Investigating and Engineering an 1,2-Propanediol-Responsive Transcription Factor-Based Biosensor.

Transcription factor (TF)-based biosensors have arisen as powerful tools in the advancement of metabolic engineering. However, with the emergence of numerous bioproduction targets, the variety of applicable TF-based biosensors remains severely limited. In this study, we investigated and engineered an 1,2-propanediol (1,2-PD)-responsive transcription activator, PocR, from Salmonella typhimurium to enrich the current biosensor repertoire. Heterologous characterization of PocR in E. coli revealed a significantly limited operational range and dynamic range, primarily attributed to the leaky binding between PocR and its corresponding promoters in the absence of the 1,2-PD inducer. Promiscuity characterization uncovered the minor responsiveness of PocR toward glycerol and 1,2-butanediol (1,2-BD). Using AlphaFold-predicted structure and protein mutagenesis, we preliminarily explored the underlying mechanism of PocR. Based on the investigated mechanism, we engineered a PcoR-F46R/G105D variant with an altered inducer specificity to glycerol, as well as a PocR-ARE (Q107A/S192R/A203E) variant with nearly a 4-fold higher dynamic range (6.7-fold activation) and a 20-fold wider operational range (0-20 mM 1,2-PD). Finally, we successfully converted PocR to a repressor through promoter engineering. Integrating the activation and repression functions established a versatile 1,2-PD-induced bifunctional regulation system based on PocR-ARE. Our work showcases the exploration and exploitation of an underexplored type of transcriptional activator capable of recruiting RNA polymerase. It also expands the biosensor toolbox by providing a 1,2-PD-responsive bifunctional regulator and glycerol-responsive activator.

Advancing microbial production through artificial intelligence-aided biology.

Microbial cell factories (MCFs) have been leveraged to construct sustainable platforms for value-added compound production. To optimize metabolism and reach optimal productivity, synthetic biology has developed various genetic devices to engineer microbial systems by gene editing, high-throughput protein engineering, and dynamic regulation. However, current synthetic biology methodologies still rely heavily on manual design, laborious testing, and exhaustive analysis. The emerging interdisciplinary field of artificial intelligence (AI) and biology has become pivotal in addressing the remaining challenges. AI-aided microbial production harnesses the power of processing, learning, and predicting vast amounts of biological data within seconds, providing outputs with high probability. With well-trained AI models, the conventional Design-Build-Test (DBT) cycle has been transformed into a multidimensional Design-Build-Test-Learn-Predict (DBTLP) workflow, leading to significantly improved operational efficiency and reduced labor consumption. Here, we comprehensively review the main components and recent advances in AI-aided microbial production, focusing on genome annotation, AI-aided protein engineering, artificial functional protein design, and AI-enabled pathway prediction. Finally, we discuss the challenges of integrating novel AI techniques into biology and propose the potential of large language models (LLMs) in advancing microbial production.

Neural basis of reward expectancy inducing proactive aggression.

Proactive aggression refers to deliberate and unprovoked behavior, typically motivated by personal gain or expected reward. Reward expectancy is generally recognized as a critical factor that may influence proactive aggression, but its neural mechanisms remain unknown. We conducted a task-based functional magnetic resonance imaging (fMRI) experiment to investigate the relationship between reward expectancy and proactive aggression. 37 participants (20 females, mean age = 20.8 ± 1.42, age range = 18-23 years) completed a reward-harm task. In the experiment, reward valence expectancy and reward possibility expectancy were manipulated respectively by varying amounts (low: 0.5-1.5 yuan; high: 10.5-11.5 yuan) and possibilities (low: 10%-30%; high: 70%-90%) of money that participants could obtain by choosing to aggress. Participants received fMRI scans throughout the experiment. Brain activation regions associated with reward expectancy mainly involve the middle frontal gyrus, lingual gyrus, inferior temporal gyrus, anterior cuneus, caudate nucleus, inferior frontal gyrus, cingulate gyrus, anterior central gyrus, and posterior central gyrus. Associations between brain activation and reward expectancy in the left insula, left middle frontal gyrus, left thalamus, and right middle frontal gyrus were found to be related to proactive aggression. Furthermore, the brain activation regions primarily involved in proactive aggression induced by reward expectancy were the insula, inferior frontal gyrus, inferior temporal gyrus, pallidum, and caudate nucleus. Under conditions of high reward expectancy, participants engage in more proactive aggressive behavior. Reward expectancy involves the activation of reward- and social-cognition-related brain regions, and these associations are instrumental in proactive aggressive decisions.

Inhibition of Nogo-B reduces the progression of pancreatic cancer by regulation NF-κB/GLUT1 and SREBP1 pathways.

Pancreatic cancer (PC) is a lethal disease and associated with metabolism dysregulation. Nogo-B is related to multiple metabolic related diseases and types of cancers. However, the role of Nogo-B in PC remains unknown. In vitro, we showed that cell viability and migration was largely reduced in Nogo-B knockout or knockdown cells, while enhanced by Nogo-B overexpression. Consistently, orthotopic tumor and metastasis was reduced in global Nogo knockout mice. Furthermore, we indicated that glucose enhanced cell proliferation was associated to the elevation expression of Nogo-B and nuclear factor κB (NF-κB). While, NF-κB, glucose transporter type 1 (GLUT1) and sterol regulatory element-binding protein 1 (SREBP1) expression was reduced in Nogo-B deficiency cells. In addition, we showed that GLUT1 and SREBP1 was downstream target of NF-κB. Therefore, we demonstrated that Nogo deficiency inhibited PC progression is regulated by the NF-κB/GLUT1 and SREBP1 pathways, and suggested that Nogo-B may be a target for PC therapy.

Neural correlates of aggression outcome expectation and their association with aggression: A voxel-based morphometry study.

BACKGROUND: Aggression outcome expectation is an important cognitive factor of aggression. Discovering the neural mechanism of aggression outcome expectation is conducive to developing aggression research. However, the neural correlates underlying aggression outcome expectation and its effect remain elusive. METHODS: We utilized voxel-based morphometry (VBM) to unravel the neural architecture of aggression outcome expectation measured by the Social Emotional Information Processing Assessment for Adults and its relationship with aggression measured by the Buss Perry Aggression Questionnaire in a sample of 185 university students (114 female; mean age = 19.94 ± 1.62 years; age range: 17-32 years). RESULTS: We found a significantly positive correlation between aggression outcome expectation and the regional gray matter volume (GMV) in the right middle temporal gyrus (MTG) (x = 55.5, y = -58.5, z = 1.5; t = 3.35; cluster sizes = 352, p < 0.05, GRF corrected). Moreover, aggression outcome expectation acted as a mediator underlying the association between the right MTG volume and aggression. CONCLUSIONS: These results revealed the neural correlates of aggression outcome expectation and its effect on aggression for the first time, which may contribute to our understanding of the cognitive neural mechanism of aggression and potentially identifying neurobiological markers for aggression.

Recent progresses in analytical method development for 210Pb in environmental and biological samples.

As a decay product of uranium series, 210Pb spreads widely in the nature and imposes strong radiological and chemical toxicity. It is vital to establish reliable and efficient radioanalytical methods for 210Pb determination to support environment and food radioactivity monitoring programs. This article critically reviews analytical methods developed for determining 210Pb in environmental and biological samples, especially new development in recent years. Techniques applied throughout different analytical steps including sample pretreatment, separation, purification, and detection are summarized and their pros and cons are discussed to provide a holistic overview for 210Pb environmental and biological assay.

Mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins.

TAX1BP1, a multifunctional autophagy adaptor, plays critical roles in different autophagy processes. As an autophagy receptor, TAX1BP1 can interact with RB1CC1, NAP1, and mammalian ATG8 family proteins to drive selective autophagy for relevant substrates. However, the mechanistic bases underpinning the specific interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins remain elusive. Here, we find that there are two distinct binding sites between TAX1BP1 and RB1CC1. In addition to the previously reported TAX1BP1 SKICH (skeletal muscle and kidney enriched inositol phosphatase (SKIP) carboxyl homology)/RB1CC1 coiled-coil interaction, the first coiled-coil domain of TAX1BP1 can directly bind to the extreme C-terminal coiled-coil and Claw region of RB1CC1. We determine the crystal structure of the TAX1BP1 SKICH/RB1CC1 coiled-coil complex and unravel the detailed binding mechanism of TAX1BP1 SKICH with RB1CC1. Moreover, we demonstrate that RB1CC1 and NAP1 are competitive in binding to the TAX1BP1 SKICH domain, but the presence of NAP1's FIP200-interacting region (FIR) motif can stabilize the ternary TAX1BP1/NAP1/RB1CC1 complex formation. Finally, we elucidate the molecular mechanism governing the selective interactions of TAX1BP1 with ATG8 family members by solving the structure of GABARAP in complex with the non-canonical LIR (LC3-interacting region) motif of TAX1BP1, which unveils a unique binding mode between LIR and ATG8 family protein. Collectively, our findings provide mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins and are valuable for further understanding the working mode and function of TAX1BP1 in autophagy.

Determination and human health risk assessment of TFWT, OBT and carbon-14 in seafood around Qinshan Nuclear Power Plant.

This work aims to evaluate the effects of the operation of Qinshan nuclear Power Plant (QNPP) on tritium (3H) and carbon-14 (14C) levels in seafood and assess the health risks caused by seafood consumption. Five kinds of seafood, including marine fish, prawn, razor clam, crabs, and seaweed, were collected from QNPP and the sea around Hangzhou Bay. The activity concentrations of tissue free water tritium (TFWT), organically bound tritium (OBT) and 14C were determined, respectively, and the annual intake and annual effective dose (AED) were calculated. The results showed that the TFWT, OBT, and 14C activity concentrations of the seafood in the surrounding area of QNPP ranged from 2.00 to 74.75 Bq/L, <1.04 to 19.68 Bq/L and 0.09 to 0.17 Bq/g·C, respectively. The TFWT, OBT, and 14C activity concentrations of the seafood in Hangzhou Bay ranged from 1.36 to 10.55 Bq/L, 1.08 to 6.78 Bq/L and 0.07 to 0.13 Bq/g·C, respectively. The differences were not statistically significant. The total AED from 3H and 14C due to the seafood consumption for the residents in the surrounding of QNPP and Hangzhou Bay were 1.96 × 10-4 and 1.61 × 10-4 mSv/year, respectively. The results showed that the operation of QNPP had no obvious effect on 3H and 14C accumulation in seafood, and the dose burden of population was low.

A self-regulated network for dynamically balancing multiple precursors in complex biosynthetic pathways.

Microbial synthesis has emerged as a promising and sustainable alternative to traditional chemical synthesis and plant extraction. However, the competition between synthetic pathways and central metabolic pathways for cellular resources may impair final production efficiency. Moreover, when the synthesis of target product requires multiple precursors from the same node, the conflicts of carbon flux have further negative impacts on yields. In this study, a self-regulated network was developed to relieve the competition of precursors in complex synthetic pathways. Using 4-hydroxycoumarin (4-HC) synthetic pathway as a proof of concept, we employed an intermediate as a trigger to dynamically rewire the metabolic flux of pyruvate and control the expression levels of genes in 4-HC synthetic pathway, achieving self-regulation of multiple precursors and enhanced titer. Transcriptomic analysis results additionally demonstrated that the gene transcriptional levels of both pyruvate kinase PykF and synthetic pathway enzyme SdgA dynamically changed according to the intermediate concentrations. Overall, our work established a self-regulated network to dynamically balance the metabolic flux of two precursors in 4-HC biosynthesis, providing insight into balancing biosynthetic pathways where multiple precursors compete and interfere with each other.

Structure-based development of potent and selective type-II kinase inhibitors of RIPK1.

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) functions as a key regulator in inflammation and cell death and is involved in mediating a variety of inflammatory or degenerative diseases. A number of allosteric RIPK1 inhibitors (RIPK1i) have been developed, and some of them have already advanced into clinical evaluation. Recently, selective RIPK1i that interact with both the allosteric pocket and the ATP-binding site of RIPK1 have started to emerge. Here, we report the rational development of a new series of type-II RIPK1i based on the rediscovery of a reported but mechanistically atypical RIPK3i. We also describe the structure-guided lead optimization of a potent, selective, and orally bioavailable RIPK1i, 62, which exhibits extraordinary efficacies in mouse models of acute or chronic inflammatory diseases. Collectively, 62 provides a useful tool for evaluating RIPK1 in animal disease models and a promising lead for further drug development.

Effects of LED Light Colors on the Growth Performance, Intestinal Morphology, Cecal Short-Chain Fatty Acid Concentrations and Microbiota in Broilers.

This study aimed to explore the effects of light-emitting diode (LED) light colors on growth, intestinal morphology, and cecal microbiota in broilers. A total of 360 healthy male Arbor Acres (AA) broilers with similar weights were selected and divided into four groups with six replicates in each group and 15 broilers in each replicate: LED white light (W), LED green light (G), LED blue light (B), and LED blue-green composite light (BG). The experimental period was 42 d, the light cycle of each treatment group was 23L:1D (23 h of light, one hour of darkness) from 1 to 3 d, and the light cycle from 4 to 42 d was 16L:8D; light intensity was 20 Lux. The results showed that the average daily feed intake and final weight of broilers receiving the B group were the highest in 21 d and 42 d compared with other groups. The average daily feed intake of the BG group was lower than that of the B group. In the same light color, small intestine villus height grows with age. On days 21 and 42, compared with other groups, the ileal villus height was higher, the crypt depth was lower, and the V/C ratio (villus to crypt ratio) was higher in the BG group. The combination of blue-green composite light was beneficial to increase the content of propionate, isobutyrate, butyrate, isovalerate, and valerate in the cecum of 21-day-old broilers and the content of isobutyrate in the cecum of 42-day-old broilers, and a decrease in cecal short-chain fatty acid concentrations with age. The B group and the BG group had higher abundances of Bacteroidetes at day 21 of age and lower abundances of Phascolarctobacterium at day 42. However, no cecal microbiota differences were detected by the Bonferroni-corrected test. In general, our research results showed that light color could promote the growth of broilers by affecting intestinal morphology, microbiota abundance (needs to be validated by further experiments), and cecal short-chain fatty acid concentrations. And blue and blue-green composite lights are more suitable for broiler growth.

Mechanistic insights into the enzymatic activity of E3 ligase HOIL-1L and its regulation by the linear ubiquitin chain binding.

Heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1L) serves as a unique E3 ligase to catalyze the mono-ubiquitination of relevant protein or sugar substrates and plays vital roles in numerous cellular processes in mammals. However, the molecular mechanism underpinning the E3 activity of HOIL-1L and the related regulatory mechanism remain elusive. Here, we report the crystal structure of the catalytic core region of HOIL-1L and unveil the key catalytic triad residues of HOIL-1L. Moreover, we discover that HOIL-1L contains two distinct linear di-ubiquitin binding sites that can synergistically bind to linear tetra-ubiquitin, and the binding of HOIL-1L with linear tetra-ubiquitin can promote its E3 activity. The determined HOIL-1L/linear tetra-ubiquitin complex structure not only elucidates the detailed binding mechanism of HOIL-1L with linear tetra-ubiquitin but also uncovers a unique allosteric ubiquitin-binding site for the activation of HOIL-1L. In all, our findings provide mechanistic insights into the E3 activity of HOIL-1L and its regulation by the linear ubiquitin chain binding.

Mechanistic Insights into the Interactions of Arl8b with the RUN Domains of PLEKHM1 and SKIP.

Arl8b, a specific Arf-like family GTPase present on lysosome, and plays critical roles in many lysosome-related cellular processes such as autophagy. The active Arl8b can be specifically recognized by the RUN domains of two Arl8b-effectors PLEKHM1 and SKIP, thereby regulating the autophagosome/lysosome membrane fusion and the intracellular lysosome positioning, respectively. However, the mechanistic bases underlying the interactions of Arl8b with the RUN domains of PLEKHM1 and SKIP remain elusive. Here, we report the two high-resolution crystal structures of the active Arl8b in complex with the RUN domains of PLEKHM1 and SKIP. In addition to elucidating the detailed molecular mechanism governing the specific interactions of the active Arl8b with the RUN domains of PLEKHM1 and SKIP, the determined complex structures also reveal a general binding mode shared by the PLEKHM1 and SKIP RUN domains for interacting with the active Arl8b. Furthermore, we uncovered a competitive relationship between the RUN domains of PLEKHM1 and SKIP in binding to the active Arl8b as well as a unique small GTPase-binding mode adopted by the PLEKHM1 and SKIP RUN domains, thereby enriching the repertoire of the RUN domain/small GTPase interaction modes. In all, our findings provide new mechanistic insights into the interactions of the active Arl8b with PLEKHM1 and SKIP, and are valuable for further understanding the working modes of these proteins in relevant cellular processes.

Identifying, Characterizing, and Engineering a Phenolic Acid-Responsive Transcriptional Factor from Bacillus amyloliquefaciens.

Transcriptional factors-based biosensors are commonly used in metabolic engineering for inducible control of gene expression and related applications such as high-throughput screening and dynamic pathway regulations. Mining for novel transcriptional factors is essential for expanding the usability of these toolsets. Here, we report the identification, characterization, and engineering of a phenolic acid responsive regulator PadR from Bacillus amyloliquefaciens (BaPadR). This BaPadR-based biosensor system showed a unique ligand preference and exhibited a high output strength comparable to that of commonly used inducible expression systems. Through engineering the DNA binding region of BaPadR, we further enhanced the dynamic range of the biosensor system. The DNA sequences that are responsible for BaPadR recognition were located by promoter truncation and hybrid promoter building. To further explore the tunability of the sensor system, base substitutions were performed on the BaPadR binding region of the phenolic acid decarboxylase promoter (PpadC) and the hybrid promoter. This novel biosensor system can serve as a valuable tool in future synthetic biology applications.

Application of Metabolite-Responsive Biosensors for Plant Natural Products Biosynthesis.

Plant natural products (PNPs) have shown various pharmaceutical activities, possessing great potential in global markets. Microbial cell factories (MCFs) provide an economical and sustainable alternative for the synthesis of valuable PNPs compared with traditional approaches. However, the heterologous synthetic pathways always lack native regulatory systems, bringing extra burden to PNPs production. To overcome the challenges, biosensors have been exploited and engineered as powerful tools for establishing artificial regulatory networks to control enzyme expression in response to environments. Here, we reviewed the recent progress involved in the application of biosensors that are responsive to PNPs and their precursors. Specifically, the key roles these biosensors played in PNP synthesis pathways, including isoprenoids, flavonoids, stilbenoids and alkaloids, were discussed in detail.

ATG16L1 is equipped with two distinct WIPI2-binding sites to drive autophagy.

The recruitment of ATG12-ATG5-ATG16L1 complex to phagophore mediated by the specific interaction between ATG16L1 and WIPI2, is pivotal to the formation of autophagosomes during macroautophagy. Recently, we reported that ATG16L1 contains two distinct WIPI2-binding sites, the previously reported WIPI2-binding site (WBS1), and the newly identified site (WBS2). By determining the crystal structures of WIPI2 with ATG16L1 WBS1 and WBS2 respectively, we uncovered that, unlike ATG16L1 WBS1, ATG16L1 WBS2 and its binding mechanism to WIPI2 are conserved from yeast to mammals. Using cell-based functional assays, we further demonstrated that the integrity of two WIPI2-binding sites of ATG16L1 is essential for normal autophagic flux. In summary, our study provided mechanistic insights into the interaction of two key autophagic proteins, ATG16L1 and WIPI2, and revealed a dual-binding-site mode adopted by ATG16L1 to associate with WIPI2.Abbreviations: ATG: autophagy-related protein; CCD: coiled-coil domain; ITC: isothermal titration calorimetry; PI3KC3-C1: class III phosphatidylinositol 3-kinase complex I; PtdIns3P: phosphatidylinositol-3-phosphate; ULK: Unc-51-like kinase; WBS: WIPI2-binding site; WIPI: WD repeat domain phosphoinositide-interacting protein.

ATG16L1 adopts a dual-binding site mode to interact with WIPI2b in autophagy.

Macroautophagy plays crucial roles in the regulation of cellular physiology and requires de novo synthesis of double-membrane autophagosomes, which relies on a specific interaction between autophagy-related 16L1 (ATG16L1) and WD repeat domain phosphoinositide-interacting protein 2b (WIPI2b). However, the molecular mechanism governing the interaction of ATG16L1 with WIPI2b remains elusive. Here, we find that ATG16L1 has two distinct binding sites for interacting with WIPI2b, the previously reported WIPI2b-binding site (WBS1) and the previously unidentified site (WBS2). We determine the crystal structures of WIPI2b with ATG16L1 WBS1 and WBS2, respectively, and elucidate the molecular mechanism underpinning the recruitment of ATG16L1 by WIPI2b. Moreover, we uncover that ATG16L1 WBS2 and its binding mode with WIPI2b is well conserved from yeast to mammals, unlike ATG16L1 WBS1. Last, our cell-based functional assays demonstrate that both ATG16L1 WBS1 and WBS2 are required for the effective autophagic flux. In conclusion, our findings provide mechanistic insights into the key ATG16L1/WIPI2b interaction in autophagy.

Governance of China's Potatso National Park Influenced by Local Community Participation.

Conservationists recognize that protected areas (PAs) have limited prospects without the involvement and support of local people. As a governance strategy, community participation is to implement the coordinated development of communities and PAs. However, the effects of community participation on national park governance have rarely been tested. Therefore, the present study used a mixed-method approach that is derived from the International Union for Conservation of Nature (IUCN) green list of protected and conserved areas (PCA) conservation outcomes framework, calibrated to the indigenous peoples and local communities' (IPLCs) self-assessments about the outcomes of community participation on national park governance to explore the community participation effects. Our results show that management efficiency controls governance outcomes. Potatso National Park's transformation from the tourism development model to national park is still ongoing, and there exists quite a few problems. We conclude that a successful national park governance as envisaged by the "ecological civilization" paradigm requires a balance of government regulation, participation of various stakeholders in decision-making and discussion, compensation, as well as sustainable access to environmental resources by the affected populations.

Exploring and engineering PAM-diverse Streptococci Cas9 for PAM-directed bifunctional and titratable gene control in bacteria.

The RNA-guided Cas9s serve as powerful tools for programmable gene editing and regulation; their targeting scopes and efficacies, however, are always constrained by the PAM sequence stringency. Most Streptococci Cas9s, including the prototype SpCas9 from S. pyogenes, specifically recognize a canonical NGG PAM via a conserved RxR PAM-binding motif within the PAM-interaction (PI) domain. Here, SpCas9-based mining unveils three distinct and rarely presented PAM-binding motifs (QxxxR, QxQ and RxQ) among Streptococci Cas9 orthologs. With the catalytically-dead QxxxR-containing SedCas9 from S. equinus, we dissect its NAG PAM specificity and elucidate its underlying recognition mechanism via computational prediction and mutagenesis analysis. Replacing the SedCas9 PI domain with alternate PAM-binding motifs rewires its PAM specificity to NGG or NAA. Moreover, a semi-rational design with minimal mutation creates a SedCas9-NQ variant showing robust activity towards expanded NNG and NAA PAMs, based upon which we engineered a compact ω-SedCas9-NQ transcriptional regulator for PAM-directed bifunctional and titratable gene control. The ω-SedCas9-NQ mediated metabolic reprogramming of endogenous genes in Escherichia coli affords a 2.6-fold increase of 4-hydroxycoumarin production. This work reveals new Cas9 scaffolds with distinct PAM-binding motifs for PAM relaxation and creates a new PAM-diverse Cas9 variant for versatile gene control in bacteria.

Starch-protein interaction effects on lipid metabolism and gut microbes in host.

The purpose of this experiment was to investigate the effects of different starch and protein levels on lipid metabolism and gut microbes in mice of different genders. A total of 160 male mice were randomly assigned to sixteen groups and fed a 4 × 4 Latin square design with dietary protein concentrations of 16, 18, 20, and 22%, and starch concentrations of 50, 52, 54, and 56%, respectively. The results of the study showed that different proportions of starch and protein had obvious effects on the liver index of mice, and there was a significant interaction between starch and protein on the liver index (p = 0.005). Compared with other protein ratio diets, 18% protein diet significantly increased the serum TBA concentration of mice (p < 0.001), and different starch ratio diets had no effect on serum TBA concentration (p = 0.442). It was proved from the results of ileal tissue HE staining that the low protein diet and the low starch diet were more favorable. There was a significant interaction between diets with different starch and protein levels on Bacteroidetes, Firmicutes and Proteobacteria abundance in feces of mice (p < 0.001). Compared with 16 and 18% protein ratio diets, both 20 and 22% protein diets significantly decreased the Parabacteroides and Alistipes abundance in feces of mice (p < 0.05), and 52% starch ratio diet significantly decreased the Parabacteroides and Alistipes abundance than 50% starch ratio diet of mice (p < 0.05). There was a significant interaction between diets with different starch and protein levels on Parabacteroides (p = 0.014) and Alistipes (p = 0.001) abundance in feces of mice. Taken together, our results suggest that a low protein and starch diet can alter lipid metabolism and gut microbes in mice.