Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses

Phosphonates (Pn), compounds with a direct C–P bond instead of the more common C–O–P ester bond, constitute a significant fraction of marine dissolved organic phosphorus and recent evidence suggests that they may be an alternative source of P for marine microorganisms. To further characterize the microorganisms and pathways involved in Pn utilization, we screened bacterioplankton genomic libraries for their ability to complement an Escherichia coli strain unable to use Pns as a P source. Using this approach we identified a phosphonatase pathway as well as a novel pair of genes that allowed utilization of 2-aminoethylphosphonate (2-AEPn) as the sole P source. These pathways are present in diverse bacteria common in marine plankton including representatives of Proteobacteria , Planctomycetes and Cyanobacteria . Analysis of metagenomic databases for Pn utilization genes revealed that they are widespread and abundant among marine bacteria, suggesting that Pn metabolism is likely to play an important role in P-depleted surface waters, as well as in the more P-rich deep-water column.     

Transport capabilities of eleven gram-positive bacteria: Comparative genomic analyses

The genomes of eleven Gram-positive bacteria that are important for human health and the food industry, nine low G + C lactic acid bacteria and two high G + C Gram-positive organisms, were analyzed for their complement of genes encoding transport proteins. Thirteen to 18% of their genes encode transport proteins, larger percentages than observed for most other bacteria. All of these bacteria possess channel proteins, some of which probably function to relieve osmotic stress. Amino acid uptake systems predominate over sugar and peptide cation symporters, and of the sugar uptake porters, those specific for oligosaccharides and glycosides often outnumber those for free sugars. About 10% of the total transport proteins are constituents of putative multidrug efflux pumps with Major Facilitator Superfamily (MFS)-type pumps (55%) being more prevalent than ATP-binding cassette (ABC)-type pumps (33%), which, however, usually greatly outnumber all other types. An exception to this generalization is Streptococcus thermophilus with 54% of its drug efflux pumps belonging to the ABC superfamily and 23% belonging each to the Multidrug/Oligosaccharide/Polysaccharide (MOP) superfamily and the MFS. These bacteria also display peptide efflux pumps that may function in intercellular signalling, and macromolecular efflux pumps, many of predictable specificities. Most of the bacteria analyzed have no pmf-coupled or transmembrane flow electron carriers. The one exception is Brevibacterium linens, which in addition to these carriers, also has transporters of several families not represented in the other ten bacteria examined. Comparisons with the genomes of organisms from other bacterial kingdoms revealed that lactic acid bacteria possess distinctive proportions of recognized transporter types (e.g., more porters specific for glycosides than reducing sugars). Some homologues of transporters identified had previously been identified only in Gram-negative bacteria or in eukaryotes. Our studies reveal unique characteristics of the lactic acid bacteria such as the universal presence of genes encoding mechanosensitive channels, competence systems and large numbers of sugar transporters of the phosphotransferase system. The analyses lead to important physiological predictions regarding the preferred signalling and metabolic activities of these industrially important bacteria.     

Transport capabilities of eleven gram-positive bacteria: comparative genomic analyses

The genomes of eleven Gram-positive bacteria that are important for human health and the food industry, nine low G+C lactic acid bacteria and two high G+C Gram-positive organisms, were analyzed for their complement of genes encoding transport proteins. Thirteen to 18% of their genes encode transport proteins, larger percentages than observed for most other bacteria. All of these bacteria possess channel proteins, some of which probably function to relieve osmotic stress. Amino acid uptake systems predominate over sugar and peptide cation symporters, and of the sugar uptake porters, those specific for oligosaccharides and glycosides often outnumber those for free sugars. About 10% of the total transport proteins are constituents of putative multidrug efflux pumps with Major Facilitator Superfamily (MFS)-type pumps (55%) being more prevalent than ATP-binding cassette (ABC)-type pumps (33%), which, however, usually greatly outnumber all other types. An exception to this generalization is Streptococcus thermophilus with 54% of its drug efflux pumps belonging to the ABC superfamily and 23% belonging each to the Multidrug/Oligosaccharide/Polysaccharide (MOP) superfamily and the MFS. These bacteria also display peptide efflux pumps that may function in intercellular signalling, and macromolecular efflux pumps, many of predictable specificities. Most of the bacteria analyzed have no pmf-coupled or transmembrane flow electron carriers. The one exception is Brevibacterium linens, which in addition to these carriers, also has transporters of several families not represented in the other ten bacteria examined. Comparisons with the genomes of organisms from other bacterial kingdoms revealed that lactic acid bacteria possess distinctive proportions of recognized transporter types (e.g., more porters specific for glycosides than reducing sugars). Some homologues of transporters identified had previously been identified only in Gram-negative bacteria or in eukaryotes. Our studies reveal unique characteristics of the lactic acid bacteria such as the universal presence of genes encoding mechanosensitive channels, competence systems and large numbers of sugar transporters of the phosphotransferase system. The analyses lead to important physiological predictions regarding the preferred signalling and metabolic activities of these industrially important bacteria.     

基于调节肠道菌群的功能性低聚糖改善肥胖的研究进展

肥胖是机体脂肪积聚过多的一种典型的能量过剩疾病,是导致2型糖尿病和心血管疾病等一系列代谢性疾病的主要原因之一,已成为威胁全球健康的重大公共卫生问题。肠道菌群作为机体能量代谢调控的重要参与者,在肥胖及相关代谢性疾病的发生发展中起着关键作用,通过饮食干预调节肠道菌群,进而改善机体健康状况将是未来的研究热点之一。已有研究表明,功能性低聚糖作为一类典型的新型益生元,可调节肠道菌群结构及其代谢产物的水平,影响机体能量代谢过程,改善肥胖及相关代谢性疾病。本文主要对肠道菌群在肥胖中的潜在作用机制,以及常见功能性低聚糖调节肠道菌群改善肥胖的作用效果进行综述,以期为通过靶向肠道菌群精准干预肥胖及相关代谢性疾病提供一些新的潜在防治策略。

     

基于NGS方法评估不同保存条件对粪便样本中菌群含量的影响

目的 评估粪便样本的不同保存条件对肠道微生态研究结果的影响.方法 设计相关实验,比较7种不同的保存方法,基于高通量测序技术比对不同时间、不同贮存温度对粪便样本DNA质量、菌群多样性及病原菌检出等结果之间的差异.结果 证实了对于粪便样本采集仍建议采取即刻提取核酸或-20℃保存的方法.同时比较多种保存方法后发现,采用不同样...     

Prebiotics: tools to manipulate the gut microbiome and metabolome

Journal of Industrial Microbiology & Biotechnology - The human gut is an ecosystem comprising trillions of microbes interacting with the host. The composition of the microbiota and their...     

Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions

Functional genomic technologies such as high density DNA microarrays allow biologists to study the structure and behavior of thousands of genes in a single experiment. One of the fields in which microarrays have had an increasingly important impact is host-pathogen interactions. Early investigations in this area over the past two years not only emphasize the utility of this approach, but also highlight the stereotyped gene expression responses of different host cells to diverse infectious stimuli, and the potential value of broad dataset comparisons in revealing fundamental features of innate immunity. The comparative analysis of recently published datasets involving human gene expression responses to two bacterial respiratory pathogens illustrates many of these points. Comparisons between these large, highly parallel sets of experimental observations also emphasize important technical and experimental design issues as future challenges.     

Use of complex DNA and antibody microarrays as tools in functional analyses

While the deciphering of basic sequence information on a genomic scale is yielding complete genomic sequences in ever-shorter intervals, experimental procedures for elucidating the cellular effects and consequences of the DNA-encoded information become critical for further analyses. In recent years, DNA microarray technology has emerged as a prime candidate for the performance of many such functional assays. Technically, array technology has come a long way since its conception some 15 years ago, initially designed as a means for large-scale mapping and sequencing.The basic arrangement, however, could be adapted readily to serve eventually as an analytical tool in a large variety of applications. On their own or in combination with other methods, microarrays open up many new avenues of functional analysis.     

斜纹夜蛾幼虫肠道细菌分离鉴定及其功能初步分析

昆虫肠道微生物对其寄主的生长发育、营养代谢、免疫以及农药抗性等方面都发挥着重要作用。为研究斜纹夜蛾Spodoptera litura幼虫肠道细菌的多样性,并为其功能验证做准备,本文利用传统微生物分离纯培养方法从斜纹夜蛾4龄幼虫肠道中共分离鉴定得到10株细菌,分别为属于变形菌门(Proteobacteria)的脱氮假单胞菌(Pseudomonas denitrificans),不动细菌(Acinetobacter sp.),肺炎克雷伯氏菌(Klebsiella pneumoniae)和肠杆菌(Enterobacter sp.);属于厚壁菌门(Firmicutes)的鸡葡萄球菌(Staphylococcus gallinarum),蒙氏肠球菌(Enterococcus mundtii),蜡样芽胞杆菌(Bacillus cereus)和枯草芽胞杆菌(Bacillus subtilis)以及放线菌门(Actinobacteria)的微杆菌(Microbacteriums sp.)和乳酪棒杆菌(Corynebacterium casei)。变形菌门和厚壁菌门是斜纹夜蛾肠道可培养细菌中的优势菌群。功能验证实验表明肠杆菌具备纤维素降解能力,微杆菌具备很强的苯酚降解能力。本研究为未来深入研究斜纹夜蛾肠道微生物的功能提供了方向和菌株材料。     

Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron–sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 10⁸ cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.     

Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp

The spirochetes of the Leptospira genus contain saprophytic and pathogenic members, the latter being responsible for leptospirosis. Despite the recent sequencing of the genome of the pathogen L. interrogans, the slow growth of these bacteria, their virulence in humans, and a lack of genetic tools make it difficult to work with these pathogens. In contrast, the development of numerous genetic tools for the saprophyte L. biflexa enables its use as a model bacterium. Leptospira spp. require iron for growth. In this work, we show that Leptospira spp. can acquire iron from different sources, including siderophores. A comparative genome analysis of iron uptake systems and their regulation in the saprophyte L. biflexa and the pathogen L. interrogans is presented in this study. Our data indicated that, for instance, L. biflexa and L. interrogans contain 8 and 12 genes, respectively, whose products share homology with proteins that have been shown to be TonB-dependent receptors. We show that some genes involved in iron uptake were differentially expressed in response to iron. In addition, we were able to disrupt several putative genes involved in iron acquisition systems or iron regulation in L. biflexa. Comparative genomics, in combination with gene inactivation, gives us significant functional information on iron homeostasis in Leptospira spp.