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PubMed2025

Bacterial immune systems as causes and consequences of microbiome structure.

Attacks from molecular parasites such as mobile genetic elements (MGEs) have driven the evolution of defense systems in bacterial genomes. Yet, despite significant advances in understanding the molecular mechanisms of these bacterial immune systems, we have only a rudimentary understanding of their ecology and evolution. Bacteria exist as part of complex microbiomes, but community ecology and microbiome research has yet to characterize the impacts of interactions between MGEs and defense mechanisms upon the structure, dynamics and evolution of microbiomes. This Essay introduces and discusses the interplay between bacterial community dynamics and bacterial immune systems, speculating about how these reciprocal interactions may shape microbial community structure and function.

Bacteria↗
PubMed2025

Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.

As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100&#x2009;nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p&#x2009;<&#x2009;0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p&#x2009;<&#x2009;0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.

Soil Microbiology↗
PubMed2002

Investigations on rhizoplane Actinobacteria communities of papyrus (Cyperus papyrus) from an Egyptian wetland.

Wetlands have important global ecological functions, which include carbon storage and water interception. Wetland contributes to the maintenance of regional and global biodiversity. Though many important wetland ecological functions are based on microbial metabolism, we have scanty knowledge on microbial diversity in wetlands. Plant rhizoplane habitats are considered to harbor highly diverse bacterial communities. Most of the floating mats on river Nile are dominated by papyrus (Cyperus papyrus). Papyrus root samples were collected from a floating mat at the "Gold Island" inside the Nile River at Cairo, Egypt in February 1996 and May 1997 in order to investigate the rhizoplane actinobacteria communities. The root-tip regions were cut off, repeatedly washed, macerated and plated. Using the plate-count technique with three actinobacteria media, an average of 2.1 x 10(4) CFUg-1 root actinobacteria were obtained. All actinobacteria colonies were isolated, purified and investigated by classical and molecular methods. In the papyrus rhizoplane Streptomyces anulatus, Micromonospora sp., Rhodococcus luteus, Verrucosispora gifhornensis and Aureobacterium liquefaciens dominated, moreover Actinoplanes utahensis, and Str. diastaticus were also present. The physiological traits of the members of dominant groups revealed that these bacteria might be active in the rhizoplane and can be present there is their vegetative forms.

Actinobacteria↗
PubMed1997

Amniotic fluid leukocytes and leukocyte esterase activity in parturients delivered by caesarean section.

Amniotic fluid specimens from parturients undergoing caesarean delivery were examined for leukocytes and leukocyte esterase activity, as well as for amniotic fluid bacteria and mycoplasmas by cultivation. The aim of this study was to evaluate the intrauterine environment in noninfected parturients and the associations between leukocyte test results, amniotic fluid microbial colonization and postcaesarean endometritis. Samples were obtained by direct aspiration at operation from 289 parturients with no clinical intrauterine infection. Among the total study population, leukocytes were found in 41% of the amniotic fluid samples by Gram staining and in 39% of the samples by the leukocyte esterase activity test. Leukocytes and leukocyte esterase activity were observed significantly more often in the amniotic fluids of parturients undergoing operation after onset of labour or ruptured membranes compared with those operated upon with intact membranes and no labour (p < 0.0001 and p < 0.0001). Of 255 amniotic fluid cultures, microbial colonization was observed in 82 (32%) parturients. Positive results in the leukocyte tests were associated significantly with amniotic fluid microbial colonization among parturients who underwent operation with intact membranes, or who underwent operation after rupture of the membranes and had cervical dilatation of < 5 cm at the operation (Gram stain: p < 0.0001; leukocyte esterase: p < 0.003). If cervical dilatation was > or = 5 cm, no such association was observed. In the population studied, endometritis developed in 2% and 4% of the parturients with positive test results. Thus, neither the presence of leukocytes nor detected leukocyte esterase activity were predictive of subsequent postoperative endometritis. In the detection of amniotic fluid microbial colonization, the tests functioned best in non-laboring parturients with intact membranes and in those operated on at the early stage of labour.

Adult↗
PubMed2025

A Graph Contrastive Learning Method for Enhancing Genome Recovery in Complex Microbial Communities.

Accurate genome binning is essential for resolving microbial community structure and functional potential from metagenomic data. However, existing approaches-primarily reliant on tetranucleotide frequency (TNF) and abundance profiles-often perform sub-optimally in the face of complex community compositions, low-abundance taxa, and long-read sequencing datasets. To address these limitations, we present MBGCCA, a novel metagenomic binning framework that synergistically integrates graph neural networks (GNNs), contrastive learning, and information-theoretic regularization to enhance binning accuracy, robustness, and biological coherence. MBGCCA operates in two stages: (1) multimodal information integration, where TNF and abundance profiles are fused via a deep neural network trained using a multi-view contrastive loss, and (2) self-supervised graph representation learning, which leverages assembly graph topology to refine contig embeddings. The contrastive learning objective follows the InfoMax principle by maximizing mutual information across augmented views and modalities, encouraging the model to extract globally consistent and high-information representations. By aligning perturbed graph views while preserving topological structure, MBGCCA effectively captures both global genomic characteristics and local contig relationships. Comprehensive evaluations using both synthetic and real-world datasets-including wastewater and soil microbiomes-demonstrate that MBGCCA consistently outperforms state-of-the-art binning methods, particularly in challenging scenarios marked by sparse data and high community complexity. These results highlight the value of entropy-aware, topology-preserving learning for advancing metagenomic genome reconstruction.

canonical correlation analysis↗
PubMed2005

TLR-dependent IL-4 production by invariant Valpha14+Jalpha18+ NKT cells to initiate contact sensitivity in vivo.

LPS stimulated B-1 cell polyclonal in vivo IgM responses depend on IL-4 release by invariant Valpha14+Jalpha18+ NKT (iNKT) cells. The IgM Abs can recruit effector T cells to mediate contact sensitivity. LPS activates the B-1 cell response just 1 day later, and depends on CD1d, iNKT cells, IL-4, TLR4, and MyD88. LPS in vivo and in vitro stimulates rapid preferential production of IL-4 in hepatic iNKT cells within 2 h. TLR4 were demonstrated in iNKT cells by flow cytometry and functional studies. Thus, innate microbial stimulation via TLR can activate iNKT cell and B-1 cell collaboration. The result is polyclonal IgM Ab responses capable of recruiting Ag-specific T cells into tissues. This may be involved in the promotion of autoimmunity by infectious agents.

Animals↗
PubMed2002

Breast-feeding, a complex support system for the offspring.

The newborn has an immune system, very limited in size at birth and its postnatal expansion and maturation takes time. In the meantime the transplacental IgG antibodies from the mother play an important role for the protection of the infant. However, these antibodies act in tissues and induce inflammation and are energy-consuming. In contrast, the milk secretory IgA antibodies stop microbes already on the mucosa preventing infection, tissue engagement and energy loss. In addition, the milk contains many protective factors such as lactoferrin and oligosacharides functioning as analogues for microbial receptors preventing mucosal attachment, the initial step of most infections. As a result, breast-feeding significantly reduces the risk of neonatal septicemia, respiratory tract infections, otitis media, diarrhea, urinary tract infections, infection-induced wheezing and necrotizing enterocolitis. Via several mechanisms it seems that human milk can actively stimulate the immune system of the breast-fed infant. This reduces the risk of infections like otitis media, respiratory tract infections, diarrhea and infection-induced wheezing for several years after the termination of breast-feeding. Furthermore, it seems that breast-feeding decreases the risk of attracting celiac disease and allergic diseases. The latter has been much debated, but a recent critical review of published reports gives good support for long-term protection of allergic diseases, especially in high-risk children.

Breast Feeding↗
PubMed1992

[What is reliable in therapy of liver fibrosis?].

Therapy of chronic active liver diseases associated with fibrotic transformation is usually restricted to unspecific antiinflammatory and immunosuppressive agents. However, recent advances in the biochemistry of collagen have allowed to define specific levels of collagen metabolism at which pharmacologic intervention can lead to reduced collagen deposition. The mode of action of some substances which interfere with collagen biosynthesis and degradation is described. However, the efficacy of these agents was tested in vitro exclusively or in animal experiments. Only few agents like colchicine were also studied in clinical trials. Reliable, safe, and specific antifibrotic agents for the clinical management of liver fibrosis do not exist up to now. Advances can be expected, however, from the development of novel inhibitors of prolyl-4-hydroxylase.

Collagen↗
PubMed2005

Effect of heavy metals on soil microbial activity and diversity in a reclaimed mining wasteland of red soil area.

The microbial biomass, basal respiration and substrate utilization pattern in copper mining wasteland of red soil area, southern China, were investigated. The results indicated that soil microflora were obviously different compared with that of the non-mine soil. Microbial biomass and basal respiration were negatively affected by the elevated heavy metal levels. Two important microbial ecophysiological parameters, namely, the ratio of microbial biomass C(Cmic)/organic C(Corg) and metabolic quotient(qCO2) were closely correlated to heavy metal stress. There was a significant decrease in the Cmic/Corg ratio and an increase in the metabolic quotient with increasing metal concentration. Multivariate analysis of Biolog data for sole carbon source utilization pattern demonstrated that heavy metal pollution had a significant impact on microbial community structure and functional diversity. All the results showed that soil microbiological parameters had great potential to become the early sensitive, effective and liable indicators of the stresses or perturbations in soils of mining ecosystems.

Analysis of Variance↗
PubMedDate not supplied

[Soil biological activity in the Chernye Zemli, Kalmykia, inhabited by gerbils Meriones tamariscinus and M. meridianus].

The influence of tamarisk (Meriones tamariscinus) and midday (M. meridianus) gerbils on soil biological activity in the Chernye Zemli, Kalmykia, was studied. Nitrogen fixation, denitrification, and CO2 emission were measured in soil samples from different parts of gerbil burrows. Functional biodiversity of the microbial community was evaluated using multisubstrate testing and comparison of bacterial group composition in samples from gerbil burrows. The impact of gerbils on soil biological activity was mediated by the changes in the group composition of microorganisms.

Animals↗
PubMed1989

Inhibition of chemotaxis Ng-monomethyl-L-arginine: a role for cyclic GMP.

The metabolism of L-arginine to nitric oxide (NO) has been shown to be important for the effector functions of many cell types, including polymorphonuclear (PMN) leukocytes. Its effect appears to be mediated at least in part by NO stimulation of soluble guanylate cyclase. We evaluated the role of this pathway in two PMN effector functions: cell movement and microbial killing, using the competitive inhibitor of L-arginine conversion to NO, NG-monomethyl-L-arginine (NMA). We also evaluated the effect of additional L-arginine and dibutyryl cyclic guanosine monophosphate (cGMP) on any NMA-associated changes. Human peripheral blood neutrophils were used and the cells were incubated with and without NMA. Chemotaxis was evaluated using a 48-well micro-Boyden chamber. Microbial killing was evaluated using S aureus strains D2C and 502A. These studies demonstrated that chemotaxis to formyl-methionyl-leucyl-phenylalanine was markedly inhibited in NMA-treated cells. This inhibition could be overcome if L-arginine or dibutyryl cGMP were added with the NMA. In contrast, microbial killing of S aureus was unaffected by NMA. These observations support the hypothesis that the L-arginine metabolism to NO and its effect on the cGMP level may be important for the dynamic changes required for neutrophil chemotaxis.

Arginine↗
PubMed1988

Enzyme activities of collagen peptidase (CP), monoaminoxidase (MAO) and N-acetyl-beta-D-glucosaminidase (beta-NAG) as fibrosis marker in chronic liver diseases.

The activities of enzymes collagen peptidase (CP), monoaminoxidase (MAO) and N-acetyl-beta-D-glucosaminidase (beta-NAG) in the serum are related to the development of hepatic fibrosis. These enzymes were determined in the sera of 121 liver-biopsied patients who were subdivided by morphological criteria into 4 different grades of fibrosis (0 to greater than or equal to 3). CP shows the best correlation with the extent of fibrosis. beta-NAG, indeed, bears of relationship to the morphologically proven extent of fibrosis, however, significant increases in activity are also encountered in patients with liver diseases, but without liver fibrosis. The validity of these fibrosis markers is calculated in order to differentiate between low- and high-grade fibrosis. With a sensitivity of 86% and a specificity of 92%, CP possesses the best predictive value of 85.7%. The results can still be improved by the combination of CP and beta-NAG.

Acetylglucosaminidase↗
PubMedDate not supplied

Suitability of polyvinylidene fluoride (PVDF) piping in pharmaceutical ultrapure water applications.

This paper discusses polyvinylidene fluoride (PVDF) as an alternative to stainless steel in pharmaceutical ultrapure water piping systems. Two leading Swiss companies, a piping systems supplier and a pharmaceutical manufacturer, teamed together to jointly carryout the research. Issues addressed are metallic contamination, microbial concerns, piping system functionally and ozone resistance. Comparisons between PVDF and stainless steel are made when necessary.

Drug Compounding↗
PubMed1997

Immunopathogenesis of gastrointestinal and hepatobiliary diseases.

The largest lymphoid organ in the body is the gut and the gut-associated lymphoid tissue. The mucosal immune system faces many challenges in protecting the body from microbial invasion. Its chief function is to maintain a diverse population of mature lymphocytes capable of responding to foreign antigens. This task is accomplished with a variety of unique features that distinguish the mucosal from the systemic immune system. In addition, the mucosal immune system plays a role in inflammatory bowel disease, Whipple disease, autoimmune gastritis, Helicobacter pylori infection, immunoproliferative small intestinal disease, hepatitis A, B, C, D, E, F, and G, autoimmune hepatitis, primary biliary cirrhosis, progressive sclerosing cholangitis, and vanishing bile duct syndrome.

Biliary Tract Diseases↗
PubMed1998

A critical, invariant chain-independent role for H2-M in antigen presentation.

Antigen presentation by MHC class II (class II) is facilitated by the accessory molecules, invariant chain (Ii) and H2-M. Ii associates with class II during biosynthesis and promotes transport of class II to Ag-loading compartments. One function of H2-M is the removal of Ii fragments from MHC class II. We have previously demonstrated that Ii-deficient mice, unlike class II-deficient mice, are resistant to L. major infection. In the present study, we found that H2-M-deficient (H2-M0) mice were susceptible to progressive infection with L. major. The dispensability of Ii for control of L. major allowed genetic analysis of whether H2-M functions by association with or independently of Ii. In contrast to Ii-deficient (Ii0) mice, Ii0H2-M0 mice were as susceptible to L. major as H2-M0 mice. Thus, H2-M has an essential, Ii-independent function during presentation of microbial pathogens.

Animals↗
PubMed2006

An experimental metagenome data management and analysis system.

The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity for microbial communities, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi.doe.gov/m.

Bacterial Physiological Phenomena↗
PubMed2026

Cationic porphyrin covalent organic framework reinforced hydroxypropyl methylcellulose films for photodynamic-photothermal sterilization and food preservation.

Microbial contamination in food necessitates effective antimicrobial packaging. While cellulose-based packaging materials suffer from limited antimicrobial efficacy, lack of active functionality, and susceptibility to inducing microbial resistance. To address these challenges, this study synthesized a cationic porphyrin-based covalent organic framework (Por-ICOF) as a multimodal photosensitizer. Por-ICOF was uniformly dispersed via non-covalent interaction within hydroxypropyl methylcellulose (HPMC), creating an HPMC/Por-ICOF composite film. This integration enhanced mechanical strength (increased by 26%), hydrophobicity (WCA 71&#xb0;), and gas barrier properties (OP reduced by 42%, WVP reduced by 36%). Under visible light, the HPMC/Por ICOF film superior absorption generated reactive oxygen species (ROS) and photothermal effects, inactivating 99.2% of Escherichia coli and 99.95% of Staphylococcus aureus within 20&#xa0;min. The composite film exhibited excellent biocompatibility and effectively extended the shelf life of strawberries. This cationic modification strategy for cellulose-based films offers a novel avenue for the design of high-performance antimicrobial food packaging materials.

Food Preservation↗