straw retention in a single season is recommended because it will not markedly sacrifice soil N availability impaired by the denitrification process.