Single-shot imaging through scattering media under strong ambient light interference.

Speckle correlation imaging (SCI) has found tremendous versatility compared with other scattering imaging approaches due to its single-shot data acquisition strategy, relatively simple optical setup, and high-fidelity reconstruction performance. However, this simplicity requires SCI experiments to be performed strictly in a darkroom condition. As background noise increases, the speckle contrast rapidly decreases, making precise interpretation of the data extremely difficult. Here, we demonstrate a method by refining the speckle in the autocorrelation domain to achieve high-performance single-shot imaging. Experiment results prove that our method is adapted to estimate objects in a low signal-to-background ratio (SBR) circumstance even if the SBR is about -23dB. Laboratory and outdoor SCI experiments are performed.

Multitarget imaging through scattering media beyond the 3D optical memory effect.

A robust method for efficient spatial separation optical imaging through scattering media regardless of the three-dimensional (3D) optical memory effect is proposed. In this method, the problems of imaging dealiasing, decomposition, and separation of speckle patterns are solved by employing independent component analysis. Multitarget imaging behind a scattering layer with diverse spatial positions is observed experimentally, for the first time, to the best of our knowledge. In this work, we demonstrate that, by knowing the number of targets and keeping each subtargets' size in the optical memory effect range while isolating them beyond this range without overlap in the axial direction, speckle dealiasing and multitarget imaging are solved effectively. The strategy provides a potentially useful means for incoherent imaging through scattering media in a wide class of fields such as optical microscopy, biomedical imaging, and astronomical imaging.

Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.

Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.

A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures.

As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.

Metagenomic comparison of gut communities between wild and captive Himalayan griffons.

Introduction: Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited. Methods: In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions. Results: Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs). Discussion: In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.

The first outbreak of feline panleukopenia virus infection in captive Pallas's cats in Xining Wildlife Park.

Introduction: In August 2021, an outbreak of Feline Panleukopenia Virus (FPV) was observed in four 3-month-old Pallas' cats at Xining Wildlife Park. Despite timely intervention, the Pallas'cat cubs continued to experience clinical symptoms including diarrhea, seizures, and decreased white blood cell count, and all four cats died. Methods: FPV clinical suspicions were initially confirmed by positive Polymerase Chain Reaction (PCR) testing. Pathological and immunohistochemical examinations (IHC) were performed on some organs, and the results showed that, encephalitis, viral enteritis, and splenitis occurred. Results: The virus replicates extensively in the cytoplasm of lymphocytes and macrophages in the lamina propria of the small intestine mucosa. A strain of FPV was successfully isolated and culture in CRFK cells. Through molecular identification, sequence analysis, and phylogenetic analysis of the VP2 gene in this strain, we have revealed the presence of a novel synonymous mutation. From July to December 2021, surveillance on stray cats and susceptible wildlife at Xining Wildlife Park indicated widespread FPV transmission. Discussion: The findings highlight the urgent need for ongoing epidemiological monitoring and active disinfection measures to prevent FPV transmission in wildlife parks.

The impact of bloodmeal and geographic region on the richness, diversity, and function of internal microbial community in Haemaphysalis qinghaiensis from the Qinghai province, China.

Background: Ticks are ectoparasites that feed on blood and pose a threat to both the livestock industry and public health due to their ability to transmit pathogens through biting. However, the impact of factors such as bloodmeal and geographic regions on the bacterial microbiota of Haemaphysalis qinghaiensis remains poorly understood. Methods: In this study, we used the v3-v4 region of the 16S rRNA gene to sequence the microbiota of Haemaphysalis qinghaiensis from eight groups (HY_M, YS_M, XH_M, LD_M, BM_M, LD_F_F, LD_F, and BM_F_F) in Qinghai Province. Results: Significant differences in bacterial richness were observed between LD_F_F, BM_F_F, and LD_F (P < 0.01), and among the five groups (HY_M, YS_M, XH_M, BM_M, and LD_M) (P < 0.05). The bacterial diversity also differed significantly between LD_F_F, LD_F, and BM_F_F (P < 0.01), as well as among the five groups (HY_M, YS_M, XH_M, LD_M, and BM_M) (P < 0.01). The group with the highest number of operational taxonomic units (OTUs) was LD_F, accounting for 23.93 % (419/1751), while BM_F_F accounted for at least 0.80 % (14/1751). At the phylum level, Firmicutes was the most abundant, with relative abundance ranging from 7.44 % to 96.62 %. At the genus level, Staphylococcus had the highest abundance, ranging from 1.67 % to 97.53 %. The endosymbiotic bacteria Coxiella and Rickettsia were predominantly enriched in LD_F_F. Additionally, the 16S gene of Coxiella showed the highest identity of 99.07 % with Coxiella sp. isolated from Xinxiang hl9 (MG9066 71.1), while the 16S gene of Rickettsia had 100 % identity with Candidatus Rickettsia hongyuanensis strains (OK 662395.1). Functional predictions for the prokaryotic microbial community indicated that the main functional categories were Metabolic, Genetic information processing, and Environmental information processing across the eight groups. Conclusion: This study provides a theoretical basis for the prevention and treatment of tick-borne diseases, which is of great significance for public health.

Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures.

Introduction: Himalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals' gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown. Methods: In this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures. Results: In total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures' gut virome. Discussion: Our findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures' gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures' response to captivity and aids in optimizing their rehabilitation and implementing protective measures.

Feline herpesvirus infection and pathology in captive snow leopard.

Feline herpesvirus type 1 (FHV-1) is a common causative agent of domestic cats' rhinotracheitis in domestic cats, and it increasingly threatens wild felids worldwide. The endangered snow leopard (Panthera uncia) belongs to the family Felidae, and it is the top predator on the Tibetan Plateau. Here we report the identification and isolation of FHV-1 from three dead captive snow leopards that presented with sneezing and rhinorrhea. To explore the relationship between FHV-1 and their deaths, organs and nasal swabs were collected for histopathology, viral isolation and sequence analysis. The results revealed that all three snow leopards were infected with FHV-1. The first animal died primarily of cerebral infarction and secondary non-suppurative meningoencephalitis that was probably caused by FHV-1. The second animal died mainly of renal failure accompanied by interstitial pneumonia caused by FHV-1. The cause of death for the third animal was likely related to the concurrent reactivation of a latent FHV-1 infection. The gD and gE gene sequence alignment of the isolated FHV-1 isolate strain revealed that the virus likely originated from a domestic cat. It was found that FHV-1 infection can cause different lesions in snow leopards than in domestic cats and is associated with high risk of disease in wild felids. This suggests that there should be increased focus on protecting wild felids against FHV-1 infections originating from domestic cats.