Correlation between the gut microbiome and neurodegenerative diseases:a review of metagenomics evidence

A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.

Lacticaseibacillus rhamnosus Probio-M9 may be vertically transmitted from mother to infant during lactation based on faeces metagenomics

Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study recruited one pregnant woman,who ingested Probio-M9 daily from 35 weeks of gestation to delivery.Feces of the mother-infant pair were regularly collected from one month before delivery to 6 months of infant's age for metagenomic sequencing.Probio-M9 genomes were mappable to all infant fecal samples,suggesting the ingested probiotics could be vertically transmitted from mother to infant.Infant-or mother-specific differential metabolic pathways were found between the maternal and infant's gut microbiome,implicating apparent differences in the intestinal metagenomic potential/function between the mother and the infant.In conclusion,maternal ingestion of Probio-M9 during the final weeks of gestation could deliver to the infant gut.The findings provided novel insights into shaping infant's gut microbiota.

Application of metagenomics in the human gut microbiome

There are more than 1000 microbial species living in the complex human intestine.The gut microbial community plays an important role in protecting the host against pathogenic microbes,modulating immunity,regulating metabolic processes,and is even regarded as an endocrine organ.However,traditional culture methods are very limited for identifying microbes.With the application of molecular biologic technology in the field of the intestinal microbiome,especially metagenomic sequencing of the next-generation sequencing technology,progress has been made in the study of the human intestinal microbiome.Metagenomics can be used to study intestinal microbiome diversity and dysbiosis,as well as its relationship to health and disease.Moreover,functional metagenomics can identify novel functional genes,microbial pathways,antibiotic resistance genes,functional dysbiosis of the intestinal microbiome,and determine interactions and co-evolution between microbiota and host,though there are still some limitations.Metatranscriptomics,metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome.This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects.The limitations of metagenomics to be overcome are also discussed.Metatranscriptomics,metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.

Viral Metagenomics Analysis of Planktonic Viruses in East Lake,Wuhan,China

East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a large number of viruses.However,little is known about their genetic diversity because of the limited techniques for culturing viruses.In this study,we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring,Summer,Autumn,and Winter.The libraries from four samples each generated 234,669,71,837,12,820,and 34,236 contigs(>90 bp each),respectively.The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families,with the majority of contigs homologous to DNA viruses,including members of Myoviridae,Podoviridae,Siphoviridae,Phycodnaviridae,and Microviridae,which infect bacteria or algae,and members of Circoviridae,which infect invertebrates and vertebrates.The highest viral genetic diversity occurred in samples collected in August,then December and June,and the least diversity in March.Most contigs have low-sequence identities with known viruses.PCR detection targeting the conserved sequences of genes(g20,psbA,psbD,and DNApol)of cyanophages further confirmed that there are novel cyanophages in the East Lake.Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.

Diagnostic value of metagenomics next-generation sequencing technology in disseminated strongyloidiasis

The symptoms of disseminated strongyloidiasis are not typical,and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas.We report a 70-year-old woman who was diagnosed with Guillain-Barrésyndrome due to autonomic disturbance,symmetrical bulbar palsy,and lower-motor-nerve damage in the extremities;her symptoms continued to worsen after hormone and immunoglobulin therapy.Later,parasitic larvae were found in the patient’s gastric fluid,and metagenomic next generation sequencing(mNGS)detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms.The patient was diagnosed with disseminated strongyloidiasis.The patient was given albendazole for anthelmintic treatment,but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden.In recent years,mNGS has been increasingly used in clinical practice,and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas.Especially during the corona virus disease 2019 pandemic,mNGS technology has irreplaceable value in identifying the source of infection.

Metagenomics and microbiome of infant:old and recent instincts

The human microbiota is made up of trillions of bacteria that live in the human being,whereas the microbiome is made up of the microbiota's genes and gene products.Bacteria have long been thought of as pathogens that eventually lead to human illness.Bacteria are increasingly recognized as generally beneficial commensal organisms and hence crucial to proper and healthy human development,thanks to breakthroughs in both cultivation-based approaches and the advent of metagenomics.This relatively new field of medical study has given more information on illnesses such as inflammatory bowel disease,obesity,metabolic and atopic disorders.However,there is a lot we don't know about the complexities of microbe-microbe and microbe-host interactions.Future work targeted at resolving crucial concerns about the early formation of the microbiome,in addition,what determines its dysbiosis,will most likely lead to long-term mitigation of health.In this article,review the research on prenatal and newborn microbiome modulations,the role of maternal and environmental variables on forming the newborn microbiome,and future issues and directions in the exciting new field of metagenomic medicine.

Metagenomics reveals the microbial community and functional metabolism variation in the partial nitritation-anammox process:From collapse to recovery

Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.

Clinical applications of metagenomics next-generation sequencing in infectious diseases

Infectious diseases are a great threat to human health.Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases.Metagenomics next-generation sequencing(mNGS)is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample.With the development of sequencing and bioinformatics technologies,mNGS is moving from research to clinical application,which opens a new avenue for pathogen detection.Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases,especially in difficult-to-detect,rare,and novel pathogens.However,there are several hurdles in the clinical application of mNGS,such as:(1)lack of universal workflow validation and quality assurance;(2)insensitivity to high-host background and low-biomass samples;and(3)lack of standardized instructions for mass data analysis and report interpretation.Therefore,a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases.This review briefly introduces the history of next-generation sequencing,mainstream sequencing platforms,and mNGS workflow,and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.

Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes

Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging.In this study,we developed a sequence-based functional metagenomics procedure for mining the diversity of copper(Cu)resistance gene copA in global microbiomes,by combining the metagenomic assembly technology,local BLAST,evolutionary trace analysis(ETA),chemical synthesis,and conventional functional genomics.In total,87 metagenomes were collected from a public database and subjected to copA detection,resulting in 93,899 hits.Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates,which were further subjected to ETA.Eventually,175 novel copA sequences of high quality were discovered.Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins,with 55 sequences from totally unknown species.Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli(DcopA).The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake.One recombinant harboring copA-like 15(copAL15)successfully restored Cu resistance of the host with a substantially enhanced Cu uptake.Two novel copA genes were fused with the gfp gene and expressed in E.coli for microscopic observation.Imaging results showed that they were successfully expressed and their proteins were localized to the membrane.The results here greatly expand the diversity of known CopA proteins,and the sequence-based procedure developed overcomes biases in length,screening methods,and abundance of conventional functional metagenomics.

METAGENOMICS COMBINED WITH HIGHTHROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORN STRAW UNDER THERMOPHILIC AND HIGH OLR

Dry corn straw(DCS)is usually used in anaerobic digestion(AD),but fresh corn straw(FCS)has been given less consideration.In this study,the thermophilic AD of single-substrate(FCS and DCS)and co-digestion(straw with cattle manure)were investigated.The results show that when FCS was used as the single-substrate for AD,the methane production was 144 mL·g^(−1)·VS^(−1),which was 7.5%and 19.6%higher than that of single DCS and FCS with cattle manure,respectively.In addition,the structure of FCS was loose and coarse,which was easier to be degraded than DCS.At the hydrolysis and acidification stages,Clostridium_sensu_stricto_1,Clostridium_sensu_stricto_7 and Sporosarcina promoted the decomposition of organic matter,leading to volatile fatty acids(VFAs)accumulation.Methanosarcina(54.4%)activated multifunctional methanogenic pathways to avoid the VFAs inhibition,which was important at the CH_(4) production stage.The main pathway was hydrogenotrophic methanogenesis,with genes encoding formylmethanofuran dehydrogenase(K00200-K00203)and tetrahydromethanopterin Smethyltransferase(K00577-K00584).Methanosarcina also activated acetotrophic and methylotrophic methanogenesis pathways,with genes encoding acetyl phosphate(K13788)and methyl-coenzyme M reductase(K04480,K14080 and K14081),respectively.In the co-digestion,the methanogenic potential of FCS was also confirmed.This provides a scientific basis for regulating AD of crop straw.

Assessment of residual chlorine in soil microbial community using metagenomics

Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic.However,at present,little is known about the impact of residual chlorine on the soil micro-ecological environment.Herein,we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water,and then analyzed the influence on the soil microbial community using metagenomics.After 14-d continuous chlorine treatment,there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil.Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment,it recovered to the original status.The abundance of several resistance genes changed by 7 d and recovered by 14 d.According to our results,the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth(shoot length and fresh weight)and soil micro-ecology.In general,our study assisted with environmental risk assessments relating to the application of chlorine-containing disinfectants and minimization of risks to the environment during disease control,such as COVID-19.

Metagenomics: Facts and Artifacts, and Computational Challenges

Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many （so-far） unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing （NGS） techniques.

Chain Elongation Using Native Soil Inocula:Exceptional n-Caproate Biosynthesis Performance and Microbial Mechanisms

This study demonstrates the feasibility and effectiveness of utilizing native soils as a resource for inocula to produce n-caproate through the chain elongation(CE)platform,offering new insights into anaerobic soil processes.The results reveal that all five of the tested soil types exhibit CE activity when supplied with high concentrations of ethanol and acetate,highlighting the suitability of soil as an ideal source for n-caproate production.Compared with anaerobic sludge and pit mud,the native soil CE system exhibited higher selectivity(60.53%),specificity(82.32%),carbon distribution(60.00%),electron transfer efficiency(165.00%),and conductivity(0.59 ms∙cm^(-1)).Kinetic analysis further confirmed the superiority of soil in terms of a shorter lag time and higher yield.A microbial community analysis indicated a positive correlation between the relative abundances of Pseudomonas,Azotobacter,and Clostridium and n-caproate production.Moreover,metagenomics analysis revealed a higher abundance of functional genes in key microbial species,providing direct insights into the pathways involved in n-caproate formation,including in situ CO_(2)utilization,ethanol oxidation,fatty acid biosynthesis(FAB),and reverse beta-oxidation(RBO).The numerous functions in FAB and RBO are primarily associated with Pseudomonas,Clostridium,Rhodococcus,Stenotrophomonas,and Geobacter,suggesting that these genera may play roles that are involved or associated with the CE process.Overall,this innovative inoculation strategy offers an efficient microbial source for n-caproate production,underscoring the importance of considering CE activity in anaerobic soil microbial ecology and holding potential for significant economic and environmental benefits through soil consortia exploration.

Soil bacterial and fungal communities resilience to long-term nitrogen addition in subtropical forests in China

Atmospheric nitrogen(N)deposition is predicted to increase,especially in the subtropics.However,the responses of soil microorganisms to long-term N addition at the molecular level in N-rich subtropical forests have not been clarified.A long-term nutrient addition experiment was conducted in a subtropical evergreen old-growth forest in China.The four treatments were:control,low N(50 kg N ha^(-1)a^(-1)),high N(100 kg N ha^(-1)a^(-1)),and combined N and phosphorus(P)(100 kg N ha^(-1)a^(-1)+50 kg P ha^(-1)a^(-1)).Metagenomic sequencing characterized diversity and composition of soil microbial communities and used to construct bacterial/fungal co-occurrence networks.Nutrient-treated soils were more acidic and had higher levels of dissolved organic carbon than controls.There were no significant differences in microbial diversity and community composition across treatments.The addition of nutrients increased the abundance of copiotrophic bacteria and potentially beneficial microorganisms(e.g.,Gemmatimonadetes,Chaetomium,and Aureobasidium).Low N addition increased microbiome network connectivity.Three rare fungi were identified as module hubs under nutrient addition,indicating that low abundance fungi were more sensitive to increased nutrients.The results indicate that the overall composition of microbial communities was stable but not static to long-term N addition.Our findings provide new insights that can aid predictions of the response of soil microbial communities to long-term N addition.

Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens

Background Dietary supplementation of xylooligosac charides(XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites.But no study investigated and compared the effect of in ovo feeding of xylobiose(XOS2) and xy lotriose(XOS3) in chickens.This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens.A total of 144 fertilized chicken eggs were divided into three groups:a) non-injected control(CON),b) XOS2,and c) XOS3.On the 17^(th) embryonic day,the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac.After hatching,the chicks were raised for 21 d.Blood was collected on d 14 to measure plasma immunoglobulin.Cecal digests were collected for measuring short-chain fatty acids(SCFA) on d 14 and 21,and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.Results The results were considered significantly different at P<0.05.ELISA quantified plasma IgA and IgG on d 14chickens,revealing no differences among the treatments.Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d 21.However;the SCFA concentrations were lower in the XOS3 than in the CON group on d 21.The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7,and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON.There was a reduction in the relative abundance of genus Clostridium sense stricto 1 in the XOS2 compared to the CON on d 7 and the genus Ruminococcus,torques in both XOS2 and XOS3 groups compared to the CON on d 21.The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation Ⅰ and L-histidine degradation Ⅰpathways,which contribute to improved gut health,respectivelyc in the microbiome on d 7.In contrast,on d 21,the XOS2 and XOS3 groups enriched the thiamin salvage Ⅱ,L-isoleucine biosynthesis Ⅳ,and O-antigen building blocks biosynthesis(E. coli) pathways,which are indicative of improved gut health.Unlike the XOS3 and CON,the microbiome enriched the pathways associated with energy enhancement,including flavin biosynthesis Ⅰ,sucrose degradation Ⅲ,and Calvin-Benson-Bassham cycle pathways,in the XOS2 group on d 21.Conclusion In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels.The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups.The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.

Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones

Background Sex hormones play important roles in the estrus return of post-weaning sows.Previous studies have demonstrated a complex and bi-directional regulation between sex hormones and gut microbiota.However,the extent to which the gut microbiota affects estrus return of post-weaning sows is largely unknown.Results In this study,we first screened 207 fecal samples from well-phenotyped sows by 16S rRNA gene sequencing and identified significant associations between microbes and estrus return of post-weaning sows.Using metagenomic sequencing data from 85 fecal samples,we identified 37 bacterial species that were significantly associated with estrus return.Normally returning sows were characterized by increased abundances of L.reuteri and P.copri and decreased abundances of B.fragilis,S.suis,and B.pseudolongum.The changes in gut microbial composition significantly altered the functional capacity of steroid hormone biosynthesis in the gut microbiome.The results were confirmed in a validation cohort.Significant changes in sex steroid hormones and related compounds were found between normal and non-return sows via metabolome analysis.An integrated analysis of differential bacterial species,metagenome,and fecal metabolome provided evidence that normal return-associated bacterial species L.reuteri and Prevotella spp.participated in the degradation of pregnenolone,progesterone,and testosterone,thereby promoting estrogen biosynthesis.Furthermore,the microbial metabolites related to sow energy and nutrient supply or metabolic disorders also showed relationships with sow estrus return.Conclusions An integrated analysis of differentially abundant bacterial species,metagenome,and fecal metabolome revealed the involvement of L.reuteri and Prevotella spp.in sow estrus return.These findings provide deep insight into the role of gut microbiota in the estrus return of post-weaning sows and the complex cross-talk between gut microbiota and sex hormones,suggesting that the manipulation of the gut microbiota could be an effective strategy to improve sow estrus return after weaning.

揭示氨对正己酸生产影响的机制——影响途径、关键酶和微生物

n-Caproate,which is produced via chain elongation(CE)using waste biomass,can supply various fossilderived products,thus advancing the realization of carbon neutrality.Ammonia released from the degradation of nitrogen-rich waste biomass can act as a nutrient or an inhibitor in anaerobic bioprocesses,including CE,with the distinction being primarily dependent on its concentration.Currently,the optimal concentration of ammonia and the threshold of toxicity for open-culture n-caproate production using ethanol as an electron donor,along with the underlying mechanisms,remain unclear.This study revealed that the optimal concentration of ammonia for n-caproate production was 2.0 g∙L^(-1),whereas concentrations exceeding this threshold markedly suppressed the CE performance.Exploration of the mechanism revealed the involvement of two forms of ammonia(i.e.,ammonium ions and free ammonia)in this inhibitory behavior.High ammonia levels(5.0 g∙L^(-1))induced excessive ethanol oxidation and suppressed the reverse β-oxidation(RBO)process,directly leading to the enhanced activities of enzymes(phosphotransacetylase and acetate kinase)responsible for acetate formation and diminished activities of butyryl-coenzyme A(CoA):acetyl-CoA transferase,caproyl-CoA:butyryl-CoA transferase,and caproyl-CoA:acetyl-CoA transferase that are involved in the syntheses of n-butyrate and n-caproate.Furthermore,the composition of the microbial community shifted from Paraclostridium dominance(at 0.1 g∙L^(-1)ammonia)to a co-dominance of Fermentimonas,Clostridium sensu stricto 12,and Clostridium sensu stricto 15 at 2.0 g∙L^(-1)ammonia.However,these CE-functional bacteria were mostly absent in the presence of excessive ammonia(5.0 g∙L^(-1)ammonia).Metagenomic analysis revealed the upregulation of functions such as RBO,fatty acid synthesis,K^(+)efflux,adenosine triphosphatase(ATPase)metabolism,and metal cation export in the presence of 2.0 g∙L^(-1)ammonia,collectively contributing to enhanced n-caproate production.Conversely,the aforementioned functions(excluding metal cation export)and K^(+)influx were suppressed by excessive ammonia,undermining both ammonia detoxification and n-caproate biosynthesis.The comprehensive elucidation of ammonia-driven mechanisms influencing n-caproate production,as provided in this study,is expected to inspire researchers to devise effective strategies to alleviate ammonia-induced inhibition.

Structure and functional heterogeneity of soil microbial communities in different farmland types on the Loess Plateau

Background,aim,and scope Soil microbes are important drivers of nutrient transformation and energy f low.Reclaiming forest land for agricultural use may have profound effects on soil properties and microbial communities.However,the response of soil microbial communities to soil reclamation in the dryland agroecosystem is less understood.Therefore,it is necessary to investigate the changes of soil microbial communities driven by land use conversion to promote nutrient cycling in reclaimed farmland.Materials and methods Based on the metagenomic technique,we evaluated the microbial composition and function of the newly created farmland(NF)after reclamation with two types of traditional farmland(slope farmland(SF),checkdam farmland(CF))on the Loess Plateau,and explored the response of nutrient cycling function to dominant genera and soil properties.Results The results showed that Proteobacteria,Actinobacteria,and Acidobacteria were prevalent in the three types of farmlands.Compared with SF and CF,NF increased the relative abundance of Actinobacteria and Nocardioides,as well as genes related to amino acid metabolism and carbohydrate metabolism.The relative abundance of functional genes related to carbon and nitrogen cycling in the NF was higher than that in the traditional farmland(SF and CF).The relative abundance of nutrient cycling functional genes was positively correlated with dominant genera in the three types of farmlands.Except for pH,soil physicochemical factors were negatively correlated with genes related to amino acid metabolism and carbon cycle.Discussion Previous studies have shown that the nutrient conditions of the soil may intensify the competition between the eutrophic and oligotrophic microbial populations.After long-term cultivation and fertilization,the soil properties of traditional farmland were significantly different from those of NF,leading to the differentiation of dominant microbial groups.Microbes usually have functional redundancy to cope with changing environments.Soil microbes in traditional farmland may contain more genes related to replication and repair,cell growth and death,and environmental adaptation in response to disturbances caused by agricultural practices.On the contrary,the NF was less disturbed by agricultural activities,and the soil properties were more similar to forest land,so the carbon and nitrogen cycle function genes were more abundant.The nutrient cycling function was affected by the abundance of microbial dominant groups and soil properties,which may be related to the availability of soil nutrients and agricultural disturbance in different farmlands.Aspects of soil microbial-driven nutrient cycling in agriculture could be regulated in sustainable method.Conclusions The change from forest land to farmland kept more carbon and nitrogen cycling function in the newly created farmland,while long-term agricultural activities have drastically changed the functional structure of traditional farmland,resulting in the nutrient cycling function more concentrated to meet the needs of crop growth.Recommendations and perspectives Hence,it is necessary to apply sustainable agricultural method to regulate microbial-driven nutrient cycling.The insights are meaningful for sustainable agricultural development and land management in arid areas.

Conservation metagenomics: a new branch of conservation biology

Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade,increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology,nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.

Metagenomic analysis revealing the metabolic role of microbial communities in the free amino acid biosynthesis of Monascus rice vinegar during fermentation

Free amino acid(FAA)is the important component of vinegar that infl uences quality perception and consumer acceptance.FAA is one of the major metabolites produced by microorganisms;however,the microbial metabolic network on FAA biosynthesis remains unclear.Through metagenomic analysis,this work aimed to elucidate the roles of microbes in FAA biosynthesis during Monascus rice vinegar fermentation.Taxonomic profiles from functional analyses showed 14 dominant genera with high contributions to the metabolism pathways.The metabolic network for FAA biosynthesis was then constructed,and the microbial distribution in different metabolic pathways was illuminated.The results revealed that 5 functional genera were closely involved in FAA biosynthesis.This study illuminated the metabolic roles of microorganisms in FAA biosynthesis and provided crucial insights into the functional attributes of microbiota in vinegar fermentation.