Relative Abundance Of Actinobacteria Research Articles

Seasonal variations in composition and function of gut microbiota in grazing yaks: Implications for adaptation to dietary shift on the Qinghai-Tibet plateau.

Gut microbiome of animals is affected by external environmental factors and can assist them in adapting to changing environments effectively. Consequently, elucidating the gut microbes of animals under different environmental conditions can provide a comprehensive understanding of the mechanisms of their adaptations to environmental change, with a particular focus on animals in extreme environments. In this study, we compared the structural and functional differences of the gut microbiome of grazing yaks between the summer and winter seasons through metagenomic sequencing and bioinformatics analysis. The results indicated that the composition and function of microbes changed significantly. The study demonstrated an increase in the relative abundance of Actinobacteria and a higher ratio of Firmicutes to Bacteroidetes (F/B) in winter, this process facilitated the adaptation of yaks to the consumption of low-nutrient forages in the winter. Furthermore, the network structure exhibited greater complexity in the winter. Forage nutrition exhibited a significant seasonal variation, with a notable impact on the gut microbiota. The metagenomic analysis revealed an increase in the abundance of enzymes related to amino acid metabolism, axillary activity, and mucin degradation in the winter. In conclusion, this study demonstrated that the gut microbiome of grazing yaks exhibits several adaptive characteristics that facilitate better nutrient accessibility and acid the host in acclimating to the harsh winter conditions. Furthermore, our study offers novel insights into the mechanisms of highland animal adaptation to external environments from the perspective of the gut microbiome.

Risk investigation and diversity of microbial contamination during slaughter processing of yellow-feathered broiler

The cleanliness of slaughter process is very pivotal to ensure the safety of broiler products, and slaughter process is prone to cause microbial contamination since it involves a highly collaborative system including different operations. The procedures in slaughter processing are primary sources of bacterial contamination, and it is crucial for poultry industry to maximize product safety and quality by understanding the connection between bacterial diversity on chicken carcasses. The commercial yellow-feathered broiler plant was investigated to analysis the risk of microbial contamination. In this study, 16S rRNA sequencing was used to evaluate microbial diversity and microbial contamination was investigated by collecting 910 samples from different processing steps. Generally, total count of bacteria colonies ranged from 3.14 log CFU/cm2 to 5.68 log CFU/cm2, and the microbial load at yellow-feathered broiler carcass samples was significantly higher than that at environmental samples; moreover, the cutting areas were the high-risk areas of cross-contamination. In addition, the relative abundance of Actinobacteria (9.61%) at water samples was significantly higher than that at contact surfaces samples. This paper provides a valuable theoretical insight into the diversity and changes in the bacterial community during slaughter beneficial for enterprise managers further enhancing yellow-feathered chicken quality.

Carbon, nitrogen, and phosphorus release characteristics and underlying mechanisms in fish manure from recirculating aquaculture systems under alternating aerobic-anaerobic conditions

To mitigate the adverse environmental impacts of aquaculture operations, recirculating aquaculture systems (RASs) have emerged as promising alternatives to traditional aquaculture methods. Fish manure is the primary pollutant in RASs, and oxygen fluctuations significantly influencing the release of pollutants. However, the release characteristics and underlying mechanisms of carbon (C), nitrogen (N), and phosphorus (P) during alternating aerobic-anaerobic conditions in RASs remain poorly understood. This study conducted batch incubation experiments to examine the release dynamics of C, N, and P from fish manure under simulated alternating aerobic-anaerobic conditions. Results showed that the overlying water exhibited anaerobic and reductive conditions, with both COD and TOC concentrations decreasing over time. NH4+-N levels significantly decreased from days 1–9, while NO3--N concentrations peaked on day 16. Furthermore, the alternating aerobic-anaerobic conditions significantly increased TP concentration in the overlying water. Soluble microbial byproduct-like substances in the overlying water transformed into humic acid-like substances over time. The relative abundance of Proteobacteria and Firmicutes decreased by 13.6 % and 6 %, respectively, while the relative abundance of Actinobacteria, Bacteroidota, and Chloroflexi increased by 7 %, 12.8 %, and 1.4 %, respectively. Overall, both abiotic and biotic factors influenced the release of C, N, and P from fish manure. The coupled effects of abiotic factors, specific bacterial communities, and functional genes played a critical role in the release and transformation of these elements. These findings provide new insights into the release behaviours and mechanisms of pollutants in RASs, contributing to improved environmental risk management in RASs.

Prevention and Control of Ginger Blast by Two Fumigants and Their Effects on a Soil Bacterial Community and the Metabolic Components of Ginger

A two-year field trial was conducted in order to assess techniques to control ginger blast and explore the effects of fumigants on soil bacterial microorganisms and ginger metabolites. This study examined the effects of dazomet and chloropicrin on the control of ginger blast and their influence on ginger yield in Luoping County, Yunnan Province, China. The results showed that in 2022, the control effectiveness of dazomet and chloropicrin treatments on ginger blast was 84.33% and 94.67%, respectively. The corresponding yields were 50,154.40 kg/hm2 and 50,296.90 kg/hm2. In 2023, the control effectiveness of dazomet and chloropicrin treatments on ginger blast were 86.33% and 93.67%, respectively, and the yields were 65,115.83 kg/hm2 and 65,337.93 kg/hm2. In both years, the incidence of ginger blast in the control group reached nearly 100%, leading to the near extinction of the crop. Additionally, in 2023, 16S rRNA high-throughput sequencing and non-targeted metabolomics techniques were used to analyze the effects of the fumigants on soil bacterial microorganisms and the metabolites in ginger. The results showed that the diversity and richness of soil bacterial communities were lower than those in the control group at 0 and 120 days after treatment with two fumigants, but the relative abundances of beneficial bacteria such as Pseudomonas increased at 60 days, and the relative abundances of Actinobacteria, Gemmatimonadetes, and Bacillus increased at 120 days. The abundance of Firmicutes also increased after 120 days of chloropicrin treatment. The non-targeted metabolic LC–MS results showed that the production of phenols and terpenoids was upregulated after dazomet and chloropicrin treatments. The contents of amino acids and their derivatives were also upregulated. This upregulation of metabolites was beneficial to the flavor quality of ginger and enhanced its anti-inflammatory, anti-tumoral, and antioxidant effects.

Exploring the Organic Acid Secretion Pathway and Potassium Solubilization Ability of Pantoea vagans ZHS-1 for Enhanced Rice Growth.

Soil potassium deficiency is a common issue limiting agricultural productivity. Potassium-solubilizing bacteria (KSB) show significant potential in mitigating soil potassium deficiency, improving soil quality, and enhancing plant growth. However, different KSB strains exhibit diverse solubilization mechanisms, environmental adaptability, and growth-promoting abilities. In this study, we isolated a multifunctional KSB strain ZHS-1, which also has phosphate-solubilizing and IAA-producing capabilities. 16S rDNA sequencing identified it as Pantoea vagans. Scanning electron microscopy (SEM) showed that strain ZHS-1 severely corroded the smooth, compact surface of potassium feldspar into a rough and loose state. The potassium solubilization reached 20.3 mg/L under conditions where maltose was the carbon source, sodium nitrate was the nitrogen source, and the pH was 7. Organic acid metabolism profiling revealed that strain ZHS-1 primarily utilized the EMP-TCA cycle, supplemented by pathways involving pantothenic acid, glyoxylic acid, and dicarboxylic acids, to produce large amounts of organic acids and energy. This solubilization was achieved through direct solubilization mechanisms. The strain also secreted IAA through a tryptophan-dependent metabolic pathway. When strain ZHS-1 was inoculated into the rhizosphere of rice, it demonstrated significant growth-promoting effects. The rice plants exhibited improved growth and root development, with increased accumulation of potassium and phosphorus. The levels of available phosphorus and potassium in the rhizosphere soil also increased significantly. Additionally, we observed a decrease in the relative abundance of Actinobacteria and Proteobacteria in the rice rhizosphere soil, while the relative abundance of genera associated with acid production and potassium solubilization, such as Gemmatimonadota, Acidobacteria, and Chloroflexi, as well as Cyanobacteria, which are beneficial to plant growth, increased. These findings contribute to a deeper understanding of the potassium solubilization mechanisms of strain ZHS-1 and highlight its potential as a plant growth-promoting rhizobacteria.

Spatiotemporal distribution of environmental microbiota around animal farms adjacent to produce fields in central coast California

This study aimed to identify different environmental microbiota in animal farms adjacent to produce fields and to understand their potential flow pattern. Soil and water samples were collected from 16 locations during the winter, spring, summer, and fall seasons. In addition, a high-resolution digital elevation model helped to create a stream network to understand the potential flow of the microbiome. Metagenomic analysis of the 16 S rRNA gene revealed that soil and water samples from the four seasons harbor diverse microbiome profiles. The phylogenetic relationship of operational taxonomic units (OTUs) is separated by a maximum of 0.6 Bray-Curtis distance. Similarly, the Principal Component Analysis (P = 0.001) demonstrated the soil and water microbiome clustering across different locations and seasons. The relative abundance of Proteobacteria, Bacteroidetes, and Firmicutes was higher in the water samples than in the soil samples. In contrast, the relative abundance of Actinobacteria and Chloroflexi was higher in the soil compared to the water samples. Soil samples in summer and water samples in spring had the highest abundance of Bacteroidetes and Firmicutes, respectively. A unique microbial community structure was found in water samples, with an increased abundance of Hydrogenophaga and Solirubrobacter. Genera that were significantly abundant at a 1% false discovery rate (FDR) among seasons and soil or water samples, include Nocardioides, Gemmatimonas, JG30-KF-CM45, Massilia, Gaiellales, Sphingomonas, KD4-96, Bacillus, Streptomyces, Gaiella, and Gemmatimonadaceae. The relative abundance of pathogenic genera, including Mycobacterium, Bacteroides, Nocardia, Clostridium, and Corynebacterium, were significantly (at 1% FDR) affected by seasons and environmental type. The elevation-based stream network model suggests the potential flow of microbiomes from the animal farm to the produce fields.

Aridity shapes distinct biogeographic and assembly patterns of forest soil bacterial and fungal communities at the regional scale

Climate change is exacerbating drought in arid and semi-arid forest ecosystems worldwide. Soil microorganisms play a key role in supporting forest ecosystem services, yet their response to changes in aridity remains poorly understood. We present results from a study of 84 forests at four south-to-north Loess Plateau sites to assess how increases in aridity level (1- precipitation/evapotranspiration) shapes soil bacterial and fungal diversity and community stability by influencing community assembly. We showed that soil bacterial diversity underwent a significant downward trend at aridity levels >0.39, while fungal diversity decreased significantly at aridity levels >0.62. In addition, the relative abundance of Actinobacteria and Ascomycota increased with higher aridity level, while the relative abundance of Acidobacteria and Basidiomycota showed the opposite trend. Bacterial communities also exhibited higher similarity-distance decay rates across geographic and environmental gradients than did fungal communities. Phylogenetic bin-based community assembly analysis revealed homogeneous selection and dispersal limitation as the two dominant processes in bacterial and fungal assembly. Dispersal limitation of bacterial communities monotonically increased with aridity levels, whereas homogeneous selection of fungal communities monotonically decreased. Importantly, aridity also increased the sensitivity of microbial communities to environmental disturbance and potentially decreased community stability, as evidenced by greater community similarity-environmental distance decay rates, narrower habitat niche breadth, and lower microbial network stability. Our study provides new insights into soil microbial drought response, with implications on the sustainability of ecosystems under environmental stress.

Impact of alternate partial root-zone irrigation on the rhizosphere microbiota of alfalfa plants inoculated with rhizobia.

Water is an important constraint on alfalfa (Medicago sativa) production in arid and semiarid areas, and alternate irrigation in root areas has water-saving potential for alfalfa production. To investigate the impact of alternate partial root-zone irrigation (APRI) on the rhizosphere soil microorganisms of alfalfa, this study subjected alfalfa plants to different irrigation methods and irrigation levels. The growth status and rhizosphere soil microbial community diversity of alfalfa plants under alternate root-zone watering treatment were analyzed through laboratory experiments and high-throughput sequencing. The results showed that at soil moisture levels of 80% field moisture capacity (FMC) and 60% FMC, APRI had no significant impact on the biomass or nodule number of alfalfa. However, 40% FMC significantly reduced the individual plant dry weight, chlorophyll content, and nodule number of the alfalfa plants. APRI increased the relative abundance of Actinomycetes in the alfalfa rhizosphere soil. Moreover, at 60% FMC, the MBC and MBN of rhizosphere, relative abundance of Actinobacteria and unclassified K fungi and Chao 1 index of bacteria significantly increased under APRI treatment. While relative abundance of Ascomycetes and Proteobacteria in the alfalfa rhizosphere significantly reduced under 60% FMC + APRI treatment. In summary, under the same irrigation conditions, APRI did not significantly affect the growth of alfalfa in the short term. And 60%FMC + APRI treatment did significantly affect the groups, structure and diversity of the rhizosphere soil microbial communities.

Long-term nitrogen deposition alters the soil bacterial community structure but has little effect on fungal communities

Subtropical Moso bamboo (Phyllostachys edulis) forests have become hot spots for nitrogen (N) deposition in China. However, the effect of long-term N deposition on the structure of soil microbial communities in different horizons of these forests remains unclear. To investigate the influence of extended N deposition on soil bacteria and fungi, a simulated N deposition field study was conducted in Fujian Province with four N deposition levels (0, 20, 40 and 80 kg N hm−2 a−1). The absolute abundances, diversity, community structure, and potential functions of soil bacteria and fungi were investigated after 10 years of simulated N deposition. The results indicated that there was no significant effect of N deposition on the abundance or diversity of soil microbes in either the organic or mineral horizons of Moso bamboo forests. However, under rates of 40 and 80 kg N hm−2 a−1, long-term N deposition altered the structure of the soil bacterial community in the organic horizon. Specifically, there was a 27.75∼36.40 % increase in the relative abundance of Actinobacteria, while that of Acidobacteria decreased by 24.40∼27.52 %. Redundancy analysis (RDA) demonstrated that soil total carbon (TC) was the key variable influencing the bacterial community structure in the organic horizon. Analysis of potential microbial functions showed that in the organic horizon, the rates of chemoheterotrophy significantly decreased under 80 kg N hm−2 a−1. However, N deposition did not noticeably impact the fungal community structure in either soil horizon. Our study suggested that under 10 years of N deposition, only the bacterial community composition and function in the organic horizon was affected, indicating that soil bacteria are more sensitive to N deposition than fungi in subtropical Moso bamboo forests. Therefore, further research is necessary to fully understand the impact of N deposition on fungal community composition in the soil organic horizon and on the microbial community in the mineral horizon of subtropical bamboo forests. This study provides valuable insights for informing future environmental management and conservation strategies.

Changes in soil bacterial community characteristics in patches of different vegetation types under different stages of restoration in the desert of northern China.

In desert areas, the process of mobile sandy land changing to semi-fixed sandy land and eventually to fixed sandy land after undergoing vegetation restoration is inevitable. The presence of shrub patches and herb patches is common in this restoration process. No relevant studies have reported the soil bacterial community characteristics of different vegetation-type patches (shrub patches and herb patches) under different stages of restoration. Therefore, we utilized long-established experimental plots to collect soil from 0-20 cm soil layer under shrub patches (dominated by Salix psammophila) and herb patches under different stages of restoration (i.e., mobile sand land, semi-fixed sand land, and fixed sand land), by determining soil physicochemical properties, enzyme activities, and soil bacterial communities. Our results found that soil bacterial α-diversity under different restoration stages showed higher shrub patches than herb patches. The dominant bacterial communities (phyla) in shrub patches and herb patches at different recovery stages were Actinobacteria, Proteobacteria, and Bacteroidota. When the mobile sandy land returned to fixed sandy land, the relative abundance of Actinobacteria and Bacteroidota gradually decreased under shrub patches and herb patches, while the relative abundance of Proteobacteria increased significantly. In addition, herb patches significantly increased the relative abundance of bacteria (genus) relative to shrub patches at different stages of recovery. Soil nutrients, soil fine particles, and soil enzyme activities were significantly higher under shrub patches than under herb patches when fixed sandy land due to differences in life form and architecture between shrub patches and herb patches. Based on this, soil bacterial community composition and diversity under shrub patches were driven by more soil properties during the restoration of sandy land. This study complements the dynamic recovery processes and driving mechanisms of soil bacterial community structure under different vegetation patches in sandy areas, especially in the context of global climate change.

Effects of Biochar-loaded Ammonia Nitrogen on Soil Carbon Emissions, Enzyme Activity, and Microbial Communities

The form of soil nitrogen input significantly affects soil CO2 emission. As a new form of nitrogen input, biochar-loaded ammonia nitrogen not only reduces the input of chemical nitrogen fertilizer in farmland but also reduces the cost of environmental treatment. It is of great significance to promote the zero growth of national chemical fertilizer, the prevention and control of farmland non-point source pollution, and the realization of the national goal of "carbon peak" and "carbon neutralization." Through an indoor culture experiment, the effects of different nitrogen input forms on soil carbon emission, enzyme activity, and microbial community were studied through four treatments:no fertilization (CK), single application of chemical nitrogen fertilizer (CF), biochar combined application of chemical nitrogen fertilizer (BF), and biochar-loaded ammonia nitrogen (BN). The results showed that compared with that in CF, BF significantly increased cumulative carbon emissions (66.24 %), whereas BN had no significant difference. It is worth noting that the cumulative carbon emissions were significantly reduced by 35.28 % compared with that in BF and BN. Compared with those in CF and BF, the activities of β-glucosidase, peroxidase, and polyphenol oxidase treated with BN significantly increased by 20.25 % and 5.20 %, respectively. Compared with that in CF, the BF treatment increased microbial community richness and community diversity, whereas the BN treatment decreased microbial community richness. Compared with that in BF, the relative abundance of Proteobacteria decreased by 11.16 %, and the relative abundance of Actinobacteria and Bacteroidota increased by 8.12 % and 5.83 %, respectively, in which xylosidase activity was the most important soil factor affecting microbial community structure. The relative abundance of Chloroflexi was significantly correlated with cellobiose hydrolase activity, and the relative abundance of Gemmatimonadetes was significantly correlated with β-glucosidase activity. There was a very significant correlation between the relative abundance of Proteobacteria and cumulative carbon emissions. To summarize, compared with those under biochar combined with chemical nitrogen fertilizer, biochar loaded with ammonia nitrogen significantly reduced cumulative carbon emissions, and its emission reduction effect was better. The results of this study will be beneficial to the landing of the national "double carbon strategy," the healthy development of the biological natural gas industry, the construction of the national green cultivation circular agriculture system, and the realization of the national zero growth strategy of chemical fertilizer.

The impact of gut microbial dysbiosis on the atrophy of the hippocampus and abnormal metabolism of N-acetyl aspartate in type 2 diabetic rats

Rationale and objectivesThis study aimed to investigate the effect of intestinal dysbiosis on the hippocampal volume using proton magnetic resonance spectroscopy (1H-MRS) in a type 2 diabetes mellitus (T2DM) rat model. Materials and methodsWe established a T2DM animal model with high-fat diet and streptozotocin (HFD/STZ) administration to Sprague-Dawley rats. Short-term ceftriaxone sodium administration was used to establish a T2DM intestinal dysbiosis (T2DM-ID) model. After establishing the model, fecal microbiota were detected using 16S rRNA sequencing. The models were then subjected to magnetic resonance imaging (MRI). Associations between MRI findings and fecal microbiota were evaluated. ResultsMagnetic resonance imaging (MRI) showed that the bilateral hippocampal voxel value and N-acetylaspartate (NAA) level were lower in the experimental group than in the normal control (NC) group (p < 0.05) and that NAA/creatine in the left hippocampus was lower in the T2DM-ID group than in the NC group (p < 0.05). α and β diversities differed significantly among the three groups (p < 0.05). In the T2DM and T2DM-ID groups, the abundance of bacteria in the phylum Proteobacteria increased significantly, whereas that of bacteria in the phylum Firmicutes decreased. The relative abundance of Actinobacteria was significantly increased in the T2DM-ID group. The Chao1 index (r = 0.33, p < 0.05) and relative abundance of Firmicutes (r = 0.48, p < 0.05) were positively correlated with the left hippocampal voxel, while the relative abundance of Proteobacteria was negatively correlated with the left hippocampal voxel (r = −0.44, p < 0.05). NAA levels, bilateral hippocampal voxels, and the relative abundance of Lactobacillus, Clostridia_UCG_014, and other genera were correlated positively (r = 0.34–0.70, p < 0.05). NAA levels and the relative abundances of Blautia and Enterococcus were correlated negatively (r = −0.32−0.44, p < 0.05). ConclusionThe T2DM-ID rat model showed hippocampal volume atrophy and decreased levels of neuronal markers (such as NAA). The abnormal content of specific gut microorganisms may be a key biomarker of T2DM-associated brain damage.

Kiwifruit resistance to gray mold is enhanced by yeast-induced modulation of the endophytic microbiome

The influence of endophytic microbial community on plant growth and disease resistance is of considerable importance. Prior research indicates that pre-treatment of kiwifruit with the biocontrol yeast Debaryomyces hansenii suppresses gray mold disease induced by Botrytis cinerea. However, the specific underlying mechanisms remain unclear. In this study, Metagenomic sequencing was utilized to analyze the composition of the endophytic microbiome of kiwifruit under three distinct conditions: the healthy state, kiwifruit inoculated with B. cinerea, and kiwifruit treated with D. hansenii prior to inoculation with B. cinerea. Results revealed a dominance of Proteobacteria in all treatment groups, accompanied by a notable increase in the relative abundance of Actinobacteria and Firmicutes. Ascomycota emerged as the major dominant group within the fungal community. Treatment with D. hansenii induced significant alterations in microbial community diversity, specifically enhancing the relative abundance of yeast and exerting an inhibitory effect on B. cinerea. The introduction of D. hansenii also enriched genes associated with energy metabolism and signal transduction, positively influencing the overall structure and function of the microbial community. Our findings highlight the potential of D. hansenii to modulate microbial dynamics, inhibit pathogenic organisms, and positively influence functional attributes of the microbial community.

The impact on Cd bioavailability and accumulation in rice (Oryza sativa L.) induced by dry direct-seeding cultivation method in field-scale experiments

Dry direct-seeded rice cultivation has gained popularity and expanded its cultivated area due to reduced labor requirements and water consumption. However, the impact of this cultivation method on cadmium (Cd) bioavailability in soil and the accumulation levels in grains remains uncertain. Field experiments were conducted in acidic soils at two locations in southern China to compare rice varieties and evaluate the dry direct-seeding method alongside the wet direct-seeding and traditional transplanting methods. Dry direct-seeded rice reached significantly higher Cd concentrations in its tissues starting from the heading stage than transplanted rice. Cd accumulation levels by the maturation stage in the brown rice of dry direct-seeded rice were 18.33 %–150.69 % higher than those of wet direct-seeded and transplanted rice, with a considerable ability to translocate Cd into brown rice. Furthermore, dry direct seeding decreased iron plaque formation, particularly in the amorphous Fe form; it resulted in high soil temperature and low moisture content during tillering, elevating Cd availability in the soil. Additionally, the proportion of ions and more labile forms of Cd in the soil solution was high. Moreover, the soil under dry direct seeding had high urease and acid phosphatase enzyme activities. However, low richness and diversity in the bacterial community were characterized by a significant increase in the relative abundance of Actinobacteria and Gammaproteobacteria at the class level, while exhibiting decreased relative abundances of Alphaproteobacteria, Bacilli, and KD4-96, along with fewer biomarkers. Nonetheless, these differences are gradually reduced during the maturation stage. Overall, although dry direct seeding offers several advantages, it is crucial to implement additional measures to mitigate the increased health risks linked to rice cultivation through this approach in Cd-contaminated areas.

Quinones-enhanced humification in food waste composting: A novel strategy for hazard mitigation and nitrogen retention

The harmless and high-value conversion of organic waste are the core problems to be solved by composting technology. This study introduced an innovative method of promoting targeted humification and nitrogen retention in composting by adding p-benzoquinone (PBQ), the composting without any additives was set as control group (CK). The results indicated that the addition of exogenous quinones led to a 30.1% increase in humic acid (HA) content during the heating and thermophilic phases of composting. Spectroscopic analyses confirmed that exogenous quinones form the core skeleton structure of amino-quinones in HA through composting biochemical reactions. This accelerated the transformation of quinones into recalcitrant HA in the early stages of composting, and reduced CO2 and NH3 by 8% and 78%, respectively. Redundancy analysis (RDA) revealed that the decrease in carbon and nitrogen losses primarily correlated with quinones enhancing HA formation and greater nitrogen incorporation into HA (P < 0.05). Furthermore, the compost treated with quinones demonstrated a decrease in phytotoxicity and earthworm mortality, alongside a significant increase in the relative abundance of actinobacteria, which are associated with the humification process. This research establishes and proposes that co-composting with quinones-containing waste is an effective approach for the sustainable recycling of hazardous solid waste.

Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome

BackgroundInfant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied.MethodsTwo hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort’s first week of life.ResultsNewborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs).ConclusionThese data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures—leading to what can be an extensive and diverse resistome.31ajk8a-14RKZLdCXmKHuwVideo

Effects of acupuncture on intestinal microbiota in mice with rheumatoid arthritis

To observe the effect of acupuncture on gut microbiota in mice with rheumatoid arthritis (RA), so as to explore its mechanisms underlying improvement of RA. Eighteen male C57BL/6J mice were randomly divided into saline, model and acupuncture groups, with 6 mice in each group. The RA model was established by injection of complete Freund's adjuvant (CFA, 50 μL) into the right hind paw. Acupuncture group received manual acupuncture stimulation of the bilateral "Zusanli" (ST36) for 30 min, once daily for 7 days. The paw withdrawal thermal latency (PWTL) was detected by using a thermal pain detector. After the last intervention, the mice's feces were collected for extracting the feces DNA, and 16S RNA sequencing was used to detect and analyze the diversity and structural composition of intestinal flora. Compared with the saline group, the PWTL from day 0 to 7 after administration of CFA was significantly decreased (P<0.01), and the paw swelling volume from day 0 to 7 significantly increased in the model group (P<0.01). In comparison with the model group, the PWTL from day 1 to 7 was significantly increased (P<0.01), and the paw swelling volume on day 7 was strikingly decreased (P<0.01) in the acupuncture group. The Alpha diversity analysis of intestinal flora showed that the Chao1 index was markedly decreased in the model group compared with the saline group (P<0.05), and markedly increased in the acupuncture group compared with the model group (P<0.05). Beta diversity principal coordinate analysis (PCoA) displayed that the intestinal microbiota community structure of each group was different, and there were some overlapping areas, but they could be distinguished (P<0.01), suggesting that the species richness and diversity of RA mice were changed after acupuncture treatment. Compared with the saline group, the relative abundance of Bacteroidota was decreased (P<0.05), and that of Desulfobacterota and Escherichia-Shigella significantly increased (P<0.05) in the model group. In comparison with the model group, the relative abundance of Actinobacteria and Lactobacillus was considerably increased (P<0.05, P<0.01), while that of Escherichia-Shigella and Faecalibacterium strikingly decreased (P<0.05) in the acupuncture group. Acupuncture treatment can significantly alleviate joint inflammation in RA mice, which may be related to its function in regulating the diversity and composition of gut microbiota.

Gut microbiota dysbiosis and protein energy wasting in patients on hemodialysis: an observational longitudinal study.

Protein energy wasting (PEW) is common in patients on hemodialysis, and its development may involve gut microbial dysbiosis. However, the exact relationship between the composition of different flora and the development of PEW remains unclear. This is an observational longitudinal study on 115 patients undergoing hemodialysis who were followed up for 1 year. All the patients were evaluated at baseline, and different microbiota compositions were determined. After a 1 year follow-up period, the correlations between clinical parameter variations and the relative abundance of different gut flora were assessed using Spearman correlation. Moreover, the associations of the abundance of different gut microbiota with decrease in lean tissue mass and the development of PEW were analyzed using ROC curve and logistical regression analyses. We found that the relative abundances of Actinobacteria and Bifidobacteriaceae were significantly lower in patients with PEW than in those who did not develop PEW (p < 0.05). The abundance of Actinobacteria and Bifidobacteriaceae correlated positively with variations in serum albumin levels (r = 0.213, p = 0.035 and r = 0.214, p = 0.034, respectively), lean tissue mass (r = 0.296, p = 0.007 and r = 0.238, p = 0.002, respectively), and lean tissue index (r = 0.377, p < 0.001 and r = 0.419, p < 0.001, respectively). The area under the ROC curve or AUC values of Actinobacteria and Bifidobacteriaceae for the prediction of lean tissue mass decrease ranged from 0.676 to 0.708 (p < 0.05). Thus, decrease in the abundance of Actinobacteria and Bifidobacteriaceae may be associated with decrease in lean tissue mass and the occurrence of PEW. The present findings imply Actinobacteria and Bifidobacteriaceae may be potential markers for predicting skeletal muscle mass decrease and PEW development in patients on hemodialysis.

Interactive dynamics between rhizosphere bacterial and viral communities facilitate soybean fitness to cadmium stress revealed by time-series metagenomics

The distinctive symbiotic relationship between rhizobacteria and soybean (Glycine max) can enhance soil fertility and assist soybean defense heavy metal stress, such as cadmium (Cd), in soils. Soil viruses are critical for modulating microbial activities and enhancing host adaptability to soil contamination by encoding auxiliary metabolic genes (AMGs). However, the community structure, functional diversity and ecological roles of soil viruses and their dynamic interactions with soil-dwelling microbes under Cd stress remain unclear. Here, we characterized the bulk and rhizosphere bacterial community in a Cd-contaminated soybean field at five growth stages and investigated the rhizosphere microbial functional traits and the viral community after flowering using metagenomics. We showed that the rhizosphere bacterial community exhibited a stronger soybean development-dependent diversity pattern relative to bulk soil and had a more critical role in predicting Cd accumulation. The relative abundance of Actinobacteria in the rhizosphere increased with soybean development, particularly in the families Nocardioidaceae and Intrasporangiaceae, which were further identified as the main contributors of amino acid transport E and secondary metabolites Q genes. Viral analysis suggested an interactive and complementary assembly between viral and bacterial communities. Importantly, viruses exhibited a broader host range during the flowering period, and infected specific functional taxa such as Bradyrhizobium and Nocardioides, highlighting their potential impact on the rhizobia-soybean symbiosis and soybean growth and fitness. Furthermore, AMGs related to element cycling and microbial metabolism were identified and functionally and phylogenetically characterized, suggesting the contribution of these virus-encoded genes to biogeochemical cycles and soybean fitness under Cd stress. Together, our results expand our understanding of the ecological functions of rhizosphere viruses in Cd pollution-stressed soils, and provide insights in developing new strategies for bioremediation of contaminated soils.

Prediction of Soil Bacterial Community Structure and Function in Minqin Desert-oasis Ecotone Artificial Haloxylon ammodendron Forest

Exploring the effects of artificial Haloxylon ammodendron forest planting on the structure and function of a desert soil bacterial community provides data reference for soil micro-ecological restoration and land quality improvement in desert oasis transition zones. Illumina high-throughput sequencing technology and PICRUSt2 functional prediction analysis were used to identify and analyze the structure and function of soil bacterial communities, and the Mantel correlation test and RDA analysis were used to explain the physicochemical factors affecting the structure and function of soil bacterial communities. The results showed that:① the soil bacterial OTU number, Chao1 index, and Shannon index were significantly higher in the H. ammodendron forest than in the mobile dune soil, and the PCoA analysis and Adonis test showed significant differences in the soil bacterial community structure between H. ammodendron and mobile dune soil (P=0.001). ② A total of 34 phyla, 89 classes, 174 orders, 262 families, and 432 genera of bacteria were detected in all samples, and the phyla Proteobacteria, Actinobacteria, Cyanobacteria, and Chloroflexi accounted for 76.05% of the relative abundance of soil bacteria, which belonged to the dominant soil bacteria, among which the relative abundance of Actinobacteria in H. ammodendron forest soil was extremely significantly higher than that in mobile dune soil (P &lt; 0.01). ③PICRUSt2 function prediction revealed that the soil bacterial community of H. ammodendron forest included six categories of primary functions and 28 categories of secondary functions, among which the metabolism of carbohydrates, metabolism of amino acids, and metabolism of cofactors and vitamins were all greater than 10% in relative abundance and were the main metabolic functions of H. ammodendron forest soil bacteria. ④ The planting of H. ammodendron forest significantly improved the nutrient content of soil organic matter and other nutrients. Soil pH, organic matter, total nitrogen, and fast-acting phosphorus were the main physicochemical factors affecting the bacterial community, with soil organic matter significantly affecting the soil bacterial community structure (P &lt; 0.05) and metabolic function (P &lt; 0.05). In conclusion, the artificial H. ammodendron forest helped to increase desert soil microbial diversity, increase the relative abundance of soil bacterial metabolic function genes, and improve the desert soil microenvironment.