The interaction of gut microbiota, genetic variation, and diet in autism spectrum disorder

The human gut is home to nearly 100 trillion microbes1,which constitute the human gut microecological system.The microbiota–gut–brain(MGB)axis is a two‐way communication pathway between gut microbiota and the brain through the immune system,metabolism,and the enteric nervous system.An increasing amount of clinical evidence indicates that abnormal MBG axis communication caused by intestinal ecosystem imbalance can affect the development of many neurological diseases,such as Parkinson's disease,Alzheimer's disease,and autism spectrum disorder(ASD)2.

Impact of the gut microbiome on atherosclerosis

Atherosclerosis is a chronic inflammatory metabolic disease with a complex pathogenesis.However,the exact details of its pathogenesis are still unclear,which limits effective clinical treatment of atherosclerosis.Recently,multiple studies have demonstrated that the gut microbiota plays a pivotal role in the onset and progression of atherosclerosis.This review discusses possible treatments for atherosclerosis using the gut microbiome as an intervention target and summarizes the role of the gut microbiome and its metabolites in the development of atherosclerosis.New strategies for the treatment of atherosclerosis are needed.This review provides clues for further research on the mechanisms of the relationship between the gut microbiota and atherosclerosis.

gcCov:Linked open data for global coronavirus studies

Impact Statement We present a method of mapping data from publicly available genomics and publication resources to the Resource Description Framework(RDF)and implement a server to publish linked open data(LOD).As one of the largest and most comprehensive semantic databases about coronaviruses,the resulted gcCov database demonstrates the capability of using data in the LOD framework to promote correlations between genotypes and phenotypes.These correlations will be helpful for future research on fundamental viral mechanisms and drug and vaccine designs.

Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics

Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems.Bathyarchaeia,which are among the most abundant microorganisms in marine sediment,have been proposed to mediate anaerobic lignin degradation.However,the mechanism of bathyarchaeial lignin degradation remains unclear.Here,we report an enrichment culture of Bathy-archaeia,named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001(Ca.B.ligniniphilus),from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions.Ca.B.ligniniphilus possesses and highly expresses novel methyltransferase 1(MT1,mtgB)for transferring methoxyl groups from lignin monomers to cob(I)alamin.MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages.Heterologous expression of the mtgB gene confirmed O-demethylation activity.The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments,and they were highly expressed in coastal sediments from the East China Sea.These findings suggest that Bathyarchaeia,capable of O-demethylation via their novel and specific methyltransferases,are ubiquitous in coastal sediments.

Inspiration and encounters:Carl Woese and my 30-year research journey

I clearly remember the day in February 1998 when I met Professor Carl Woese for the first time at his laboratory in the Department of Microbiology,the University of Illinois at Urbana–Champaign.Prof.Woese kindly gave me the reprint of his seminal review paper with his signature(Microbiological Reviews in 1987)1.A veritable treasure,I keep this paper in my office,having started research on the molecular biology of Archaea in 1992 and having always aspired to meet him someday.In this essay,I highlight the remarkable achievements of Carl Woese and share my memories of him,while looking back at my own research on Archaea and related aspects in Japan.

Integrated identification of growth pattern and taxon of bacterium in gut microbiota via confocal fluorescence imaging‐oriented single‐cell sequencing

Despite the fast progress in our understanding of the complex functions of gut microbiota,it is still challenging to directly investigate the in vivo microbial activities and processes on an individual cell basis.To gain knowledge of the indigenous growth/division patterns of the diverse mouse gut bacteria with a relatively high throughput,here,we propose an integrative strategy,which combines the use of fluorescent probe labeling,confocal imaging with single‐cell sorting,and sequencing.Mouse gut bacteria sequentially labeled by two fluorescent D‐amino acid probes in vivo were first imaged by confocal microscopy to visualize their growth patterns,which can be unveiled by the distribution of the two fluorescence signals on each bacterium.Bacterial cells of interest on the imaging slide were then sorted using a laser ejection equipment,and the collected cells were then sequenced individually to identify their taxa.Our strategy allows integrated acquirement of the growth pattern knowledge of a variety of gut bacteria and their genomic information on a single‐cell basis,which should also have great potential in studying many other complex bacterial systems.

Human skin bacterial microbiota homeostasis:A delicate balance between health and disease

As the largest organ of the body,the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria.Furthermore,the skin bacterial microbiota plays a vital role in health and disease.Disruption of the barrier or an imbalance between symbionts and pathogens can lead to skin disorders or even systemic diseases.In this review,we first provide an overview of research on skin bacterial microbiota and human health,including the composition of skin bacteria in a healthy state,as well as skin bacterial microbiota educating the immune system and preventing the invasion of pathogens.We then discuss the diseases that result from skin microbial dysbiosis,including atopic dermatitis,common acne,chronic wounds,psoriasis,viral transmission,cutaneous lupus,cutaneous lymphoma,and hidradenitis suppurativa.Finally,we highlight the progress that utilizes skin microorganisms for disease therapeutics,such as bacteriotherapy and skin microbiome transplantation.A deeper knowledge of the interaction between human health and disease and the homeostasis of the skin bacterial microbiota will lead to new insights and strategies for exploiting skin bacteria as a novel therapeutic target.

RsaL is a self-regulatory switch that controls alternative biosynthesis of two AHL-type quorum sensing signals in Pseudomonas aeruginosa PA1201

Pseudomonas aeruginosa is a ubiquitous and metabolically versatile microorganism naturally found in soil and water.It is also an opportunistic pathogen in plants,insects,animals,and humans.In response to increasing cell density,P.aeruginosa uses two acylhomoserine lactone(AHL)quorum-sensing(QS)signals(i.e.,N-3-oxo-dodecanoyl homoserine lactone[3-oxo-C12-HSL]and Nbutanoyl-homoserine lactone[C4-HsL]),which regulate the expression of hundreds of genes.However,how the biosynthesis of these two QS signals is coordinated remains unknown.We studied the regulation of these two QS signals in the rhizosphere strain PA1201.PA1201 sequentially produced 3-oxo-C12-HSL and C4-HSL at the early and late growth stages,respectively.The highest 3-oxo-C12-HSL-dependent elastase activity was observed at the early stage,while the highest C4-HSL-dependent rhamnolipid production was observed at the late stage.The atypical regulator RsaL played a pivotal role in coordinating 3-oxo-C12-HSL and C4-HSL biosynthesis and QS-associated virulence.RsaL repressed las/transcription by binding the-10 and-35 boxes of the lasl promoter.In contrast,RsaL activated rhll transcription by binding the region encoding the 5'-untranslated region of the rhll mRNA.Further,RsaL repressed its own expression by binding a nucleotide motif located in the-35 box of the rsaL promoter.Thus,RsaL acts as a molecular switch that coordinates the sequential biosynthesis of AHL QS signals and differential virulence in PA1201.Finally,C4-HSL activation by RsaL was independent of the Las and Pseudomonas quinolone signal(PQS)QS signaling systems.Therefore,we propose a new model of the QS regulatory network in PA1201,in which RsaL represents a superior player acting at the top of the hierarchy.

Reprogramming the endogenous type I CRISPR-Cas system for simultaneous gene regulation and editing in Haloarcula hispanica

The type I system is the most widely distributed CRISPR-Cas system identified so far.Recently,we have revealed the natural reprogramming of the type I CRISPR effector for gene regulation with a crRNA-resembling RNA in halophilic archaea.Here,we conducted a comprehensive study of the impact of redesigned crRNAs with different spacer lengths on gene regulation with the native type I-B CRISPR system in Haloarcula hispanica.When the spacer targeting the chromosomal gene was shortened from 36 to 28 bp,transformation efficiencies of the spacer-encoding plasmids were improved by over three orders of magnitude,indicating a significant loss of interference.However,by conducting whole-genome sequencing and measuring the growth curves of the hosts,we still detected DNA cleavage and its influence on cell growth.Intriguingly,when the spacer was shortened to 24 bp,the transcription of the target gene was downregulated to 10.80%,while both interference and primed adaptation disappeared.By modifying the lengths of the spacers,the expression of the target gene could be suppressed to varying degrees.Significantly,by designing crRNAs with different spacer lengths and targeting different genes,we achieved simultaneous gene editing(cdc6E)and gene regulation(crtB)for the first time with the endogenous type I CRISPR-Cas system.

Design of microaerobically inducible miniR1 plasmids

Plasmid DNA(pDNA)is the active pharmaceutical ingredient in the so-called DNA vaccines1 and in gene therapy products.The first pDNA vaccine for use in humans,which has shown high protection against SARS-CoV-2,was recently approved in India2.Furthermore,pDNA is often used as a template for in vitro transcription to produce mRNA vaccines3.

Legionella pneumophila temporally regulates the activity of ADP/ATP translocases by reversible ADP-ribosylation

The mitochondrion is an important signaling hub that governs diverse cellular functions,including metabolism,energy production,and immunity.Among the hundreds of effectors translocated into host cells by the Dot/Icm system of Legionella pneumophila,several are targeted to mitochondria but the function of most of them remains elusive.Our recent study found that the effector Ceg3 inhibits the activity of ADP/ATP translocases(ANTs)by ADP-ribosylation(ADPR).Here,we show that the effect of Ceg3 is antagonized by Larg1,an effector encoded by lpg0081,a gene that is situated next to ceg3.Larg1 functions to reverse Ceg3-mediated ADPR of ANTs by cleaving the N-glycosidic bond between the ADPR moiety and the modified arginine residues in ANTs,leading to restoration of their activity in ADP/ATP exchange.Structural analysis of Larg1 and its complex with ADPR reveals that this ADPR glycohydrolase harbors a unique macrodomain that catalyzes the removal of ADPR modification on ANTs.Our results also demonstrate that together with Ceg3,Larg1 imposes temporal regulation of the activity of ANTs by reversible ADPR during L.pneumophila infection.

Delivery of an Rhs-family nuclease effector reveals direct penetration of the gram-positive cell envelope by a type VI secretion system in Acidovorax citrulli

The type VI secretion system(T6SS)is a double-tubular nanomachine widely found in gram-negative bacteria.Its spear-like Hcp tube is capable of penetrating a neighboring cell for cytosol-to-cytosol protein delivery.However,gram-positive bacteria have been considered impenetrable to such T6SS action.Here we report that the T6SS of a plant pathogen,Acidovorax citrulli(AC),could deliver an Rhsfamily nuclease effector RhsB to kill not only gram-negative but also gram-positive bacteria.Using bioinformatic,biochemical,and genetic assays,we systematically identified T6SS-secreted effectors and determined that RhsB is a crucial antibacterial effector.RhsB contains an N-terminal PAAR domain,a middle Rhs domain,and an unknown C-terminal domain.RhsB is subject to self-cleavage at both its N-and C-terminal domains and its secretion requires the upstream-encoded chaperone EagT2 and VgrG3.The toxic Cterminus of RhsB exhibits DNase activities and such toxicity is neutralized by either of the two downstream immunity proteins,RimB1 and RimB2.Deletion of rhsB significantly impairs the ability of killing Bacillus subtilis while ectopic expression of immunity proteins RimB1 or RimB2 confers protection.We demonstrate that the AC T6SS not only can effectively outcompete Escherichia coli and B.subtilis in planta but also is highly potent in killing other bacterial and fungal species.Collectively,these findings highlight the greatly expanded capabilities of T6SS in modulating microbiome compositions in complex environments.

Bacillus subtilis produces(p)ppGpp in response to the bacteriostatic antibiotic chloramphenicol to prevent its potential bactericidal effect

Antibiotics combat bacteria through their bacteriostatic(by growth inhibition)or bactericidal(by killing bacteria)action.Mechanistically,it has been proposed that bactericidal antibiotics trigger cellular damage,while bacteriostatic antibiotics suppress cellular metabolism.Here,we demonstrate how the difference between bacteriostatic and bactericidal activities of the antibiotic chloramphenicol can be attributed to an antibiotic-induced bacterial protective response:the stringent response.Chloramphenicol targets the ribosome to inhibit the growth of the Gram-positive bacterium Bacillus subtilis.Intriguingly,we found that chloramphenicol becomes bactericidal in B.subtilis mutants unable to produce(p)ppGpp.We observed a similar(p)ppGpp-dependent bactericidal effect of chloramphenicol in the Gram-positive pathogen Enterococcus faecalis.In B.subtilis,chloramphenicol treatment induces(p)ppGpp accumulation through the action of the(p)ppGpp synthetase RelA.(p)ppGpp subsequently depletes the intracellular concentration of GTP and antagonizes GTP action.This GTP regulation is critical for preventing chloramphenicol from killing B.subtilis,as bypassing(p)ppGpp-dependent GTP regulation potentiates chloramphenicol killing,while reducing GTP synthesis increases survival.Finally,chloramphenicol treatment protects cells from the classical bactericidal antibiotic vancomycin,reminiscent of the clinical phenomenon of antibiotic antagonism.Taken together,our findings suggest a role of(p)ppGpp in the control of the bacteriostatic and bactericidal activity of antibiotics in Gram-positive bacteria,which can be exploited to potentiate the efficacy of existing antibiotics.

Heme homeostasis and its regulation by hemoproteins in bacteria

Heme is an important cofactor and a regulatory molecule involved in various physiological processes in virtually all living cellular organisms,and it can also serve as the primary iron source for many bacteria,particularly pathogens.However,excess heme is cytotoxic to cells.In order to meet physiological needs while preventing deleterious effects,bacteria have evolved sophisti-cated cellular mechanisms to maintain heme homeostasis.Recent advances in technologies have shaped our understanding of the molecular mechanisms that govern the biological processes crucial to heme homeostasis,including synthesis,acquisition,utilization,degradation,trafficking,and efflux,as well as their regulation.Central to these mechanisms is the regulation of the heme,by the heme,and for the heme.In this review,we present state-of-the-art findings covering the biochemical,physio-logical,and structural characterization of important,newly identified hemoproteins/systems involved in heme homeostasis.

Climate warming suppresses abundant soil fungal taxa and reduces soil carbon efflux in a semi-arid grassland

Soil microorganisms critically affect the ecosystem carbon(C)balance and C-climate feedback by directly controlling organic C decomposition and indirectly regulating nutrient availability for plant C fixation.However,the effects of climate change drivers such as warming,precipitation change on soil microbial communities,and C dynamics remain poorly understood.Using a long-term field warming and precipitation manipulation in a semi-arid grassland on the Loess Plateau and a complementary incubation experiment,here we show that warming and rainfall reduction differentially affect the abundance and composition of bacteria and fungi,and soil C efflux.Warming significantly reduced the abundance of fungi but not bacteria,increasing the relative dominance of bacteria in the soil microbial community.In particular,warming shifted the community composition of abundant fungi in favor of oligotrophic Capnodiales and Hypocreales over potential saprotroph Archaeorhizomycetales.Also,precipitation reduction increased soil total microbial biomass but did not significantly affect the abundance or diversity of bacteria.Furthermore,the community composition of abundant,but not rare,soil fungi was significantly correlated with soil CO_(2) efflux.Our findings suggest that alterations in the fungal community composition,in response to changes in soil C and moisture,dominate the microbial responses to climate change and thus control soil C dynamics in semi-arid grasslands.

Electrobiocorrosion by microbes without outer-surface cytochromes

Anaerobic microbial corrosion of iron-containing metals causes extensive economic damage.Some microbes are capable of direct metal-to-microbe electron transfer(electrobiocorrosion),but the prevalence of electrobiocorrosion among diverse methanogens and acetogens is poorly understood because of a lack of tools for their genetic manipulation.Previous studies have suggested that respiration with 316L stainless steel as the electron donor is indicative of electrobiocorrosion,because,unlike pure Fe^(0),316L stainless steel does not abiotically generate H_(2) as an intermediary electron carrier.Here,we report that all of the methanogens(Methanosarcina vacuolata,Methanothrix soehngenii,and Methanobacterium strain IM1)and acetogens(Sporomusa ovata and Clostridium ljungdahli)evaluated respired with pure Fe^(0)as the electron donor,but only M.vacuolata,Mx.soehngeni,and S.ovata were capable of stainless steel electrobiocorrosion.The electrobiocorrosive methanogens re-quired acetate as an additional energy source in order to produce methane from stainless steel.Cocultures of S.ovata and Mx.soehngeni demonstrated how acetogens can provide acetate to methanogens during corrosion.Not only was Meth-anobacterium strain IM1 not capable of electrobiocorrosion,but it also did not accept electrons from Geobacter metal-lireducens,an effective electron-donating partner for direct interspecies electron transfer to all methanogens that can directly accept electrons from Fe^(0).The finding that M.vacuolata,Mx.soehngeni,and S.ovata are capable of electrobiocorrosion,despite a lack of the outer-surface c-type cytochromes previously found to be important in other electrobiocorrosive microbes,demonstrates that there are multiple microbial strategies for making electrical contact with Fe^(0).

Staphylococcus aureus SoS response:Activation,impact,and drug targets

Staphylococcus aureus is a common cause of diverse infections,ranging from superficial to invasive,affecting both humans and animals.The widespread use of antibiotics in clinical treatments has led to the emergence of antibiotic-resistant strains and small colony variants.This surge presents a significant challenge in eliminating infections and undermines the efficacy of available treatments.The bacterial Save Our Souls(Sos)response,triggered by genotoxic stressors,encompasses host immune defenses and antibiotics,playing a crucial role in bacterial survival,invasiveness,virulence,and drug resistance.Accumulating evidence underscores the pivotal role of the Sos response system in the pathogenicity of S.aureus.Inhibiting this system offers a promising approach for effective bactericidal treatments and curbing the evolution of antimicrobial re-sistance.Here,we provide a comprehensive review of the activation,impact,and key proteins associated with the Sos response in S.aureus.Additionally,perspectives on therapeutic strategies targeting the Sos response for S.aureus,both individually and in combination with traditional antibiotics are proposed.

Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus

Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous proteins.Improving the yield in K.marxianus remains a challenge and incorporating large-scale functional modules poses a technical obstacle in engineering.To address these issues,linear and circular yeast artificial chromosomes of K.marxianus(KmYACs)were constructed and loaded with disulfide bond formation modules from Pichia pastoris or K.marxianus.These modules contained up to seven genes with a maximum size of 15 kb.KmYACs carried telomeres either from K.marxianus or Tetrahymena.KmYACs were transferred successfully into K.marxianus and stably propagated without affecting the normal growth of the host,regardless of the type of telomeres and configurations of KmYACs.KmYACs increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous proteins.In high-density fermentation,the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l,the highest reported level to date in K.marxianus.Transcriptomic and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis,enhanced flux entering the tricarboxylic acid cycle,and a preferred demand for lysine and arginine as features of cells overexpressing heterologous proteins.Consistently,supplementing lysine or arginine further improved the yield.Therefore,KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental research.Transferring the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins,and this strategy may be applied to optimize other microbial cell factories.

MomL inhibits bacterial antibiotic resistance through the starvation stringent response pathway

Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats.The role of the N-acyl homoserine lactone(AHL)-mediated signaling pathway,which is widespread in gram-negative bacteria,in the bacterial resistance process should be studied in depth.Here,we report a degrading enzyme of AHLs,MomL,that inhibits the antibiotic resistance of Pseudomonas aeruginosa through a novel mechanism.The MomL-mediated reactivation of kanamycin is highly associated with the relA-mediated starvation stringent response.The degradation of AHLs by MomL results in the inability of LasR to activate relA,which,in turn,stops the activation of downstream rpoS.Further results show that rpoS directly regulates the type VI secretion system H2-T6SS.Under MomL treatment,inactivated RpoS fails to regulate H2-T6SS;therefore,the expression of effector phospholipase A is reduced,and the adaptability of bacteria to antibiotics is weakened.MomL in combination with kanamycin is effective against a wide range of gram-negative pathogenic bacteria.Therefore,this study reports a MomL-antibiotic treatment strategy on antibiotic-resistant bacteria and reveals its mechanism of action.

Elucidating microbial iron corrosion mechanisms with a hydrogenase-deficient strain of Desulfovibrio vulgaris

Sulfate-reducing microorganisms extensively contribute to the corrosion of ferrous metal infrastructure.There is substantial debate over their corrosion mechanisms.We investigated Fe^(0) corrosion with Desulfovibrio vulgaris,the sulfate reducer most often employed in corrosion studies.Cultures were grown with both lactate and Fe^(0) as potential electron donors to replicate the common environmental condition in which organic substrates help fuel the growth of corrosive microbes.Fe^(0) was corroded in cultures of a D.vulgaris hydrogenase-deficient mutant with the 1:1 correspondence between Fe^(0) loss and H_(2) accumulation expected for Fe^(0) oxidation coupled to H+reduction to H_(2).This result and the extent of sulfate reduction indicated that D.vulgaris was not capable of direct Fe^(0)-to-microbe electron transfer even though it was provided with a supplementary energy source in the presence of abundant ferrous sulfide.Corrosion in the hydrogenase-deficient mutant cultures was greater than in sterile controls,demonstrating that H_(2) removal was not necessary for the enhanced corrosion observed in the presence of microbes.The parental H_(2)-consuming strain corroded more Fe^(0) than the mutant strain,which could be attributed to H_(2) oxidation coupled to sulfate reduction,producing sulfide that further stimulated Fe^(0) oxidation.The results suggest that H_(2) consumption is not necessary for microbially enhanced corrosion,but H_(2) oxidation can indirectly promote corrosion by increasing sulfide generation from sulfate reduction.The finding that D.vulgaris was incapable of direct electron uptake from Fe^(0) reaffirms that direct metal-to-microbe electron transfer has yet to be rigorously described in sulfate-reducing microbes.