Bacterial Community Richness Research Articles

Gut microbiota distinct between colorectal cancers with deficient and proficient mismatch repair: A study of 230 CRC patients.

Colorectal cancers (CRCs) with deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) exhibit heterogeneous tumor characteristics, distinct responses to immunotherapy, and different survival outcomes. However, it is unclear whether gut microbiota is distinct between CRCs with different MMR status. In this study, we used immunohistochemistry for four major MMR proteins to determine the MMR status in 230 CRC patients. The gut microbiota was profiled in cancerous and adjacent normal tissues by using bacterial 16S rRNA sequencing. The differences in microbiota diversity, composition and related metabolic pathways between patients with dMMR and pMMR CRCs were explored. Linear discriminant analysis effect size (LEfSe) analysis was further applied to validate the significant taxonomic differences at the genus level. In our study cohort, dMMR status was identified in 29 of 230 (12.61%) tumors. The richness (alpha-diversity) of gut microbiome in dMMR tumor tissue was higher compared with pMMR tumor tissues. The microbial community composition (beta-diversity) between the two groups was significantly different. The dMMR group was enriched considerably for some microbiota, including Fusobacteria, Firmicutes, Verrucomicrobia, and Actinobacteria at the phylum level and Fusobacterium, Akkermansia, Bifidobacterium, Faecalibacterium, Streptococcus, and Prevotella bacteria at the genus level. However, the pMMR group was dominated by Proteobacteria at the phylum level and Serratia, Cupriavidus and Sphingobium at the genus level. Moreover, a wide variety of microbiota associated functional pathways were observed with different MMR status. KEGG pathway analysis indicated a higher abundance of the biosynthesis and metabolic pathways of glycan and nucleotide, cell growth and death pathways, genetic replication and repair pathways in dMMR samples compared with the pMMR group. These findings demonstrate that CRC patients with different MMR status have distinct gut bacterial community richness, compositions and related metabolic pathways, suggesting basis that may explain the effectiveness of immunotherapy in dMMR tumors.

Comparative analysis of the endophytic bacteria inhabiting the phyllosphere of aquatic fern Azolla species by high-throughput sequencing

BackgroundAzolla is a small floating fern living in symbiosis with nitrogen-fixing cyanobacteria and provides a variety of important ecosystem benefits. Previous studies have presented that Azolla harbors diverse bacteria that may play a key role in host fitness and productivity. However, the characteristics of endophytic bacteria inhabiting the phyllosphere of different species of Azolla have not yet been fully understood.ResultsIn this study, the 16S ribosomal DNA (rDNA) V5-V7 region of bacteria was determined by Illumina high-throughput sequencing platform to study the diversity and richness of endophytic bacterial communities in the phyllosphere of five Azolla species collected from different countries. A total of 1150 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. According to the α diversity indices, the diversity of bacteria was ordered as Azolla imbricata > A. pinnata > A. filiculoides > A. mexicana > A. caroliniana. The PCoA results displayed that the bacterial communities of A. mexicana and A. caroliniana shared the highest similarity, followed by the similarity between A. pinnata and A. imbricata, and they were significantly distinct from the community of A. filiculoides. The dominant bacteria of Azolla mainly belonged to the phylum of Proteobacteria, followed by Actinobacteria, Chlorobillobacteria, and Firmicutes. In detail, the relative abundance of Proteobacteria in A. imbricata was 52.23%, whereas it was more than 80.00% in the other four species of Azolla. Notably, Herbaspirillum (45.91%, 44.08%) and Methylophilus (29.97%, 37.96%) were the main genera inhabiting A. mexicana and A. caroliniana respectively. Ferrovibrio (18.54%) and Rhizobium (16.68%) were the dominant genera inhabiting A. filiculoides. The group of unidentified genera (41.63%, 44.92%) consisted most of the bacteria in A. imbricata and A. pinnata respectively. Further analysis suggested that the significant different bacteria identified in LDA Effect Size analysis existed Azolla species-specific patterns.ConclusionsIn summary, all results suggested that the diversity and composition of the endophytic bacterial communities were different in Azolla species.

New insight for purifying polluted river water using the combination of large-scale rotating biological contactors and integrated constructed wetlands in the cold season

Ecological treatment technologies, applied to deal with polluted river water in the low temperature season, remain limited. In this study, a new insight was put forward for purifying polluted river water using a combination system (CS) of large-scale rotating biological contactors (RBCs) and integrated constructed wetlands in autumn and winter. The treatment performance, average removal contribution (RC), nitrification and denitrification rates, microbial community structure, and ecosystem service value were considered to estimate the combination system. Results revealed that the average removal efficiencies of ammonium (NH4+–N), total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (COD) reached 93.9%, 20.8%, 36.5%, and 37.1%, respectively. The combination system showed excellent removal efficiency of NH4+–N regardless of the effect of low temperature. The maximum values of nitrification and denitrification rates were 59.57 g N/(m3·d) and 0.78 g N/(m2·d), respectively. Considerable differences in bacterial community diversity, richness and relative abundance of functional microbes were observed in the main treatment units, resulting in different average RC to pollutants. The unit capital cost of CS purifying polluted river water was 260 USD/m3 and the operation and maintenance cost was 0.144 million USD/yr. Meanwhile, the ecosystem service value of the CS was 0.334 million USD in autumn and winter. CS not only possessed excellent pollutant purifying efficiencies, but also achieved high ecological service value in the cold season.

Dynamics of microbial communities of fresh broad bean pods and screening of biological preservatives

This study aimed to determine the dynamics of the microbiome of fresh broad bean pods stored at 10 °C and select targeted and efficient biological preservatives. Culture-dependent 16S rRNA and ITS (Internal Transcribed Spacer) sequencing combined with high-throughput sequencing (HTS) were used to analyze the microbial diversity. The biological preservatives were chosen by antimicrobial analysis and their effects on maintaining freshness. The bacterial and fungal community richness decreased with prolonged storage. The microbial diversity of samples collected on day 0 was clearly distinct from that of samples collected on day 30. The dominant spoilage bacteria were Pseudomonas, Pantoea, Stenotrophomonas and Flavobacterium and the dominant spoilage fungi Pseudogymnoascus, Cladosporium, and Beauveria. Clove essential oil (0.5%) and β-glucan from naked barley (1%) were selected as targeted and efficient biological preservatives for fresh broad bean pods. The results provide a basis for developing technology to prolong the shelf-life of fresh broad bean pods.

Nitrogen fertilization modulates rice seed endophytic microbiomes and grain quality

The intensive use of chemical fertilizer, particularly nitrogen (N) has resulted in not only markedly increased crop yields but also detrimental effects on ecosystems. Plant microbiomes represent an eco-friendly alternative for plant nutrition and productivity, and the effect of N fertilization on plant and soil microbes has been well studied. However, if and how N fertilization modulates seed endophytic microbiomes and grain quality remains largely unknown. Here, we investigated the effect of different N fertilization rates on rice seed endophytic bacterial and fungal communities as well as on grain quality. Higher bacterial and fungal community diversity and richness, but lower grain protein and amino acid contents were found in seeds of rice treated moderate N fertilization than those treated insufficient or excessive N input. There were also more complex co-occurrence networks, and an enrichment of putative beneficial bacterial taxa in seeds under moderate N application, while there was an opposite trend under the excessive N treatment. In addition, the grain amylose and amylopectin contents were positively correlated with the relative abundance of bacterial and fungal dominant genera, while the grain amino acid contents were negatively correlated with the bacterial dominant genera but positively associated with fungal dominant genera. Together, we demonstrate that moderate N fertilization can enhance bacterial and fungal community colonization in seeds and improve grain eating and cooking qualities. This study extends our knowledge regarding the significant role of rational fertilization on seed-microbe interactions in sustainable agriculture.

Composted invasive plant Ageratina adenophora enhanced barley (Hordeum vulgare) growth and soil conditions.

Ageratina adenophora originating from central America has flooded forests, pastures, and farmland in more than 40 tropical and subtropical countries, causing huge ecological disasters and economic losses. In this paper, we intended to use a complex inoculum composed of Pseudomonas putita and Clostridium thermocellum to in-situ compost A. adenophora debris and then to compare the phytotoxicity of extracts from uncomposted and composted A. adenophora (UCA and CA respectively) to barley seed germination and young seedling growth. A field experiment was finally conducted to reveal the effects of UCA and CA on barley nutrients uptake, yield, grain quality, soil enzyme activities, microbial biomass and biodiversity. In-situ composting sharply decreased 4,7-dimethyl-1-(propan-2-ylidene)-1,4,4a,8a-tetrahydronaphthalene- 2,6(1H,7H)-dione(DTD) and 6-hydroxy-5-isopropyl-3,8-dimethyl-4a,5,6,7,8,8a-hexahydronaphthal en-2(1 H)-one(HHO) from 2096.3 and 743.7 mg kg-1 in uncomposted A. adenophora to 194.4 and 68.19 mg kg-1 in composted A. adenophora. UCAE showed negative influences on seed germination performances (except lower rates on germination percentage). The mechanism may be the inhibition of bio-macromolecules hydrolysis (including proteins, starch, and phytin) in endosperms and their hydrolysates for forming new plants. CAE promoted seed germination and seedling growth, increased chlorophyll levels in leaves, and stimulated dehydrogenase and nitrate reductase activities in plants, while UCAE got opposite performance. Compared with chemical fertilizers, application of CA in combination with chemical fertilizers significantly improved plant nutrient uptake (nitrogen, phosphorus, and potassium), yield, grain quality, quantity of 16S rDNA sequences, richness and diversity of bacterial communities in contrast to UCA which behaved otherwise. Taken together, the use of the microbial agent to in-situ compost A. adenophora may be an effective approach for agricultural use of A. adenophora debris as a plant-friendly organic fertilizer, being undoubtedly worth advocating.

Effects of Broad-Spectrum Antibiotic (Florfenicol) on Resistance Genes and Bacterial Community Structure of Water and Sediments in an Aquatic Microcosm Model.

This study evaluates the effects of a broad-spectrum antibiotic (florfenicol) on antibiotic resistance genes (ARGs) and bacterial community structure in aquatic environments. We constructed an indoor aquatic microcosm model, adding different concentrations of florfenicol (0.1, 1, 10, 100 mg L−1), and water and sediment samples were collected after 0, 7, 30, and 60 days. qPCR and 16S rDNA amplicon sequencing were used to study the changes in the ARGs and bacterial community structure of the collected samples. The results show that the inclusion of florfenicol resulted in an increased abundance of the floR and optrA genes. Adding 100 mg L−1 florfenicol to the water increased the abundance of optrA gene copies with the maximum on the Day 7, and increased the abundance of floR gene copies with the maximum on Day 30. Adding 100 mg L−1 florfenicol to the sediment increased the abundance of floR and optrA genes by one order of magnitude on Day 60. Meanwhile, the average number of operational taxonomic units (OTUs) in the water samples was 257, and the average number of OTUs in sediment samples was 823. The bacterial community diversity and richness in sediments were higher than those in water. The difference between the maximal and minimal values of the Shannon diversity index in the water and sediment samples was 4.36 and 1.95, respectively. The effect of florfenicol on the bacterial community structure in water was much higher than that in sediment. At 30 days, the diversity index and richness index of the florfenicol treatment groups with 1 and 10 mg L−1 concentrations began to increase; at 60 days, the diversity and richness indices of the 100 mg L−1 florfenicol treatment group began to increase. The samples at the same sampling time in the sediments clustered closer together. The results of this study provide a scientific basis for guiding the rational use of florfenicol in aquaculture, maintaining a healthy and stable microecological environment in aquaculture, and provide theoretical data for environmental ecological risk assessment and safety management caused by microbial resistance under the abuse of florfenicol.

Changes in Soil Properties, Bacterial Communities and Wheat Roots Responding to Subsoiling in South Loess Plateau of China

This study was carried out to investigate effects of subsoiling on the diversity and composition of the bacterial community in a wheat–maize rotation field in the Guanzhong area of Shaanxi Province, China. After the wheat harvest, surface soil samples were collected under two tillage methods (single rotary tillage (RT) and subsoiling + rotary tillage (ST)) to perform high-throughput sequencing and bioinformatics analysis. Soil properties and root length density (RLD) of winter wheat at booting and flowering stages were also studied. Results showed that ST treatment significantly raised the water storage, organic carbon and total nitrogen contents of deep soil (>40 cm), and notably increased the total soil pH, ammonium nitrogen content and RLD in the tillage layer from 0–70 cm at booting stage and 0~100 cm at flowering stage, but the residual nitrate nitrogen significantly decreased by 17.74%. Compared with RT, soil bacterial richness and diversity in the 10~20 cm layer of ST treatment showed a significantly decreased trend. The relative abundances of GAL15, Actinobacteria, Nitrospirae, Rhizobiales, Burkholderiales, Pseudomonas and Serratia in the 10–20 cm layer were remarkably increased in ST. Principal Component Analysis (PCA) and Redundancy Analysis (RDA) results showed that surface soil pH, ammonium nitrogen and nitrate nitrogen contents have the strongest effect on the bacterial structure. In addition, there were positive correlations between the RLD and the relative abundances of Rhizobiales, Burkholderiales, Pseudomonas and the ammonium nitrogen content. In conclusion, although subsoiling was not conducive to improving soil bacterial community richness and diversity, it significantly increased soil beneficial bacteria (biological nitrogen-fixing bacteria, ammonifying bacteria, nitrobacteria) abundances, reduced the nitrogen loss caused by denitrifying bacteria, promoted earlier root development and improved the plant utilization ratio of soil nutrients.

Urbanization and greenspace type as determinants of species and functional composition of collembolan communities

Urban regions are rapidly expanding worldwide resulting in biotic homogenization and loss of ecological functions in urban ecosystems due to management practices targeting at satisfying aesthetic and health demands of urban residents. These practices also modify living conditions and food recourses of soil invertebrates thereby affecting the structure and functional diversity of soil animal communities including collembolans. Here, we assessed the response of the community composition and functional diversity of collembolans as a major component of soil food webs to urbanization (suburban vs urban region) and greenspace types (including forest and four park-associated greenspaces: lawn, lawn with shrubs, lawn with trees, and lawn with shrubs and trees). Our results highlight that both urbanization and greenspace type significantly affect soil properties and community structure of collembolans. The negative effect of urbanization and park-associated greenspaces on species and functional composition of collembolan communities were likely due to both changes in soil abiotic conditions and bacterial community composition, whereas the reduction of collembolan functional traits likely resulted from changes in soil abiotic conditions and fungal community composition. In park-associated greenspaces richness and diversity of bacterial communities were highest in lawns with trees and lowest in forests. By contrast, species richness and diversity of fungal communities were highest in lawns with shrubs, but, similar to bacteria, lowest in forests. Community composition and functional traits of collembolans were more homogeneous in urban than suburban greenspaces pointing to reduced functioning of collembolan assemblages in urban areas. Overall, our results suggest that changes in soil properties and bacterial communities caused by urbanization and greenspace type are important factors contributing to taxonomic homogenization of collembolan communities, while the loss of functional traits of collembolan communities in urban greenspaces is likely caused by changes in soil properties and fungal community composition.

Intestinal Microbiome Richness of Coral Reef Damselfishes (Actinopterygii: Pomacentridae).

Fish gastro-intestinal system harbors diverse microbiomes that affect the host's digestion, nutrition, and immunity. Despite the great taxonomic diversity of fish, little is understood about fish microbiome and the factors that determine its structure and composition. Damselfish are important coral reef species that play pivotal roles in determining algae and coral population structures of reefs. Broadly, damselfish belong to either of two trophic guilds based on whether they are planktivorous or algae-farming. In this study, we used 16S rRNA gene sequencing to investigate the intestinal microbiome of 5 planktivorous and 5 algae-farming damselfish species (Pomacentridae) from the Great Barrier Reef. We detected Gammaproteobacteria ASVs belonging to the genus Actinobacillus in 80% of sampled individuals across the 2 trophic guilds, thus, bacteria in this genus can be considered possible core members of pomacentrid microbiomes. Algae-farming damselfish had greater bacterial alpha-diversity, a more diverse core microbiome and shared 35 ± 22 ASVs, whereas planktivorous species shared 7 ± 3 ASVs. Our data also highlight differences in microbiomes associated with both trophic guilds. For instance, algae-farming damselfish were enriched in Pasteurellaceae, whilst planktivorous damselfish in Vibrionaceae. Finally, we show shifts in bacterial community composition along the intestines. ASVs associated with the classes Bacteroidia, Clostridia, and Mollicutes bacteria were predominant in the anterior intestinal regions while Gammaproteobacteria abundance was higher in the stomach. Our results suggest that the richness of the intestinal bacterial communities of damselfish reflects host species diet and trophic guild.

Intestinal Microflora Characteristics of Antheraea pernyi (Lepidoptera: Saturniidae) Larvae With Vomit Disease.

Antheraea pernyi Guérin-Méneville (Lepidoptera: Saturniidae) is of high economic value as a source of silk, food, and bioactive substances with medicinal properties. A. pernyi larvae are prone to A. pernyi vomit disease (AVD), which results in substantial economic losses during cultivation; however, the relationship between AVD and A. pernyi gut microbiota remains unclear. Here, we investigated the bacterial community in the midgut and feces of A. pernyi larvae with and without AVD using 16S rRNA gene sequencing with Illumina MiSeq technology. Compared with healthy larvae, intestinal bacterial diversity and community richness increased and decreased in larvae with mild and severe AVD, respectively. In addition, the proportion of gut Enterobacter Hormaeche and Edwards(Enterobacteriales: Enterobacteriaceae) and Enterococcus Thiercelin and Jouhaud (Lactobacillales: Enterococcaceae) was higher and lower, respectively, in larvae with mild AVD than those in healthy larvae. A. pernyi vomit disease infection significantly increased the genera with abundance <1%. In the gut of larvae with severe AVD, the proportion of Turicibacter Bosshard et al. (Erysipelotrichales: Turicibacteraceae) increased significantly to 81.53-99.92%, whereas that of Enterobacter decreased compared with healthy larvae. However, the diversity of fecal bacteria was similar between healthy larvae and those with mild AVD. Overall, the findings demonstrate that intestinal microflora in A. pernyi larvae are altered by AVD infection and may cause secondary bacterial infection. This is the first report of the presence of Turicibacter in the intestinal tract of lepidopterans.

Determining why continuous cropping reduces the production of the morel Morchella sextelata.

Artificial cultivation of Morchella sextelata and other morels is expanding in China, but continuous cropping reduces Morchella for unknown reasons. Here, we investigated soil that had been used or not used for M. sextelata cultivation for 0, 1, and 2 years. We found that the continuous cropping of M. sextelata substantially reduced the pH and the nutrient content of the hyphosphere soil and increased sclerotia formation by M. sextelata. Changes in the structure of bacterial and fungal communities were associated with levels of available nitrogen (N) and phosphorus in the soil. With continuous cropping, the richness and diversity of fungal and bacterial communities increased, but the abundance of Bacillus and Lactobacillus decreased and the abundance of pathogenic fungi increased. FAPROTAX analysis indicated that N cycle functions were enriched more with than without continuous cultivation, and that enrichment of N cycle and sulfate respiration functions was higher in the second than in the first year of cultivation. FunGuild analysis indicated that the functions related to pathotrophs and wood saprotrophs were enriched by M. sextelata cultivation. Overall, the results suggest that continuous cropping may reduce M. sextelata production by acidifying the soil and increasing the abundance of pathogenic fungi. Additional research is needed to determine whether increases in the abundance of pathogenic fungi and changes in soil chemistry result in the declines in production that occur with continuous M. sextelata cultivation.

Associated bacteria of a pine sawyer beetle confer resistance to entomopathogenic fungi via fungal growth inhibition

BackgroundThe entomopathogenic Beauveria bassiana is a popular fungus used to control the Japanese pine sawyer, Monochamus alternatus Hope, the key vector of pine wood nematode (Bursaphelenchus xylophilus) that is the causal agent of pine wilt disease, resulting in devastating losses of pines in China and Portugal. However, recent studies have demonstrated that some insect-associated bacteria might decrease fungal toxicity and further undermine its biological control efficacy against M. alternatus. Thus, it is of great significance to uncover whether and how associated bacteria of M. alternatus become involved in the infection process of B. bassiana.ResultsHere, we show that axenic M. alternatus larvae died significantly faster than non-axenic larvae infected by four increasing concentrations of B. bassiana spores (Log-rank test, P < 0.001). The infection of B. bassiana significantly changed the richness and structure of the beetle-associated bacterial community both on the cuticle and in the guts of M. alternatus; meanwhile, the abundance of Pseudomonas and Serratia bacteria were significantly enriched as shown by qPCR. Furthermore, these two bacteria genera showed a strong inhibitory activity against B. bassiana (One-way ANOVA, P < 0.001) by reducing the fungal conidial germination and growth rather than regulating host immunity.ConclusionsThis study highlights the role of insect-associated bacteria in the interaction between pest insects and entomopathogenic fungi, which should be taken into consideration when developing microbial-based pest control strategies.

Source and acquisition of rhizosphere microbes in Antarctic vascular plants.

Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.

Analysis on bacterial community structure of new and old fermented pit mud of Shedian Liquor

The richness and diversity of bacterial community in the fermented pit mud from the new and old distilleries of Shedian Liquor were analysed via the Illumina Miseq PE300 high-throughput sequencing technology, so as to further understand the differences of bacterial community structure in fermented pit muds with different pit ages. The results show that the bacterial community is mainly distributed into five dominant phyla (> 1.0%): Firmicutes, Synergistes, Bacteroidetes, Proteobacteria and Verrucomicrobia. There are 13 dominant genera (> 1.0%), of which Lactobacillus is dominant in both samples with a higher content in the new pit (61.12%) and lower in the old pit (1.15%). Caproiciproducens accounting for 43.53% and Syntrophomonas accounting for 6.20%, norank_f__Family_XIV (17.68%), Aminobacterium (17.68%), Sedimentibacter (1.89%), Caldicoprobacter (1.52%) and Sporanaerobacter (1.29%) are the dominant bacteria in the old pit mud. Bacillus accounting for 6.02%, Bacteroides (6.27%), Akkermansia (1.51%), Hydrogenispora (2.15%) and norank_f__Bacteroidales_S24-7_group (1.15%) are the dominant bacteria in the new pit mud. The results showed that there is a great difference in the bacterial community structure of in the new and old pit mud. In addition, compared with the bacterial community composition in the pit mud of Luzhou flavour Baijiu in Sichuan, it was found that the microorganisms that formed caproic acid and butyric acid were different.

Improvement of gut microbiome and intestinal permeability following splenectomy plus pericardial devascularization in hepatitis B virus-related cirrhotic portal hypertension.

The gut microbiome is an essential component of the intestinal mucosal barrier, critical in regulating intestinal permeability. Microbiome dysbiosis and intestinal permeability changes are commonly encountered conditions in patients with cirrhosis and are closely related to its development and further complications. However, alterations in the gut microbiome and intestinal permeability in chronic hepatitis B virus (HBV) patients with cirrhotic portal hypertension after undergoing a splenectomy plus pericardial devascularization (SPD) have not been investigated. This study recruited 22 patients who were measured against themselves on the study parameters before and after an SPD, along with 20 healthy controls. Methodologically, fecal samples were collected for gut microbiome analysis by 16S ribosomal DNA sequencing, and peripheral blood samples were obtained to examine the liver function and intestinal permeability. This study showed that the community structure of the gut microbiomes in patients before the SPD exhibited obvious differences from those in the healthy control group. They also exhibited a decreased bacterial community richness, increased intestinal permeability, and enhanced inflammation compared with the healthy controls. These issues were further aggravated two weeks after the SPD. There was also evidence of significantly higher abundances of Streptococcaceae, Enterobacteriaceae, and Enterococcaceae than those in the healthy control group. However, 12 months after the surgery, 12 of the 16 patient-associated genera recovered, of which 10 reached normal levels. Additionally, the microbiome diversity increased; the bacterial composition was back to a level similar to the healthy controls. Liver function, intestinal permeability, and inflammation levels all improved compared with preoperative levels. Furthermore, correlation analyses indicated that the five recovered bacterial taxa and the Shannon diversity index were correlated with several improved clinical indicators. Altogether, the improvements in the liver function and intestinal permeability in HBV-related cirrhotic patients may be related to the restoration of the gut microbiome after an SPD.

The diversity, structure and function of microbial communities changes across aging process of tobacco leaves

Microbial communities that inhabit aging tobacco leaves play a key role in improving products quality. A better understanding of microbial communities on the aging of tobacco leaves could provide an important microbial repository for the industrial applications. Here, we examined the structural and compositional changes of microbial communities throughout the aging process of by tobacco leaves 16 S and ITS rRNA amplicon sequencing techniques and identified the potential metabolic pathways of bacteria and fungi using Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Fungi Functional Guild (FUNGuild), respectively. The results showed that the diversity and structure of the microbial communities keep changing along with the aging process went on. The richness and diversity of bacterial community decreased, while the richness of fungal community was in an inverse trend. At the phylum level, the bacterial community was dominated by Proteobacteria, Actinobacteria, and Firmicutes, while Ascomycota and Basidiomycota were the dominant species in the fungal community. In the bacterial community, metabolic functions related to the carbon and nitrogen cycles which response to the degradation of harmful components, and the metabolism of aromatic hydrocarbons showed extremely dynamic at different aging periods. The change of the main nutritional mode of the fungal community also led to an increase in the abundance of saprophytic fungi. These results provide information on the succession of microbial community structure and function in the whole process of tobacco aging and suggest that the aging process of tobacco leaves can be a natural microbial collection for target microorganism and their metabolites. It also enables the further investigation of coordination mechanisms between beneficial microbial regulation and pathogenicity during aging process.

Performance exploration and microbial dynamics of urine diverting composting toilets in rural China

The ongoing "toilet revolution” in China provides new opportunities to improve the rural living environment and sanitation, and the introduction of new sanitation facilities such as urine diverting composting toilets (UDCTs) is conducive to the effective treatment and resource utilization of feces. This study revealed the degradation performance and microbial community dynamics of UDCTs and clarified the influence mechanism of fecal volume in aerobic composting treatment. The results showed that UDCTs could effectively decompose human feces, with an organic matter degradation rate of 25%⁓30%. The temperature, water content, NH4+-N and nutrient accumulation were higher in the high fecal volume treatment than in the low fecal volume treatment. Bacterial community composition and structure in UDCTs varied with composting stage and fecal volume. The diversity and richness of bacterial community in compost were changed with different fecal volumes, but the dominant groups were similar. Redundancy analysis (RDA) showed that nitrogen and organic carbon were the main drivers of bacterial community changes during composting. Highly nutritious and non-phytotoxic compost products were suitable for agronomic uses. Based on these results, UDCTs can be an effective way to solve the problem of fecal pollution in rural areas, and fecal dosage is a potential influencing factor in the operation and maintenance of composting systems.

Variations of rhizosphere and bulk soil microbial community in successive planting of Chinese fir (Cunninghamia lanceolata).

Successive planting and monoculture, as common forest management methods, are widely used globally, especially in Chinese fir plantations in the subtropical areas of southern China. Although soil fertility depletion and productivity decline caused by successive planting have been widely reported, the underlying mechanism is still ambiguous. In this study, the composition and diversity of soil microorganisms (rhizosphere and bulk soils) in Chinese fir seedlings exposed to successive planting soils (first-generation Chinese fir seedings, FCP. second-generation Chinese fir seedings, SCP. third-generation Chinese fir seedings, TCP) and broadleaf tree species soil (Phoebe zhennan S. Lee et F. N. Wei, CK) were examined with high-throughput sequencing technology. Our findings revealed that the diversity and richness of bacterial and fungal communities were remarkably reduced in TCP than FCP and SCP, and were remarkably different between FCP and SCP. At the phylum level, the fungi with greatest relative abundance were Basidiomycota (5.74–32.88%) and Ascomycota (57.63–87.38%), while the bacteria with the greatest relative abundance were Acidobacteria (23.16–31.17%) and Proteobacteria (24.71–29.32%) for all treatments in both soil types. Additionally, the relative abundance of some pathogens (Penicillium and Burkholderia) was significantly higher in TCP than in FCP and SCP, suggesting that the presence of pathogens is an important factor in increasing the incidence of soil-borne sickness. Moreover, changes in fungal and bacterial communities were predominantly driven by soil dissolved organic carbon (DOC), DOC/DON ratio (DOCN), NO3–-N, microbial biomass carbon (MBC), and MBC/MBN ratio (MBCN). Overall, the long-term monoculture of Chinese fir promotes the microecological imbalance of rhizosphere and bulk soil, and remarkably reduced soil microbial community diversity. These results can provide a scientific support for the implementation of future management measures for fir plantations (e.g., fertilization, addition of microbial fungicides, and construction of mixed forests).

Shifts in Bacterial and Archaeal Community Composition in Low-Permeability Oil Reservoirs by a Nutrient Stimulation for Enhancing Oil Recovery

Indigenous microbial enhanced oil recovery technology by selective nutrient injection is a potential alternative that leads to oil production improvement in low-permeability oil reservoirs. Nutrient flooding in oil reservoirs can shift the balance of microorganisms within a population; an in-depth exploration of this phenomenon can enable us to selectively activate particularly beneficial microbial species for enhancing oil recovery. In this study, high-throughput sequencing was employed to analyse indigenous microorganisms (e.g., archaea and bacteria) in an oil production well (W226), compared to a control well (W202), in the Xingzichuan Oil Recovery Plant (Ansai, Shaanxi, China). According to alpha diversity analysis and community composition, the nutrient injection exhibited a significant impact on indigenous archaea at the genus level. The predominant archaeal genus Methanolobus (more than 66%) in the control well shifted to Methanocalculus (50.8%) and Methanothermococcus (30.6%) genera in the oil production well. Conversely, the activators increased bacterial community richness but reduced its evenness. Bacterial community analysis at the genus level revealed that nutrient injections significantly increased specific populations with the potential to emulsify, lower interfacial tension, and lower oil viscosity, including the genera Arcobacter, Halomonas, and Thalassolituus. At the same time, some microbial species that are harmful for the oil recovery process (e.g., the sulphate-reducing bacteria Desulfovibrus, Desulfocurvus, Desulfocarbo, and Desulfoglaeba), were inhibited. In conclusion, nutrient flooding reduced the abundance of harmful microorganisms and increased beneficial functional microbial populations linked to beneficial functions, contributing to the enhancement of oil recovery in low-permeability oil reservoirs.