Changes In Microbial Diversity Research Articles

Characterization of microbial diversity and important off-odor compounds in fermented Ma bamboo shoots (Dendrocalamus latiflorus Munro)

Ma bamboo shoots (Dendrocalamus latiflorus Munro) are widely distributed in southern China and play an important role as a valuable natural resource. However, the inherent odor produced during fermentation is not accepted by most consumers, which limits the use of fermented Ma bamboo shoots as popular foods. Therefore, reducing the inherent odor of fermented Ma bamboo shoots is still a bottleneck problem in processing.In general, indigenous microorganisms play an important role in the formation of volatile compounds in various fermented products. Therefore, the change of microbial diversity in Ma bamboo shoots during fermentation was studied to establish the relationship between microbial diversity and fermentation odor formation. The results showed that the abundance of Lactobacillus, Weissella, and Lactococcus increased significantly during fermentation. Five significantly different volatile compounds were detected. Among them, two highly regulated VOCs, methylpyrazine and p-cresol, were identified as the major odor components. In general, lactic acid bacteria showed increased abundance and were the possible producer of off-odors. These results will provide new ideas and strategies for the removal or attenuation of off-odors by microbiological methods.

Effects of ferrous sulfate modification on the fate of phosphorous in sewage sludge biochar and its releasing mechanisms in heavy metal contaminated soils.

Modifications of sludge biochar with metal-based materials can enhance its fertilizing efficiency and improve safety. To elucidate the effects of ferrous sulfate modification on the fate of phosphorus in sludge biochar and its effect on phosphorus fractionation in soil, we investigated the changes in fractionation and bioavailability of phosphorus in modified sludge biochar and studied the changes in soil characteristics, microbial diversity and response, bioavailability, plant uptake of phosphorus, and heavy metals in contaminated soils after treatment with ferrous sulfate modified sludge biochar. The results demonstrated that ferrous sulfate modifications were conducive to the formation of moderately labile phosphorus in sludge biochar, and the concentrations increased by a factor of 2.7 compared to control. The application of ferrous sulfate-modified sludge biochar to alkaline heavy metal-contaminated soils enhanced the bioavailable, labile, and moderately labile phosphorus contents by a factor of 2.9, 3.0, and 1.6, respectively, whereas it obviously reduced the leachability and bioavailability of heavy metals in soils, exhibited great potentials in the fertilization and remediation of actual heavy metal-contaminated soils in mining areas. The biochar-induced reduction in soil pH, enhancement of organic matter, surface oxygen-containing functional groups, the abundance of Gammaproteobacteria, and its phosphonate degradation activity were primarily responsible for the solubilization of phosphorus from modified biochar in heavy metal-contaminated soils.

Impacts of various amendments on the microbial communities and soil organic carbon of coastal saline-alkali soil in the Yellow River Delta.

The utilization of industrial and agricultural resources, such as desulfurization gypsum and straw, is increasingly favored to improve saline alkali land. However, there is still a lack of comprehensive study on the mechanism of organic carbon turnover under the conditions of desulfurization gypsum and straw application. We studied the changes in soil chemical performance, microbial diversity, and microbial community structure in soils with the addition of various levels of straw (no straw, S0; low straw, Sl; medium straw, Sm; and high straw, Sh) and gypsum (no gypsum, DG0; low gypsum, DGl; and high gypsum, DGh) in a 120-day incubation experiment. The bacterial and fungal community richness was higher in the SmDGl treatment than in the SmDG0 treatment. The microbial community evenness showed a similar pattern between the SmDGl and SmDG0 treatments. The combination of the straw and desulfurization gypsum treatments altered the relative abundance of the main bacterial phyla Bacteroidetes and Firmicutes and the dominant fungal class Sordariomycetes, which increased with the enhancement of the SOC ratio. The combination of the straw and desulfurization gypsum treatments, particularly SmDGl, significantly decreased the soil pH and exchangeable sodium percentage (ESP), while it increased the soil organic carbon, microbial biomass carbon, and activities of soil enzymes. Improvement in the soil salinization environment clearly drove the changes in bacterial α-diversity and community, particularly those in the soil carbon fractions and ESP. In conclusion, these findings provide a strong framework to determine the impact of application practices on soil restoration, and the information gained in this study will help to develop more sustainable and effective integrated strategies for the restoration of saline-alkali soil.

The effect of polyvinyl chloride (PVC) color on biofilm development and biofilm-heavy metal chemodynamics in the aquatic environment

Plastic surfaces are colonized by microorganisms and biofilms are formed in the natural aquatic environment. As the biofilm develops, it changes the density and buoyancy of the plastic-biofilm complex, results in plastic sinking, and increases the heavy metals accumulated by biofilm's mobility and availability in aquatic ecosystems. In this experiment, biofilms were cultured on five colors of polyvinyl chloride (PVC; transparent, green, blue, red, black) in an aquatic environment to investigate the effects of plastic color on biofilm formation and development (Phase 1) and to study the effects of being sunk below the photic zone on biofilm (Phase 2). The PVC color significantly affected the biofilm formation rate but had no impact on the final biofilm biomass. After sinking the biofilm-PVC below the photic zone in Phase 2, the layer of diatoms on the biofilm surface began to disintegrate, and the biomass and Chlorophyll-a (Chla) content of the biofilm decreased, except on the red PVC. Below the photic zone, the microbial community of the biofilm changed from primarily autotrophic microbes to mostly heterotrophic microbes. Microbial diversity increased and extracellular polymeric substances (EPS) content decreased. The primary factor leading to microbial diversity and community structure changes was water depth rather than PVC color. The changes induced in the biofilm led to an increase in the concentration of all heavy metals in the biofilm, related to the increase in microbial diversity. This study provides new insights into the biofilm formation process and the effects on a biofilm when it sinks below the photic zone.

High carbohydrate to protein ratio promotes changes in intestinal microbiota and host metabolism in rainbow trout (Oncorhynchus mykiss) fed plant-based diet

To ensure the sustainability of aquaculture, it is necessary to change the “menu” of carnivorous fish such as rainbow trout from a fish-based diet to one with plant-based ingredients. However, there is a major problem with the growth performance decrease of fish fed with a 100% plant-based diet due to the reduction in feed intake and feed efficiency. For the first time, we incorporated high levels of digestible carbohydrates (high-starch diet) in a 100% plant-based diet during a 12-week feeding trial in order to improve protein utilization for growth (protein sparing effect) and reduce nitrogen waste.We measured the changes in the intestinal microbiota, Short-Chain Fatty Acid (SCFA) levels and metabolic responses in liver. Dietary carbohydrates had a strong effect on alpha and beta diversity and abundance of 12 genera, including Ralstonia and Bacillus in digesta associated microbiota whereas mucosa associated microbiota was less affected. The change in microbial diversity might be linked to the change observed in SCFA production. High levels of Mycoplasma were observed in the intestinal mucosa. Overall, hepatic gene expression was significantly altered by the CHO/protein ratio. Up-regulation of genes involved in glucose metabolism (gcka, gckb, g6pcb2a), down-regulation of genes involved in lipid metabolism (hadh, acox3, srebp2a, and cyp51a) were associated with higher enzymatic activities (such as glucokinase or pyruvate kinase) and higher glycogen levels in the liver, suggesting adequate adaptation to diet. Interestingly, strong correlations were observed between abundances of certain bacterial OTUs and gene expression in the liver.The inclusion of digestible carbohydrates in combination with a 100% plant-based diet, could be a promising way to improve and reduce the use of plant proteins in rainbow trout. In addition, the relationship between intestinal microbiota and host metabolism needs further investigation to better understand fish nutrition.

Metagenomic signatures reveal the key role of phloretin in amelioration of gut dysbiosis attributed to metabolic dysfunction-associated fatty liver disease by time-dependent modulation of gut microbiome.

The importance of gut-liver axis in the pathophysiology of metabolic dysfunction-associated fatty liver disease (MAFLD) is being investigated more closely in recent times. However, the inevitable changes in gut microbiota during progression of the disease merits closer look. The present work intends to assess the time-dependent gut dysbiosis in MAFLD, its implications in disease progression and role of plant-derived prebiotics in its attenuation. Male C57BL/6J mice were given western diet (WD) for up to 16 weeks and phloretin was administered orally. The fecal samples of mice were collected every fourth week for 16 weeks. The animals were sacrificed at the end of the study and biochemical and histological analyses were performed. Further, 16S rRNA amplicon sequencing analysis was performed to investigate longitudinal modification of gut microbiome at different time points. Findings of our study corroborate that phloretin alleviated the metabolic changes and mitigated circulating inflammatory cytokines levels. Phloretin treatment resists WD induced changes in microbial diversity of mice and decreased endotoxin content. Prolonged exposure of WD changed dynamics of gut microbiota abundance and distribution. Increased abundance of pathogenic taxa like Desulfovibrionaceae, Peptostreptococcus, Clostridium, and Terrisporobacter was noted. Phloretin treatment not only reversed this dysbiosis but also modulated taxonomic signatures of beneficial microbes like Ruminococcus, Lactobacillus, and Alloprevotella. Therefore, the potential of phloretin to restore gut eubiosis could be utilized as an intervention strategy for the prevention of MAFLD and related metabolic disorders.

Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes

Understanding the rapid responses of marine microbiomes to environmental disturbances is paramount for supporting early assessments of harm to high-value ecosystems, such as coral reefs. Yet, management guidelines aimed at protecting aquatic life from environmental pollution remain exclusively defined for organisms at higher trophic levels. In this study, 16S rRNA gene amplicon sequencing was applied in conjunction with propidium monoazide for cell-viability assessment as a sensitive tool to determine taxon- and community-level changes in a seawater microbial community under copper (Cu) exposure. Bayesian model averaging was used to establish concentration-response relationships to evaluate the effects of copper on microbial composition, diversity, and richness for the purpose of estimating microbiome Hazard Concentration (mHCx) values. Predicted mHC5 values at which a 5 % change in microbial composition, diversity, and richness occurred were 1.05, 0.72, and 0.38 μg Cu L−1, respectively. Threshold indicator taxa analysis was applied across the copper concentrations to identify taxon-specific change points for decreasing taxa. These change points were then used to generate a Prokaryotic Sensitivity Distribution (PSD), from which mHCxdec values were derived for copper, suitable for the protection of 99, 95, 90, and 80 % of the marine microbiome. The mHC5dec guideline value of 0.61 μg Cu L−1, protective of 95 % of the marine microbial community, was lower than the equivalent Australian water quality guideline value based on eukaryotic organisms at higher trophic levels. This suggests that marine microbial communities might be more vulnerable, highlighting potential insufficiencies in their protection against copper pollution. The mHCx values proposed here provide approaches to quantitatively assess the effects of contaminants on microbial communities towards the inclusion of prokaryotes in future water quality guidelines.

Influence of tree residue retention in Mediterranean forest on soil microbial communities responses to frequent warming and drying events

In the coming decades, Mediterranean forests are likely to experience higher heat-wave frequency that may severely affect soil microbial functioning. Here, we studied the effects of warming intensification on soil microbial communities and tested whether certain types of Mediterranean plant residues favor soil biological resistance to frequent drying and warming events (FDW). To this aim, we set-up mesocosms in which soils originating from six Mediterranean forest stands (i.e, Quercus ilex and Q. pubescens and Pinus halepensis and P. sylvestris monospecific and mixed stands) were amended with corresponding coarse (crushed branches) and fine (crushed twigs with leaves/needles) woody debris. A quantity of residues corresponding to five-fold the equivalent of the quantity left on the floor after tree harvesting/logging (equivalent to 35 gC.kg−1 soil DW) was added to each pot, and mesocosms were laid out into a split-plot design and subjected to FDW. After nineteen months, soil physico-chemical properties and changes in microbial communities' diversity and structure, biomass and extracellular enzymatic activities were measured. We showed that FDW reduced the richness of the soil fungal community by ca. 11% and functional diversity by ca. 4% and increased bacterial richness by ca. 40%. We observed a drastic down-regulation of extracellular enzyme activities related with N and C cycles (respectively -44% for protease, -54% for cellulase and -31% for tyrosinase activities). We also found that residues inputs types (fine vs. coarse) only slightly mitigate those effects, while species origin did. Our study showed that residues retention could alleviate the consequences of hydric and thermic stresses on microbial communities by modulating communities’ resistance in specific stands. These results suggest that tree residues retention, in specific stands, could contribute to sustain soil biological properties in the context of Mediterranean climate intensification.

Effects of polyethylene microplastics on properties, enzyme activities, and the succession of microbial community in Mollisol: At the aggregate level

Soil, as a heterogeneous body, is composed of different-sized aggregates. There is limited data available on the potential role of microplastics (MPs) in microbial properties at the soil aggregate level. In this study, changes in microbial construction and diversity in farmland bulk soil and aggregates induced by polyethylene MPs (PE-MPs) were investigated at a dose of 0.5% (w/w) through 16s rDNA sequencing and enzyme activity measurements of different particle size aggregates in incubated soil. The presence of low-dose PE-MPs increased the proportion of >1 mm soil aggregates fraction, and decreased soil available nitrogen and available phosphorus in bulk soils. Furthermore, low-dose PE-MPs increased bacterial richness and diversity in 1–0.5 and < 0.25 mm fractions and decreased operational taxonomic unit, abundance-based coverage estimator, and Chao1 indices in bulk soil and >1 mm fractions. The levels of predicted functional genes taking part in the biodegradation and metabolism of exogenous substances also increased. At the phylum level, PE-MPs changed the proportion of Proteobacteria and Actinobacteria. The variations in soil aggregate properties were significantly correlated with the bacterial communities’ composition and diversity. This study deepens our perception of the soil microenvironment, microbial community composition, and diversity in response to PE-MPs.

Discrepant diversity patterns and function of bacterial and fungal communities on an earthquake-prone mountain gradient in Northwest Sichuan, China.

Patterns of microbial diversity on elevational gradients have been extensively studied, but little is known about those patterns during the restoration of earthquake-fractured alpine ecosystems. In this study, soil properties, soil enzyme activities, abundance and diversity of soil bacterial and fungal communities at four positions along a 2.6-km elevational gradient in the Snow Treasure Summit National Nature Reserve, located in Pingwu County, Southwest China. Although there were no significant changes in the soil chemical environment, bacterial and fungal communities were significantly different at different elevations. The overall fungal community presented an N-shaped diversity pattern with increasing elevation, while bacterial diversity decreased significantly with elevation. Changes in microbial diversity were associated with soil phosphorus, plant litter, and variations in dominant microbial taxa. Differences in enzyme activities among elevations were regulated by microbial communities, with changes in catalase and acid phosphatase activities mainly controlled by Acidobacteria and Planctomycetaceae bacteria, respectively (catalase: p < 0.001; acid phosphatase: p < 0.01), and those in β-glucosidase, sucrase, and urease activities mainly controlled by fungi. The β-glucosidase and sucrase were both positively correlated with Herpotrichiellaceae, and urease was positively correlated with Sebacinaceae (p < 0.05). These findings contribute to the conservation and management of mountain ecosystems in the face of changing environmental conditions. Further research can delve into the specific interactions between microbial communities, soil properties, and vegetation to gain deeper insights into the intricate ecological dynamics within earthquake-prone mountain ecosystems.

Examining the Interaction between Exercise, Gut Microbiota, and Neurodegeneration: Future Research Directions.

Physical activity has been demonstrated to have a significant impact on gut microbial diversity and function. Emerging research has revealed certain aspects of the complex interactions between the gut, exercise, microbiota, and neurodegenerative diseases, suggesting that changes in gut microbial diversity and metabolic function may have an impact on the onset and progression of neurological conditions. This study aimed to review the current literature from several databases until 1 June 2023 (PubMed/MEDLINE, Web of Science, and Google Scholar) on the interplay between the gut, physical exercise, microbiota, and neurodegeneration. We summarized the roles of exercise and gut microbiota on neurodegeneration and identified the ways in which these are all connected. The gut-brain axis is a complex and multifaceted network that has gained considerable attention in recent years. Research indicates that gut microbiota plays vital roles in metabolic shifts during physiological or pathophysiological conditions in neurodegenerative diseases; therefore, they are closely related to maintaining overall health and well-being. Similarly, exercise has shown positive effects on brain health and cognitive function, which may reduce/delay the onset of severe neurological disorders. Exercise has been associated with various neurochemical changes, including alterations in cortisol levels, increased production of endorphins, endocannabinoids like anandamide, as well as higher levels of serotonin and dopamine. These changes have been linked to mood improvements, enhanced sleep quality, better motor control, and cognitive enhancements resulting from exercise-induced effects. However, further clinical research is necessary to evaluate changes in bacteria taxa along with age- and sex-based differences.

Coronavirus Disease 2019 (COVID-19) Pandemic Lifestyle Changes May Have Influenced Small Bowel Microbial Composition and Microbial Resistance

BackgroundThe coronavirus disease 2019 (COVID-19) global pandemic necessitated many severe lifestyle changes, including lockdowns, social distancing, altered food consumption and exercise patterns, and extensive hygiene practices. These extensive changes may have affected the human gut microbiome, which is highly influenced by lifestyle.AimsTo examine the potential effects of pandemic-related lifestyle changes on the metabolically relevant small bowel microbiome.MethodsAdult subjects presenting for upper endoscopy without colonoscopy were identified and divided into two matched groups: pre-pandemic (February 2019–March 2020) and intra-pandemic (April 2021–September 2021, all COVID-19 negative). Duodenal aspirates and blood samples were collected. Duodenal microbiomes were analyzed by 16S rRNA sequencing. Serum cytokine levels were analyzed by Luminex FlexMap3D.ResultsFifty-six pre-pandemic and 38 COVID-negative intra-pandemic subjects were included. There were no significant changes in duodenal microbial alpha diversity in the intra-pandemic vs. pre-pandemic group, but beta diversity was significantly different. The relative abundance (RA) of phylum Deinococcus-Thermus and family Thermaceae, which are resistant extremophiles, was significantly higher in the intra-pandemic vs. pre-pandemic group. The RA of several Gram-negative taxa including Bacteroidaceae (phylum Bacteroidetes) and the Proteobacteria families Enterobacteriaceae and Pseudomonadaceae, and the RA of potential disruptor genera Escherichia-Shigella and Rothia, were significantly lower in the intra-pandemic vs. pre-pandemic group. Circulating levels of interleukin-18 were also lower in the intra-pandemic group.ConclusionsThese findings suggest the small bowel microbiome underwent significant changes during the pandemic, in COVID-19-negative individuals. Given the key roles of the small bowel microbiota in host physiology, this may have implications for human health.

Behaviour and sun exposure in holidaymakers alters skin microbiota composition and diversity.

Introduction: The skin microbiota plays a crucial role in maintaining epidermal homeostasis. Ultraviolet radiation (UVR) and other environmental challenges can impact the skin microbiota through direct and indirect mechanisms. This study aimed to investigate the effects of sun exposure on the skin microbiota and its relationship with individual skin phototypes. Methods: Healthy volunteers (n = 21 [4M, 17F], mean age 33.2years) holidayed in a sunny destination for a minimum of 7days with swabs taken pre-holiday and up to 84days post-holiday. Participant group was categorised by individual typology angle (ITA) classification and the composition of the skin microbiota was examined using 16S rRNA gene sequencing. Results: In the entire cohort and at all time points, the major bacterial phyla were Actinobacteria, Proteobacteria and Firmicutes. There was a significant change in microbial beta diversity at day 28 post-holiday, compared to baseline, for all participants. However, when participants were segregated into three cohorts dependent on the degree of skin tanning response between baseline (pre-holiday) and immediately one-day post-holiday, there was a reduction in Proteobacteria in the sun-seeking participants 1day after the holiday, which recovered over time. Discussion: These findings suggest that sun exposure can affect the diversity and composition of the skin microbiota, which may have downstream effects on skin health.

Investigating the changes of texture, physicochemical properties, microbial diversity, and volatile compounds of quinoa fresh noodles during storage time

AbstractBackgroundQuinoa was suggested to substitute in noodles with positive effects of cardiovascular disease, metabolic, and gastrointestinal systems. However, quinoa fresh noodles (QFN) were hard to preserve but constrain industrial production. The deteriorative changes in the quality and relative parameters of QFN at 25 ± 1°C are lacking and needed to investigate.FindingsIn this study, QFN was sampled every 12 h at 25 ± 1°C, and found that the total plate count exceeded safety limit (5 log10 CFU/g) in 24 h. Bacillus, Staphylococcus, Aspergillus, and Filobasidium were the dominant spoilage microorganisms, where Bacillus was significantly increased and accounted over 90% of bacteria after spoilage. The volatile compounds changed significantly, where aldehydes decreased from 58.25% to 30.09%, while easters and alcohols increased from 2.29% to 14.84%, and 7.78% to 20.28% separately. With increasing of storage time, the water content and water activity decreased. Besides, strongly bound water decreased from 12.51% to 7.63%, weakly bound water and free water increased. The color of QFN turned to dark and red, where a value increased from 2.11 to 3.82, while L value decreased from 75.20 to 64.56. pH of QFN also decreased during storage. The quality index of QFN was qualified with decreased texture properties (hardness, springiness, and chewiness) and significantly increased cooking loss rate (8.65%–12.74%) and cooked broken rate (0%–26.67%).ConclusionsThe storage time of QFN was 24 h at 25 ± 1°C. The textural changes and certain indexes changed significantly after spoilage. And relative indexes of QFN qualities presented significant correlation with microorganisms.Significance and NoveltyBacillus in QFN may contribute significant changes in spoilage. The correlation analysis figured out the possible reasons for qualities changes of QFN.

Changes in quality and microbial diversity of refrigerated carp fillets treated by chitosan/zein bilayer film with curcumin/nisin-loaded pectin nanoparticles

The quality of freshwater fish is easy to deteriorate during postmortem storage, so it is necessary to find an effective method to extend the shelf life of fish fillets. The aim of this study is mainly to develop a novel bilayer active film with curcumin/nisin-loaded pectin nanoparticles (CZ-NPs) and evaluate its effect on the quality of fish fillets. The selected sensory, physicochemical (pH, color qualities, TVB-N, TBARS, biogenic amines, moisture state) and microbial properties (microbial enumeration and high-throughput sequencing) were analyzed to confirm the preservative mechanism of films on the fillets. During storage at 4 °C, better sensory evaluation feedback and lower total volatile base nitrogen in the film treated samples was observed when compared to the control samples. Additionally, CZ-NPs film effectively inhibited oxidation, with the final reductions of 1.04 mg MDA/kg flesh when compared to control. As suggested by low-field NMR and magnetic resonance imaging, film treated fillets presented higher water holding capacity by controlling transformation from immobilized to free water. Meanwhile, lower microbial enumerations were also recorded in the CZ-NPs film treated group, which was reduced by a range of 1.8–2.3 log CFU/g on day 10 when compared to control. High-throughput sequencing results showed that the Pseudomonas constituted the main spoilage bacteria of fillets, and CZ-NPs film contributed to the notably suppressed growth of Pseudomonas. As a result, CZ-NPs film showed a desirable application to extend the shelf life of refrigerated flesh, as an alternative for fishery product packaging and preservation.

Fine root litter quality regulates soil carbon storage efficiency in subtropical forest soils

Decomposing root litter is a major contributor to soil carbon (C) storage in forest soils. During decomposition, the quality of root litter could play a critical role in soil C storage. However, it is unclear whether root litter quality influences soil C storage efficiency. We conducted a two-year greenhouse decomposition experiment using 13C-labeled fine root litter of two tree species to investigate how root litter quality, represented by C to nitrogen (C/N) ratios, regulates decomposition and C storage efficiency in subtropical forest soils in China. ‘High-quality’ root litter (C/N ratio = 26) decayed faster during the first year (0–410 days), whereas ‘low-quality’ root litter (C/N ratio = 46) decomposed faster toward the end of the two-year period (598–767 days). However, over the two years of the study, mass loss from high-quality root litter (29.14 ± 1.42%) was lower than ‘low-quality’ root litter (33.01 ± 0.54%). Nonetheless, root litter C storage efficiency (i.e., the ratio of new root litter-derived soil C to total mineralized root litter C) was significantly greater for high-quality root litter, with twice as much litter-derived C stored in soils compared to low-quality root litter at the end of the experiment. Root litter quality likely influenced soil C storage via changes in microbial diversity, as the decomposition of high-quality litter declined with increasing bacterial diversity, whereas the amount of litter-derived soil C from low-quality litter increased with fungal diversity. Our results thus reveal that root litter quality mediates decomposition and C storage in subtropical forest soils in China and future work should consider the links between root litter quality and soil microbial diversity.

Back to the 'roots' of research: a hypothesis-driven approach provides predictive understanding of plant-herbivore-microbe interactions.

This article is a Commentary on Böttner et al. (2023), 239: 1475–1489.

Alterations of the gut microbiota associated with the occurrence and progression of viral hepatitis.

Gut microbiota is the largest population of microorganisms and is closely related to health. Many studies have explored changes in gut microbiota in viral hepatitis. However, the correlation between gut microbiota and the occurrence and progression of viral hepatitis has not been fully clarified. PubMed and BioProject databases were searched for studies about viral hepatitis disease and 16S rRNA gene sequencing of gut microbiota up to January 2023. With bioinformatics analyses, we explored changes in microbial diversity of viral hepatitis, screened out crucial bacteria and microbial functions related to viral hepatitis, and identified the potential microbial markers for predicting risks for the occurrence and progression of viral hepatitis based on ROC analysis. Of the 1389 records identified, 13 studies met the inclusion criteria, with 950 individuals including 656 patient samples (HBV, n = 546; HCV, n = 86; HEV, n = 24) and 294 healthy controls. Gut microbial diversity is significantly decreased as the infection and progression of viral hepatitis. Alpha diversity and microbiota including Butyricimonas, Escherichia-Shigella, Lactobacillus, and Veillonella were identified as the potential microbial markers for predicting the risk of development of viral hepatitis (AUC>0.7). Microbial functions including tryptophan metabolism, fatty acid biosynthesis, lipopolysaccharide biosynthesis, and lipid metabolism related to the microbial community increased significantly as the development of viral hepatitis. This study demonstrated comprehensively the gut microbiota characteristics in viral hepatitis, screened out crucial microbial functions related to viral hepatitis, and identified the potential microbial markers for predicting the risk of viral hepatitis.

Changes in the Bacterial Community Composition of Cultivated Soil after Digging up Operations for Laying a Pipeline

Our study aimed to evaluate the impact of the pipeline installation on the bacterial composition in cultivated soil by metagenomic analyses performed before the excavation and in the following three years. Differential abundance analysis was obtained using DESeq2 from the GAIA pipeline to verify the bacteriological diversity in soils collected after the reference year (2013). Soil samples presented a different distribution of taxa, especially in 2014, in which a further allocation at the phylum and family levels was observed compared to the previous year (2013). The phyla Bacteroidetes and Firmicutes increased significantly, while the phylum Actinobacteria, most abundant in 2013, showed reduced abundance; moreover, Chloroflexi and Planctomycetes decreased considerably, and Verrucomicrobia was absent. The significant differences in the taxonomic composition and structure of the soil microbial community were due to critical stress conditions following the soil excavations. The bacterial communities were capable of profound physiological and genetic changes, implementing different mechanisms for survival and adaptation to an environment with changed conditions. The implication of changes in microbial diversity before and after the mechanical insult of soil has been determined.

Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration.

Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.