Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes.

Ruminococcus gnavus is prevalent in the intestines of humans and animals, and ambiguities have been reported regarding its relations with the development of diseases and host well-being. We postulate the ambiguities of its function in different cases may be attributed to strain-level variability of genomic features of R. gnavus . We performed comparative genomic and pathogenicity prediction analysis on 152 filtered high-quality genomes, including 4 genomes of strains isolated from healthy adults in this study. The mean G+C content of genomes of R. gnavus was 42.73±0.33 mol%, and the mean genome size was 3.46±0.34 Mbp. Genome-wide evolutionary analysis revealed R. gnavus genomes were divided into three major phylogenetic clusters. Pan–core genome analysis revealed that there was a total of 28 072 predicted genes, and the core genes, soft-core genes, shell genes and cloud genes accounted for 3.74 % (1051/28 072), 1.75 % (491/28 072), 9.88 % (2774/28 072) and 84.63 % (23 756/28 072) of the total genes, respectively. The small proportion of core genes reflected the wide divergence among R. gnavus strains. We found certain coding sequences with determined health benefits (such as vitamin production and arsenic detoxification), whilst some had an implication of health adversity (such as sulfide dehydrogenase subunits). The functions of the majority of core genes were unknown. The most widespread genes functioning in antibiotic resistance and virulence are tetO (tetracycline-resistance gene, present in 75 strains) and cps4J (capsular polysaccharide biosynthesis protein Cps4J encoding gene, detected in 3 genomes), respectively. Our results revealed genomic divergence and the existence of certain safety-relevant factors of R. gnavus . This study provides new insights for understanding the genomic features and health relevance of R. gnavus , and raises concerns regarding predicted prevalent pathogenicity and antibiotic resistance among most of the strains.

An oval to rod-shaped, Gram-stain-positive, strictly anaerobic bacterium, designated LFL-14^T, was isolated from the faeces of a healthy Chinese woman. Cells of the strain were non-spore-forming, grew optimally at 37 °C (growth range 30–45 °C) and pH 7.0 (growth range 6.0–9.0) under anaerobic conditions in the liquid modified Gifu anaerobic medium (mGAM). The result of 16S rRNA gene-based analysis indicated that LFL-14^T shared an identity of 94.7 0% with Eubacterium ventriosum ATCC 27560^T, indicating LFL-14^T represented a novel taxon. The results of genome-based analysis revealed that the average nucleotide identity (ANI), the digital DNA–DNA hybridisation (dDDH) and average amino acid identity (AAI) between LFL-14^T and its phylogenetically closest neighbour, Eubacterium ventriosum ATCC 27560^T, were 77.0 %, 24.6 and 70.9 %, respectively, indicating that LFL-14^T represents a novel species of the genus Eubacterium. The genome size of LFL-14^T was 2.92 Mbp and the DNA G+C content was 33.14 mol%. We analysed the distribution of the genome of LFL-14^T in cohorts of healthy individuals, type 2 diabetes patients (T2D) and patients with non-alcoholic fatty liver disease (NAFLD). We found that its abundance was higher in the T2D cohort, but it had a low average abundance of less than 0.2 % in all three cohorts. The percentages of frequency of occurrence in the T2D, healthy and NAFLD cohorts were 48.87 %, 16.72 % and 13.10 % respectively. The major cellular fatty acids of LFL-14^T were C_16 : 0 (34.4 %), C_17 : 0 2-OH (21.4 %) and C_14 : 0 (11.7 %). Additionally, the strain contained diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE), as well as unidentified phospholipids and unidentified glycolipids. The glucose fermentation products of LFL-14^T were acetate and butyrate. In summary, On the basis of its chemotaxonomic, phenotypic, phylogenetic and phylogenomic properties, strain LFL-14^T (= CGMCC 1.18005^T = KCTC 25580^T) is identified as representing a novel species of the genus Eubacterium, for which the name Eubacterium album sp. nov. is proposed.

Two bacterial strains, designated BSP-53 ^T and BSP-153 ^T , were isolated from soil samples collected from Beijing Olympic Forest Park, China. Phylogenomic reconstruction based on core genes robustly positioned the strains as two distinct evolutionary lineages within the genus Acinetobacter . Both strains were Gram-negative, aerobic, non-motile and short rods. Their major cellular fatty acids consisted of summed feature 3 (C _16 : 1  ω 7 c /C _16 : 1  ω 6 c ), C _18 : 1  ω 9 c , C _16 : 0 , C _12 : 0 and C _12 : 0 3-OH. The predominant polar lipids included diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The average nucleotide identity values between the novel strains and their closest Acinetobacter type strains were below 95%, with corresponding digital DNA–DNA hybridization values below 70%. Based on polyphasic taxonomic characterization, including chemotaxonomic, phenotypic, phylogenetic and genomic analysis, we propose that strains BSP-53 ^T and BSP-153 ^T represent two novel species of the genus Acinetobacter , for which the names Acinetobacter uliginosus sp. nov. and Acinetobacter halobius sp. nov. are designated. The type strains are BSP-53 ^T (=CGMCC 1.62070 ^T =KCTC 8190 ^T ) and BSP-153 ^T (=CGMCC 1.62071 ^T =KCTC 8191 ^T ), respectively.