Discovery of antimicrobial peptides in the global microbiome with machine learning.

Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and 87,920 prokaryotic genomes from environmental and host-associated habitats to create the AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, few of which match existing databases. AMPSphere provides insights into the evolutionary origins of peptides, including by duplication or gene truncation of longer sequences, and we observed that AMP production varies by habitat. To validate our predictions, we synthesized and tested 100 AMPs against clinically relevant drug-resistant pathogens and human gut commensals both in vitro and in vivo. A total of 79 peptides were active, with 63 targeting pathogens. These active AMPs exhibited antibacterial activity by disrupting bacterial membranes. In conclusion, our approach identified nearly one million prokaryotic AMP sequences, an open-access resource for antibiotic discovery.

Effect of zein-pectin composite particles on the stability and rheological properties of gelatin/hydroxypropyl methylcellulose water-water systems.

To improve the compatibility of gelatin (GA) and hydroxypropyl methylcellulose (HPMC), we investigated the effects of zein-pectin composite particles (ZCPs) with various zein/pectin ratios (1:0, 1:0.5, 1:1, 1:1.5, and 1:2) on the physical stability, microstructure, and rheological properties of the GA/HPMC water-water systems. With increasing pectin ratio, the particle size of the composite particles increased from 234.53 ± 1.48 nm to 1111.00 ± 26.91 nm, and their zeta potential decreased from 20.60 mV to below -34.77 mV. Macroscopic and microstructure observations indicated that pectin-modified ZCPs could effectively inhibit phase separation behavior between GA and HPMC. Compared to pure HPMC, the GA/HPMC water-water systems possessed a higher viscosity and dynamic modulus at room temperatures but lower gel temperatures (reduction of about 11 %). The viscosity and modulus of the water-water systems increased with increasing pectin ratio in ZCPs. However, the ratio had no impact on the gel-sol (sol-gel) transition temperatures (not statistically significant (P < 0.05)). This study may serve as a reference for advancing the processability of HPMC.

Correlation between acoustic characteristics and sensory evaluation of puffed-grain food based on energy analysis.

Puffed-grain food is a crispy snack whose consumer satisfaction depends on snack crispness and crunchiness, which can be characterized by the sound and the acoustic signals of food breaking. This study aimed to evaluate whether acoustic characteristics can be used to predict the crispness of various puffed-grain food. Sensory evaluation was performed on puffed-grain products with varying hygroscopic durations and different types. The relation between sensory evaluation and acoustic characteristics of nine different types of food was examined. The Hilbert-Huang transform was used to perform energy segmentation of the acoustic signal of puffed-grain food and observe its energy migration process. The results showed that energy release was more concentrated in the low-frequency range for grain-puffed foods with different hygroscopic durations. No notable correlation was observed between the low-frequency interval and sensory crispness for the different types of puffed-grain foods. However, the acoustic features extracted from their inherent low-frequency intervals showed a significantly improved correlation with sensory crispness. Therefore, it provides a theoretical reference for applying acoustic characteristics to describe food texture.

Computational exploration of the global microbiome for antibiotic discovery.

Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes. This led to the creation of AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, the majority of which were previously unknown. We observed that AMP production varies by habitat, with animal-associated samples displaying the highest proportion of AMPs compared to other habitats. Furthermore, within different human-associated microbiota, strain-level differences were evident. To validate our predictions, we synthesized and experimentally tested 50 AMPs, demonstrating their efficacy against clinically relevant drug-resistant pathogens both in vitro and in vivo. These AMPs exhibited antibacterial activity by targeting the bacterial membrane. Additionally, AMPSphere provides valuable insights into the evolutionary origins of peptides. In conclusion, our approach identified AMP sequences within prokaryotic microbiomes, opening up new avenues for the discovery of antibiotics.

A Study on the Amelioration of Circadian Rhythm Disorders in Fat Mice Using High-Protein Diets.

This innovative study investigates the effects of high-protein diets (milk protein) on the circadian rhythm of hepatic lipid metabolism. We aimed to understand how high-protein interventions regulate biological clock genes, maintain lipid metabolism balance, and affect the circadian rhythm of antioxidant levels in vivo. We divided 120 SPF-class C57BL/6J mice into the control, high-fat/low-protein (HF-LP), and high-fat/high-protein (HF-HP) groups. Mice were sacrificed during active (2 a.m. and 8 a.m.) and rest periods (2 p.m. and 8 p.m.). In the HF-LP group, hepatic lipid anabolic enzymes were consistently expressed at high levels, while key lipolytic enzymes slowly increased after feeding with no significant diurnal differences. This led to an abnormal elevation in blood lipid levels, a slow increase in and low levels of superoxide dismutase, and a rapid increase in malondialdehyde levels, deviating from the diurnal trend observed in the control group. However, high-protein interventions in the HF-HP group restored lipid synthase activity and the expression of key catabolic enzymes, exhibiting a precise circadian rhythm. It also improved the lipid-metabolism rhythm, which was disrupted by the high-fat diet. Overall, high-protein interventions restored the expression of key enzymes involved in lipid metabolism, improving the lipid-metabolism rhythm, which was disrupted by the high-fat diet.

Metagenomic association analysis of cognitive impairment in community-dwelling older adults.

The gut microbiota is reportedly involved in neurodegenerative disorders, and exploration of differences in the gut microbiota in different cognitive status could provide clues for early detection and intervention in cognitive impairment. Here, we used data from the Taizhou Imaging Study (N = 516), a community-based cohort, to compare the overall structure of the gut microbiota at the species level through metagenomic sequencing, and to explore associations with cognition. Interestingly, bacteria capable of producing short-chain fatty acids (SCFAs), such as Bacteroides massiliensis, Bifidobacterium pseudocatenulatum, Fusicatenibacter saccharivorans and Eggerthella lenta, that can biotransform polyphenols, were positively associated with better cognitive performance (p < 0.05). Although Diallister invisus and Streptococcus gordonii were not obviously related to cognition, the former was dominant in individuals with mild cognitive impairment (MCI), while the later was more abundant in cognitively normal (CN) than MCI groups, and positively associated with cognitive performance (p < 0.05). Functional analysis further supported a potential role of SCFAs and lactic acid in the association between the gut microbiota and cognition. The significant associations persisted after accounting for dietary patterns. Collectively, our results demonstrate an association between the gut microbiota and cognition in the general population, indicating a potential role in cognitive impairment. The findings provide clues for microbiome biomarkers of dementia, and insight for the prevention and treatment of dementia.

The effects of altered DNA damage repair genes on mutational processes and immune cell infiltration in esophageal squamous cell carcinoma.

BACKGROUND: Defects in DNA damage repair (DDR) pathways lead to genomic instability and oncogenesis. DDR deficiency is prevalent in esophageal squamous cell carcinoma (ESCC), but the effects of DDR alterations on mutational processes and tumor immune microenvironment in ECSS remain unclear. METHODS: Whole-exome and transcriptome sequencing data of 45 ESCC samples from Taizhou, China, were used to identify genomic variations, gene expression modulation in DDR pathways, and the abundance of tumor-infiltrating immune cells. Ninety-six ESCC cases from The Cancer Genome Atlas (TCGA) project were used for validation. RESULTS: A total of 57.8% (26/45) of the cases in the Taizhou data and 70.8% (68/96) of the cases in the TCGA data carried at least one functional impact DDR mutation. Mutations in the DDR pathways were associated with a high tumor mutation burden. Several DDR deficiency-related mutational signatures were discovered and were associated with immune cell infiltration, including T cells, monocytes, dendritic cells, and mast cells. The expression levels of two DDR genes, HFM1 and NEIL1, were downregulated in ESCC tumor tissues and had an independent effect on the infiltration of mast cells. In the Taizhou data, increased expression of HFM1 was associated with a poor prognosis, and the increased expression of NEIL1 was associated with a good outcome, but no reproducible correlation was observed in the TCGA data. CONCLUSION: This research demonstrated that DDR alterations could impact mutational processes and immune cell infiltration in ESCC. The suppression of HFM1 and NEIL1 could play a crucial role in ESCC progression and may also serve as prognostic markers.

The role of metabolites under the influence of genes and lifestyles in bone density changes.

Purpose: Osteoporosis is a complex bone disease influenced by numerous factors. Previous studies have found that some metabolites are related to bone mineral density (BMD). However, the associations between metabolites and BMD under the influence of genes and lifestyle have not been fully investigated. Methods: We analyzed the effect of metabolites on BMD under the synergistic effect of genes and lifestyle, using the data of 797 participants aged 55-65 years from the Taizhou Imaging Study. The cumulative sum method was used to calculate the polygenic risk score of SNPs, and the healthful plant-based diet index was used to summarize food intake. The effect of metabolites on BMD changes under the influence of genes and lifestyle was analyzed through interaction analysis and mediation analysis. Results: Nineteen metabolites were found significantly different in the osteoporosis, osteopenia, and normal BMD groups. We found two high-density lipoprotein (HDL) subfractions were positively associated with osteopenia, and six very-low-density lipoprotein subfractions were negatively associated with osteopenia or osteoporosis, after adjusting for lifestyles and genetic factors. Tea drinking habits, alcohol consumption, smoking, and polygenic risk score changed BMD by affecting metabolites. Conclusion: With the increased level of HDL subfractions, the risk of bone loss in the population will increase; the risk of bone loss decreases with the increased level of very-low-density lipoprotein subfractions. Genetic factors and lifestyles can modify the effects of metabolites on BMD. Our results show evidence for the precise prevention of osteoporosis.

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments.

Metagenomic binning is the step in building metagenome-assembled genomes (MAGs) when sequences predicted to originate from the same genome are automatically grouped together. The most widely-used methods for binning are reference-independent, operating de novo and enable the recovery of genomes from previously unsampled clades. However, they do not leverage the knowledge in existing databases. Here, we introduce SemiBin, an open source tool that uses deep siamese neural networks to implement a semi-supervised approach, i.e. SemiBin exploits the information in reference genomes, while retaining the capability of reconstructing high-quality bins that are outside the reference dataset. Using simulated and real microbiome datasets from several different habitats from GMGCv1 (Global Microbial Gene Catalog), including the human gut, non-human guts, and environmental habitats (ocean and soil), we show that SemiBin outperforms existing state-of-the-art binning methods. In particular, compared to other methods, SemiBin returns more high-quality bins with larger taxonomic diversity, including more distinct genera and species.

Hypoglycemia and mortality in sepsis patients: A systematic review and meta-analysis.

BACKGROUND: Hypoglycemia frequently occurs in patients with sepsis. The status of prognosis of sepsis patients varies with the cause of hypoglycemia. OBJECTIVE: A meta-analysis was performed to obtain a reliable basis for assessing the severity of disease in sepsis patients. METHODS: A search of electronic databases was performed. The random-effects model was employed to calculate the overall odds ratio (OR) and 95% CI. RESULTS: Five cohort studies were included. Decreased blood glucose level was associated with an increased risk of death [OR:1.68; 95% CI (1.12-2.53)]. Incidents of mortality were analyzed based on the causative factor of hypoglycemia. Patients with spontaneous hypoglycemia showed a significantly higher mortality rate than the control subjects[OR 1.65; 95% CI (1.20-2.28); p = 0.002]. CONCLUSION: In the early stages of sepsis, the occurrence of spontaneous hypoglycemia may be associated with the severity of the disease.

The gut microbiome in subclinical atherosclerosis: a population-based multiphenotype analysis.

OBJECTIVES: An altered microbiota, which can be described quantitatively, has been identified as playing a pivotal role in host vascular physiology, and it may contribute to various diseases. The aim of this study was to better understand the role of the gut microbiota in vascular physiology in a subclinical elderly population, and to investigate how lifestyle affects the composition of host gut microbiota to further impact the pathogenesis of vascular diseases. METHODS: We performed a population-based faecal metagenomic study over 569 elderly asymptomatic subclinical individuals in rural China. An association network was built based on clinical measurements and detailed epidemiologic questionnaires, including blood chemistry, arterial stiffness, carotid ultrasonography, and metagenomic datasets. RESULTS: By analyzing the breadth, depth and impact of each node of the association network, we found carotid arterial atherosclerosis indices, including intima-media thickness (IMT), were essential in the network, and were significantly associated with living habits, socio-economic status, and diet. Using mediation analysis, we found that higher frequency of eating fresh fruits and vegetables, and more exercise significantly reduced carotid atherosclerosis in terms of IMT, peak systolic velocity and end-diastolic velocity values through the mediation of Alistepes, Oligella and Prevotella. Gut microbes explained 16.5% of the mediation effect of lifestyle on the pathogenesis of carotid atherosclerosis. After adjustment, Faecalicatena [odds ratio (OR) = 0.12 ∼0.65] was shown to be protective against the formation of carotid atherosclerosis, independently, while Libanicoccus (OR = 1.46 ∼4.20 ) was associated with increased carotid arterial IMT. KEGG/KO Kyoto Encyclopedia of Genes and Genomes/ KEGG Orthology (KEGG/KO) analyses revealed a loss of anti-inflammation function in IMT subjects. CONCLUSION: Our study revealed a Chinese population-wide phenotype-metagenomic association network and a mediation effect of gut microbiota on carotid artery atherosclerosis, hinting at potential therapeutic and preventive uses for microbiota in vascular diseases.

ALDH2 rs671 polymorphisms and the risk of cerebral microbleeds in Chinese elderly: the Taizhou Imaging Study.

BACKGROUND: Cerebral microbleeds (CMBs) are more prevalent in Asian populations, and have been associated with increased risk of stroke, dementia and mortality. So far, risk factors for CMBs other than hypertension were merely known. Previous studies have shown that polymorphisms at aldehyde dehydrogenase 2 (ALDH2) gene were independently associated with the risk of stroke. Its role in CMBs, however, remains unclear. This study aimed to evaluate the associations of ALDH2 gene polymorphisms with CMBs in Chinese elderly. METHODS: Using bio-specimen and data collected at baseline survey of the population-based Taizhou Imaging Study (TIS) (phase I), we genotyped the single nucleotide polymorphisms (SNPs) at ALDH2 among 549 individuals aged 55-65 years, and rs671 was used as surrogate marker of ALDH2. CMBs were detected on brain magnetic resonance imaging (MRI), and further categorized as strictly lobar or as deep/mixed. Logistic regression models were used to evaluate the associations of the variants at ALDH2 and CMBs. RESULTS: CMBs were present in 103 individuals (18.8%). Forty-one point three percent participants were with ALDH2 *2 allele and 5.1% had ALDH2 *2/*2 genotype. Subjects with ALDH2 *1 allele were more likely to be drinker, have hypertension or CMBs than those with *2 allele (all P<0.05). Multivariate logistic regression model showed that the ALDH2 *1/*1 genotype was independently associated with CMBs (P=0.013), particularly for deep/mixed CMBs (P=0.008), and the association was more pronounced in men, non-drinkers or hypertension patients. CONCLUSIONS: The results suggest that Han Chinese with ALDH2 *1/*1 genotype may be more susceptible to CMBs than those with ALDH2 *2 allele.

Associations of Arterial Stiffness and Carotid Atherosclerosis with Cerebral Small Vessel Disease in a Rural Community-Based Population.

AIMS: We aimed to examine the associations of four extracranial artery indicators with cerebral small vessel disease (CSVD) and its total burden. METHODS: A total of 904 individuals aged 55-65 years old were included from the Taizhou Imaging Study. CSVD markers, including lacunes (LAC), white matter hyperintensities (WMH), cerebral microbleeds (CMB), and perivascular spaces (PVS), were rated based on brain magnetic resonance imaging. We also measured extracranial artery indices, including the brachial-ankle pulse wave velocity (baPWV), the ankle-brachial index, the carotid intima-media thickness (IMT), and carotid plaque. Linear and binary logistic regressions were adopted to test the associations among these four artery indicators and each CSVD marker when appropriate. Additionally, ordinal and multinomial logistic regressions were performed to assess the relationships between artery indicators and total CSVD score (range from 0-4 points). RESULTS: A total of 443 (49.0%) participants were found to have at least one of the CSVD markers, including 172 (19.0%) with WMH, 184 (20.4%) with LAC, 147 (16.3%) with CMB, and 226 (25.0%) with PVS. Increased baPWV was significantly associated with each CSVD marker, increasing carotid IMT was associated with LAC and PVS, and the presence of carotid plaque was associated with WMH volume and PVS. Moreover, per SD increment of baPWV (odds ratio [OR]: 1.29, 95% confidence interval [CI]: 1.11-1.50) and the presence of carotid plaque (OR: 1.42, 95% CI: 1.05-1.92) were significantly associated with greater total CSVD scores. CONCLUSION: Increased baPWV and the presence of carotid plaque appear to be associated with total CSVD burden in rural regions in China.

Role of Virtual Touch Tissue Imaging Quantification in the Assessment of Hepatic Sinusoidal Obstruction Syndrome in a Rat Model.

OBJECTIVES: To investigate the value of liver stiffness in rats with various degrees of hepatic sinusoidal obstruction syndrome (HSOS) induced by monocrotaline by comparing liver histopathologic findings. METHODS: Seventy rats were randomly divided into a control group (n = 10), a low-dose monocrotaline group (n = 30), and a high-dose monocrotaline group (n = 30). After successful modeling, the liver shear wave velocity (SWV) by Virtual Touch tissue imaging quantification (Siemens Medical Solutions, Mountain View, CA) and the alanine aminotransferase (ALT), aspartate aminotransferase (AST), and total bilirubin levels of the groups were obtained on days 3 and 5, and the intergroup differences were compared. Liver histopathologic characteristics were analyzed to evaluate the degrees of HSOS, and the scores were recorded. RESULTS: On days 3 and 5, the total bilirubin, AST, and ALT, levels and liver SWV in the low- and high-dose groups were elevated; the portal vein velocity (PVV) of these groups was decreased compared with the control group; and the high-dose rats showed higher serum AST and ALT levels than the low-dose rats. The high-dose rats had a lower PVV than the low-dose rats at day 3. The liver SWV values had significant correlations with the histologic score and PVV. In a multivariate analysis, the liver SWV (ß = 0.813; P < .001) was independently associated with the histopathologic score. CONCLUSIONS: Liver stiffness as measured by Virtual Touch tissue imaging quantification increases with the severity of HSOS and can be recommended as a marker for diagnosis and assessment of HSOS.

Out-of-Plane Designed Soft Metasurface for Tunable Surface Plasmon Polariton.

Reliable and repeatable tunability gives functional diversity for reconfigurable plasmonics devices, while reversible and large mechanical deformation enabled by soft materials provides a new way for the global or partial regulation of metadevices. Here, we demonstrate a soft metasurface with an out-of-plane design for tuning the energy of surface plasmon polaritons (SPPs) bloch wave using theory, simulation, and experiments. Our metasurface is composed of two-layered gold nanoribbon arrays (2GNRs) on a soft substrate. The out-of-plane coupling mechanism is systematically analyzed in terms of separation height effect. Moreover, by harnessing mechanical deformation, continuously tunable plasmonic resonance has been achieved in the visible and near-infrared ranges. We further studied the angle-dependent reflection spectra of our metastructure. Compared with its planar counterpart, our soft and two-layered metastructure exhibits diverse tunability and significant field enhancement by out-of-plane interactions. Our approach in designing soft metasurface with out-of-plane structures can be extended to more-complex photonic devices and finds prominent applications such as biosensing, high-density plasmonic circuits, surface-enhanced luminescence, and surface-enhanced Raman scattering.