Bacterial Community Composition Research Articles

Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic

Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical–chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000–2020), intermediate (1978–2000), and late (1954–1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil’s higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.

Effects of Nitrogen Addition and Drought on Soil Microbial Diversity and Community Composition in a Young Tree Community

Soil microorganisms are well known to play a crucial role in carbon and nutrient cycling within terrestrial ecosystems. Numerous research efforts have demonstrated that nitrogen deposition can change forest soil microbial diversity and community composition; however, it is still unclear how nitrogen deposition will affect the soil microbial diversity and community composition in subtropical forests under the background of increasing drought. Consequently, over a period of 2.5 years, we carried out an experiment using two N addition regimes and three soil water treatment levels to reveal the effects of nitrogen, drought, and the influence of their interaction on the diversity and community composition of soil microorganisms. Overall, we found that both N addition and drought decreased the bacterial Shannon and Simpson indices yet had no significant effect on fungal diversity. In the well-watered treatments, nitrogen addition did not significantly reduce bacterial diversity, while in the moderate drought and severe drought treatments, N addition significantly decreased bacterial diversity, reducing the Shannon and Simpson indices by 27.05% and 0.13%, respectively, in the severe drought treatment. Drought significantly altered the community composition of bacteria regardless of N addition. N addition significantly changed the community composition of bacteria under moderate drought treatments, while both N addition and drought had less significant effects on the fungal community composition. The soil water content, fine root biomass, and soil pH were significantly correlated with bacterial community composition, which explained 53.3%, 11.1%, and 8.7% of the changes in soil bacterial community composition, respectively. These results suggest that drought may intensify the inhibitory effect of nitrogen on bacterial diversity and change the magnitude and direction of the impact of nitrogen on the composition of the bacterial community.

Impacts of pseudomonas fluorescent bacterial fertilizer addition on the soil environment and fruit yield under water stress in greenhouse grape

Bacterial fertilizers, which contain beneficial soil microorganisms, are becoming more widely used as they can mitigate the problems of crop yields reduction and soil environment degradation caused by the overuse of chemical fertilizer. However, the impact of bacterial fertilizer on greenhouse grape yields and the rhizosphere soil environment has not been assessed in arid and semi-arid region of Northwest China. Thus, a 2-year field trial was conducted with five treatments: adequate water supply without bacterial fertilizer (CK); mild (W1), moderate (W2) water stress and small (F1), maximize (F2) fertilizer cross-combination, respectively. The results indicated that water stress had a negative impact on the accumulation of dissolved organic carbon (DOC), microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN) in the rhizosphere soil. The addition of pseudomonas fluorescent bacterial fertilizer significantly increased the content of available phosphorus (AP), DOC, MBC and MBN content. The W1F2 treatment significantly increased the activities of urease, catalase and sucrase (p < 0.05). The W1F1 and W1F2 treatments increased fungal and bacterial diversity. Bacterial community composition was closely related to soil total organic carbon (TOC), soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), MBC, and sucrase, while fungi community composition was significantly related to Nitrate-N (NO3−-N), TN, and sucrase. Additionally, compared with CK treatment the yield and economic benefit of the W1F2 treatment increased by 35.44 and 44.04%, respectively. Therefore, W1F2 is recommended as the optimal water and fertilizer management scheme for efficient greenhouse grape production in the arid and semi-arid region of Northwest China.

Microbiota of Punctuated Snake Eel Ophichthus remiger (Valenciennes, 1842) Reared in Recirculation System Is Dominated by Latilactobacillus

Research on microbiota has underscored the crucial influence of microbial communities on numerous biological functions that yield positive outcomes for the host, such as digestion, nutrient metabolism, resistance against pathogen invasion, and growth performance. Concurrently, numerous variables, including the host’s diet, genetics, and physiological condition and environmental factors, influence the gut microbiota. Our study aims to characterize the bacterial community composition of the common snake eel (Ophichthus remiger), captured wild and then reared under controlled conditions. We employed a 16S rRNA gene-based approach facilitated by next-generation sequencing to conduct this analysis. The gut microbiota of the snake eel was highly dominated by bacteria from the phylum Firmicutes, comprising over 80% of the relative abundance, with Lactilactobacillus being the most important genus. The results suggest that feed-associated bacteria may influence the composition of the microbiota, contributing the most relevant bacteria within the intestinal content. This study provides the first comprehensive analysis of the gut microbiota in Ophichthus remiger, offering novel insights into the potential roles of Firmicutes and Lactilactobacillus in marine eels.

Responses of a soil-inhabiting collembolan (Entomobrya proxima Folsom) to organic fertilizer addition illustrated by functional traits and gut bacterial community

IntroductionOrganic fertilizer offers significant advantages for sustainable agricultural development compared to inorganic fertilizers and is increasingly becoming the predominant fertilizer strategy. Functional traits and gut microbiota of soil fauna are recognized as potential indicators of environmental changes. However, there is a dearth of research examining the correlation between functional traits and intestinal microorganisms in response to organic fertilizer.MethodsIn this study, we selected Entomobrya proxima Folsom, a predominant soil collembolan species found in cropland across North China, as our subject of study. We set treatments with no organic fertilizer (CK) and three different concentrations of organic fertilizer at 1% (O1), 6% (O2), and 10% (O3). Stereomicroscopy and high-throughput amplicon sequencing were employed to elucidate the response of soil fauna to organic fertilizer through host functional traits and associated gut microbial communities.ResultsThe results indicated that the impact of organic fertilizer on the functional traits of collembolans was closely linked to the input concentration. Specifically, low input concentrations positively influenced all functional traits of Entomobrya proxima Folsom; conversely, higher input concentrations exerted an overall detrimental effect. For the gut bacterial community, the addition of organic fertilizer resulted in a significant decrease in abundance, adversely affected α-diversity, and significantly altered the structure of the gut bacterial community compared to CK. However, there was no significant effect of fertilizer concentration on these three parameters. The composition of the gut bacterial community varied due to the addition of organic fertilizer, with significant changes observed in the relative abundances of six phyla and three genera. Furthermore, body length and foreleg length may serve as potential indicators for characterizing the proportions of Alcanivorax and Sphingobacterium of gut bacterial community. Additionally, the assembly process of the gut bacterial community was strongly influenced by the amount of organic fertilizer added; this led to a narrowing niche width that is believed to contribute to an increase in species richness.DiscussionIn conclusion, adding organic fertilizer exerted multiple impacts on soil fauna, with effect sizes related to its concentration. These findings provide insights for conserving soil animals while maximizing their ecological functions and offer perspectives on optimizing sustainable agricultural management practices.

Correlating Feed Efficiency with Ruminal Bacterial, Fungal, and Archaeal Community Composition in Dairy Cows over Two Lactations

Dairy cows rely on their complex rumen microbial community to convert host-indigestible feed into nutrients usable for host growth, maintenance, and milk production. Previous work by our group found that the rumen bacterial community is dynamic over the course of two lactations and that cows with high and low milk production efficiency (MPE) have different taxa associated with either phenotype. Here, we characterized the ruminal fungal and archaeal communities to determine if these microbial populations exhibit properties similar to that of the rumen bacteria with respect to MPE over time. Our results show a decrease in fungal diversity over the course of both lactation cycles with an increase during the transition period. The fungal community had only a few taxa associated with efficiency. For the ruminal archaea, we found no change in diversity across both lactation cycles and only taxa in the genus Methanospera were found to be more abundant in high-MPE cows. Given that our previous study used 454 pyrosequencing, we also sought to determine if a resequencing of these communities using Illumina-based technology would alter our previous findings. We found that resequencing showed no significant deviation from our original broad conclusions, with the exception of some minor taxonomic associations.

Cultivation of Genetically Modified Soybeans Did Not Alter the Overall Structure of Rhizosphere Soil Microbial Communities

Herbicide-tolerant soybeans are the most extensively cultivated genetically modified (GM) crop globally. The effects of GM soybean and associated agronomic practices on soil microbial communities remain poorly understood. This study aimed to investigate the impact of planting GM soybeans with a glyphosate application on soil microbial diversity. The main bacterial and fungal community compositions (phylum level) were consistent for GM and non-GM soybeans. The alpha diversity analysis indicated that the bacterial Shannon index was significantly higher in GM rhizosphere soil during flowering compared to non-GM soil. There were no significant differences in the Shannon, Simpson, or ACE indices of the soil fungal communities between GM and non-GM soybeans in the same period. The PCoA analysis showed no significant differences in community structure between the GM and non-GM soybean soil for either fungi or bacteria during the same period. Although the relative abundance of Bradyrhizobium at the seedling stage was significantly lower in those GM than in those non-GM, it did not affect the final number of root nodules in either soybean type. The relative abundance of Frankia was significantly lower in GM rhizosphere soil during the seedling and flowering stages, whereas that of Thelebolus was significantly higher during flowering and pod filling. The abundance and ecological functions of these taxa warrant continuous monitoring.

Net cage aquaculture alters the co-occurrence network and functions of bacterial communities in offshore areas

A better understanding of bacterial communities and the factors that drive them is essential to maintain their functions and services. As an ecosystem closely linked to human activities, the health of offshore aquaculture depends on the diversity and functions of bacteria in its environment. However, little attention has been paid to the vertical interface of the offshore aquaculture areas with shellfish net cages. In this study, high-throughput sequencing was used to analyze bacterial communities in different water layers of a net cage scallop farm in the offshore area of Northeast of China. Based on the results, an increased richness of bacterial communities was observed in the water adjacent to the net cages. Meanwhile, apparently different bacterial community compositions were observed among the water layers, with an enrichment of Cyanobacteria, Bacteroidota, and Firmicutes in the water layers above, parallel to, and below the net cages, respectively. According to the predicted functions, the bacterial communities of the water layers above, parallel to, and below the net cages were identified as phototrophy-, chemoheterotrophy-, and nitrogen respiration-dominated. Furthermore, network analysis revealed a complex but unstable bacterial community in the water layer containing the net cage. Finally, partial least squares path modelling revealed that the net cage aquaculture directly influenced the environmental variables and bacterial richness, which further induced the variations in bacterial community composition, and ultimately affected their ecological functions. These results provide a basic understanding of bacterial communities in net cage scallop farms and highlight the effects of offshore aquaculture on variations in ecological functions.

Long-term biochar-based fertilizer substitution promotes carbon, nitrogen, and phosphorus acquisition enzymes in dryland soils by affecting soil properties and regulating bacterial community

Biochar-based fertilizers have shown positive effects on soil function, an understanding of how long-term biochar-based fertilizers substitution affects soil properties, microbial communities, and enzyme activities in dryland is lacking. We investigated the impacts of seven years biochar-based fertilizer substitution on the soil properties, bacterial community, and carbon (C), nitrogen (N), and phosphorus (P) acquisition-related enzymes in a dryland cauliflower-maize rotation. Four fertilization strategies were set up: no fertilizer (CK), chemical fertilizer (CF), 30 % replacement of chemical N with biochar-based fertilizer (LBF), and 60 % replacement of chemical N with biochar-based fertilizer (HBF). Results elucidated that biochar-based fertilizer substitution treatments had higher soil organic C (SOC) and nutrients (N, P, and potassium (K)) than non-biochar-based fertilizer treatments. Biochar-based fertilizer substitution improved C-, N-, and P-acquiring enzyme activities and C:N enzyme ratio, but decreased C:P and N:P enzyme ratios. We further found that biochar-based fertilizer substitution altered the soil bacterial community diversity and composition. Soil properties and bacterial community explained most variations in C-, N-, and P-acquiring enzymes. Modeling analysis revealed that biochar-based fertilizer substitution had positive effects on soil properties and bacterial community, which further positively regulated soil C-, N-, and P-acquiring enzymes. Key factors driving enzyme variations included available P, SOC, available K, available N, total K, and total N, as well as soil bacterial community composition and diversity. In conclusion, biochar-based fertilizer substitution could enhance C-, N-, and P-acquiring enzyme activities by boosting soil nutrient levels and altering bacterial community in dryland fields.

Insights into the functionality of biofilm-forming bacterial consortia as bioavailability enhancers towards biodegradation of pyrene in hydrocarbon-contaminated soil.

Hydrophobic organic compounds (HOCs), such as pyrene, pose significant challenges for microbial-based remediation in soil due to limited substrate availability and the sustainability of augmented microbes. Research targets are to investigate the potential of biofilm-forming bacterial cells to enhance pyrene bioavailability and biodegradation in two different hydrocarbon-contaminated soil microcosms, employing microbiological, molecular, and chemical analysis validated through statistical tools. The microcosm augmented with strong biofilm bacterial consortia (A) significantly enhanced pyrene availability by 1-1.5% compared to the weak biofilm consortia (B) and mixed consortia (AB). Analysis of 16S rDNA amplicons revealed notable differences in bacterial community composition between consortia A and B augmented soil, with Proteobacteria as the dominant phylum. Taxonomic composition of soil microbiome predicted enhanced xenobiotic biodegradative potential of strong biofilm consortia (A) up to 20 days, exhibiting a higher abundance of functional genes related to upstream degradative pathway of PAHs, such as naphthalene dioxygenase (nahAa), PAH dioxygenase subunit genes (nidA, nidB), extradiol dioxygenase (phdF) and aldehyde dehydrogenase (nidD). Our study highlights the significant role of biofilm-forming bacteria as "bioavailability enhancers," for high molecular weight PAHs like pyrene, in contaminated soils with their implications for designing future sustainable bioremediation programs.

Bacterial community composition and metabolic characteristics of three representative Marine areas in northern China

Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.

Spatial distribution of bacteria in response to phytoplankton community and multiple environmental factors in surface waters in Sanggou Bay.

Coastal bays link terrestrial and oceanic carbon reservoirs and play important roles in marine carbon cycles. Particulate organic carbon (POC) produced by phytoplankton is a major autochthonous carbon source in coastal bays. Previous studies on the fate of POC produced by phytoplankton mainly focused on the relationship between phytoplankton and zooplankton in classic food webs, while our knowledge on the roles of bacterioplankton is still limited, particularly in bays under highly intensive aquaculture activities. Here, we investigated bacterial community structure, and the influence of environmental factors and phytoplankton biomass and community structure based on samples collected in August 2022 from Sanggou Bay, a typical aquaculture bay in northern China. Environmental conditions, phytoplankton and bacterial community structure differed significantly between different aquaculture areas, showing higher relative abundance of Synechococcus sp. in the mixing area of shellfish and kelp culture (Area II) than the shellfish culture area (Area I). In contrast, Marivita cryptomonadis was more abundant in Area I, associated with elevated dissolved inorganic nitrogen (DIN), POC, POC/PN (the molar ratio of POC to particulate nitrogen) and sterol-derived total phytoplankton biomass. The strong correlation between total phytoplankton biomass and particle-associated bacteria indicated the important role of this bacterial fraction in processing organic compounds produced by phytoplankton. Significant correlations between bacterial community composition and POC/PN suggested more organic carbon potentially entering detrital biomass pools in Area I compared to Area II. Our results suggest that spatial distribution patterns of bacterial community structure were regulated by multiple abiotic and biotic factors and had a profound impact on the fate of organic carbon under highly intensive aquaculture activities in Sanggou Bay.

Elevational patterns in the diversity and composition of soil archaeal and bacterial communities depend on climate, vegetation, and soil properties in an arid mountain ecosystem

Elevational patterns in the diversity and composition of soil archaeal and bacterial communities depend on climate, vegetation, and soil properties in an arid mountain ecosystem

Microbial recruitment and microbial ecological roles in soil nutrient cycling of Populus cathayana males and females

Soil nitrogen (N) availability influences plant production and soil nutrient cycling. However, how it influences sex-specific microbial community composition and rhizosphere nutrient cycling in dioecious plant species is poorly understood. We examined the rhizospheric bacterial and fungal community assemble and their influences on soil nutrient cycling under different N backgrounds in 30-year-old experimental stands and a soil microbial reshaping-controlled experiment. In comparison to male trees, female trees increased fungal community diversity, and the relative abundance of taxa related to nutrient availability; elevated phosphorus (P) mobilization by increasing acidic phosphatase activity and carboxylic acid release; and decreased the counts of denitrification nirS, nirK, and nosZ genes at high N supply. Males increased the nifH gene counts related to microbial N fixation at high N supply. Low N supply increased N fixation nifH gene counts in the rhizosphere of females. Males decreased bacterial and fungal diversity, increased enzymatic activities related to organic N and P mineralization, and elevated soil nitrate-nitrogen levels at low N supply. Our results indicate that sex-specific responses to N availability are associated with rhizospheric bacterial and fungal community composition and diversity and their effects on rhizospheric nutrient cycling, which may explain sex-specific resource utilization and niche differentiation.

Warming reduces bacterial diversity and stability in Lake Bosten.

Understanding the effects of warming on bacterial communities is essential for predicting microbial responses to climate change in aquatic ecosystems. However, the mechanisms through which warming influences bacterial diversity and stability in lake ecosystems remain poorly understood. To address this gap, we conducted a mesocosm experiment in Lake Bosten, a climate change hotspot, with three temperature scenarios (26°C, 29°C, and 32°C), and investigated bacterial diversity, community composition, potential functions, and stability. Our findings revealed that temperature, time, and their interactions significantly reduced bacterial α-diversity (two-way ANOVA: P<0.05). Warming altered bacterial potential metabolic functions, with decreases in methanotrophy and methylotrophy and increases in phototrophy and photoheterotrophy. Warming also increased species replacement within bacterial communities, indicating a dynamic shift in community composition. Network analysis indicated heightened complexity under higher temperatures but also a decrease in bacterial stability, evidenced by higher average variation degree (AVD), increased vulnerability, and reduced robustness. Overall, our study highlights the profound effects of warming on the ecological dynamics of lake bacterial communities, underscoring the need for further research to understand and mitigate the impacts of global climate change on aquatic ecosystems.

Interactions Between Bacterivorous Nematodes and Bacteria Reduce N2O Emissions.

Trophic interactions in micro-food webs, such as those between nematodes and their bacterial prey, affect nitrogen cycling in soils, potentially changing nitrous oxide (N2O) production and consumption. However, how nematode-mediated changes in soil bacterial community composition affect soil N2O emissions is largely unknown. Here, microcosm experiments are performed with the bacterial feeding nematode Protorhabditis to explore the potential of nematodes in regulating microbial communities and thereby soil N2O emissions. Removal of nematodes by defaunation resulted in increased N2O emissions, with the removal of Protorhabditis contributing most to this increase. Further, inoculation with Protorhabditis altered bacterial community composition and increased the relative abundance of Bacillus, and the abundance of the nosZ gene in soil. In vitro experiments indicated that Protorhabditis reinforce the reduction in N2O emissions by Bacillus due to suppressing competitors and producing bacteria growth stimulating substances such as betaine. The results indicate that interactions between nematodes and bacteria modify N2O emissions providing the perspective for the mitigation of greenhouse gas emissions via manipulating trophic interactions in soil.

Nisin A-producing Lactococcus cremoris formulations for pre- and post-milking teat disinfection modulate the bovine milk microbiota

BackgroundBovine mastitis is a major challenge in dairy farms. Since the agents commonly used for pre- and post-dipping can affect the udder health by modifying milk microbiota, alternative products are needed. This study aimed to evaluate the effect of the use of pre- and post-dipping formulations containing the fermented broth of Nisin A-producing Lactococcus cremoris FT27 strain (treated group, TR) on the abundance and biodiversity of milk microbiota as compared to iodine-based commercial disinfectants (control group, CTR) during a three-month trial. The experiment was conducted on 20 dairy cows, divided into two groups (CTR and TR) of 10 lactating cows each. Milk samples were collected from two selected healthy quarters of each cow at 3 time-points. Microbial communities were investigated by cultural and sequence-based methods, and analyzed through bioinformatic and statistical approaches.ResultsClear differences in bacterial community composition were observed among groups, with higher species richness in TR, especially of Staphylococcus, Enterococcus, Lactococcus, and Streptococcus genera. The microbiota was dominated by Firmicutes, followed by Actinobacteriota, Proteobacteria, and Bacteroidota. Staphylococcaceae family was significantly higher in TR (p < 0.009), whereas Carnobacteriaceae, Mycobacteriaceae, and Pseudomonadaceae were significantly lower (p = 0.005, p = 0.001, and p = 0.040, respectively). CTR had considerably higher abundances of the genera Alkalibacterium (p = 0.011), Pseudomonas_E (p = 0.045), Corynebacterium (p = 0.004), and Alloiococcus (p = 0.004), and lower abundances of Staphylococcus (p < 0.009). Milk microbiota changed noticeably during the experimental period, regardless of treatment. A significant decrease was observed in both groups for Firmicutes_A phylum, with an increment in Actinobacteriota phylum, Propionibacteriaceae family, and Cutibacterium genus. Streptococcaceae significantly decreased in CTR (p = 0.013) and rose in TR (p = 0.001). Several differences were observed between the two groups during the experimental period. Streptococcus genus almost disappeared in CTR (p = 0.013), whereas it significantly increased in TR (p = 0.001). Three and twelve enriched groups were significantly identified respectively in CTR and TR using LEfSe.ConclusionsThe use of Nisin A-based teat dip formulations could be linked to greater microbial diversity compared to commercial products. Despite the influence of seasonality, the experimental formulations maintained higher milk biodiversity, suggesting that lactic acid bacteria metabolites prevent alterations in the milk microbiota.

Alterations in fecal bacteriome virome interplay and microbiota-derived dysfunction in patients with schizophrenia

Rising studies have consistently reported gut bacteriome alterations in schizophrenia (SCZ). However, little is known about the role of the gut virome on shaping the gut bacteriome in SCZ. Here in, we sequenced the fecal virome, bacteriome, and host peripheral metabolome in 49 SCZ patients and 49 health controls (HCs). We compared the gut bacterial community composition and specific abundant bacteria in SCZ patients and HCs. Specific gut viruses and host peripheral metabolites co-occurring with differential bacteria were identified using Multiple Co-inertia Analysis (MCIA). Additionally, we construct a latent serial mediation model (SMM) to investigate the effect of the gut virome on SCZ through the bacteriome and host metabolic profile. SCZ patients exhibited a decreased gut bacterial β-diversity compared to HCs, with seven differentially abundant bacteria, including Coprobacillaceae, Enterococcaceae etc. Gut viruses including Suoliviridae and Rountreeviridae, co-occur with these SCZ-related bacteria. We found that the viral-bacterial transkingdom correlations observed in HCs were dramatically lost in SCZ. The altered correlations profile observed in SCZ may impact microbiota-derived peripheral metabolites enriched in the bile acids pathway, eicosanoids pathway, and others, contributing to host immune dysfunction and inflammation. The SMM model suggested potential causal chains between gut viruses and SCZ, indicating that the effect of gut virome on SCZ is significantly mediated by bacteriome and metabolites. In conclusion, these findings provide a comprehensive perspective on the role of gut microbiota in the pathogenesis of SCZ. They reveal that patients with schizophrenia harbor an abnormal virome-bacteriome ecology, shedding light on the potential development of microbial therapeutics.

In vitro modeling of feline gut fermentation: a comprehensive analysis of fecal microbiota and metabolic activity

The gut microbiota (GM) is a large and diverse microbial community that plays essential roles in host health. The in vitro fermentation model of the fecal GM serves as a valuable complement to food and health research in both humans and animals. Despite advancements in standardized protocols for culturing human GM, research concerning animals—particularly companion animals—remains limited. This study aims to identify the optimal in vitro fermentation method for cat gut microbiota by comprehensively analyzing fecal microbiota and fermentation characteristics. We evaluated seven culture media previously used to simulate the gut microenvironment in humans, dogs, and cats: anaerobic medium base (AMB), Minimum medium (MM), Pet medium (PM), VI medium (VI), VL medium (VL), Yeast culture medium (JM), and yeast casitone fatty acid agar medium (YCFA). Fresh fecal samples were fermented in these media for 48 h, followed by 16S rRNA sequencing to assess bacterial community composition and targeted metabolite monitoring during fermentation. The results revealed that the substrate composition in the medium differentially impacts bacterial community structure and fermentation characteristics. High levels of carbon and nitrogen sources can substantially increase gas production, particularly CO2, while also significantly enhancing the production of short-chain fatty acids (SCFAs). Additionally, substrates with a high carbon-to-nitrogen ratio promote the production of more SCFAs and biogenic amines, and enrich the Bacteroidaceae family, even when the total substrate amount is lower. Comprehensive analysis of gut microbiota and metabolites reveals that PM medium effectively simulates a nutrient-deficient microenvironment in the cat gut during in vitro fermentation. This simulation maintains bacterial community stability and results in lower metabolite levels. Therefore, using PM medium to culture cat gut microbiota for 48 h, without focusing on specific bacterial genera, represents the most suitable in vitro model. This finding contributes to understanding the optimal conditions for simulate cat gut microbiota and may provide a new approach for investigating the food pharmaceuticals on the cat gut microbiota and related health.

Effects of baculovirus-killed cadavers on plant defenses and insect behavior

Baculoviruses are a group of entomopathogenic viruses that are important natural enemies of insects, particularly lepidopteran larvae. An important component of baculovirus transmission efficiency is the frequency with which hosts encounter patchily distributed virions on plants. Little is known about the ecology and bacterial composition of virus-killed cadavers. We used a baculovirus and host Trichoplusia ni caterpillars to study the effects of virus-killed cadavers on tomato plant defenses and T. ni behavior. We also compared bacterial communities associated with virus-killed and uninfected (freeze-killed) cadavers and found that there was no significant difference in community composition and membership between tomato-fed virus-killed or freeze-killed cadavers. Comparison of virus-killed cadavers from two separate experiments revealed significant differences in bacterial community composition, suggesting that host plant could play a more important role in shaping bacterial communities than virus infection status. Culture-dependent plating indicated that virus-killed cadavers had significantly higher bacterial titers compared with uninfected cadavers. We found that virus-killed cadavers suppressed polyphenol oxidase activity, an important plant defense protein, in mechanically damaged plants, but not in plants damaged by herbivory. Although cadavers did not influence plant defenses induced by feeding damage inflicted by healthy or infected T. ni, this study provides the first evidence that baculoviruses could influence plant defenses through host cadavers. When applied to intact plants, neither virus-killed or freeze-killed cadavers influenced T. ni oviposition, larval choice, or larval consumption, indicating these insects did not discriminate cadaver cues. Virus-killed cadavers could play important roles in mediating interactions between plants, herbivores, and other trophic levels, with potential implications for viral transmission dynamics.