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PubMedDate not supplied

Establishment of cellulolytic bacteria and development of fermentative activities in the rumen of gnotobiotically-reared lambs receiving the microbial additive Saccharomyces cerevisiae CNCM I-1077.

We studied the effects of a yeast additive used in ruminant nutrition on the establishment of cellulolytic bacteria, on plant cell wall degradation and on digestive functions in the rumen of gnotobiotically-reared lambs. Cellulolytic bacteria inoculated to the lambs tended to become established earlier in the presence of Saccharomyces cerevisiae CNCM I-1077 (SC). In addition, their population was maintained at a higher level, when the physico-chemical conditions of the biotope were altered. In these lambs, specific activities of fibrolytic enzymes were greater, and in sacco degradation of wheat straw tended to increase. In the presence of SC there was a decrease in ruminal ammonia concentration and a higher volatile fatty acid (VFA) concentration when lambs were 20 to 50 days old. These data suggest that this yeast strain may stimulate the development of cellulolytic microflora and enhance microbial activity in the rumen of young ruminants. Such activity could be beneficial in preventing microbial imbalance and a reduction of rumen function efficiency in the case of nutritional transitions. Further studies with conventional animals will soon be performed in order to verify these dings.

Ammonia↗

PubMed1996

[Gastrointestinal mucus].

Gastrointestinal mucus (GIMu) is a viscoelastic gel, which covers the surface of the entire digestive tract. The main component of GIMu is mucin, which is a high molecular weight glycoprotein. Mucin is composed of a central peptide core with polysaccharide chains arranged radially from the core ("bottle brushappearance"). The carbohydrates are very hydrophilic and, therefore, able to bind large amounts of water, which partly accounts for the gel-forming properties of GIMu. GIMu has an important function as a barrier against large particles, H+ ions and pepsin, carcinogens, certain macromolecules and microorganisms. GIMu seems to be involved in the pathogenesis of gastroduodenal ulceration, inflammatory bowel disease, gastrointestinal malignancies, gallbladder stones and infectious diarrhoeal diseases. GIMu is also an important factor in maintaining the normal microbial intestinal homeostasis. In the future, a more detailed knowledge about the molecular structure and function of GIMu may lead to new diagnostic and therapeutic strategies for gastrointestinal diseases.

Gastric Mucosa↗

PubMed1977

[Barrier-fixing function in germ-free animals].

The state of barrier-fixative function was studied in germfree and conventional guinea pigs and rats. Under conditions of conventional animals contamination with E. coli 055 (in doses of 500 million and 10 milliard microbial bodies for subcutaneous and oral inoculation, respectively) only an early transitory bacteremia developed at the early postinfection periods. As to bacteriemia in gnotobiotes, it increased progressively leading to the animal death in the course of 2 to 3 days. A decreased fixative and bactericidal capacity of the regional lymphatic apparatus and deep structures of the mononuclear-phagocytic system was revealed in germfree animals. An experimental confirmation of the participance of antibodies in the manifestation of the barrier-fixative function to E. coli was obtained. These studies demonstrated an important role of the microbial factor in the formation of the macroorganism barrier-fixative function.

Animals↗

PubMed2006

Exocellular electron transfer in anaerobic microbial communities.

Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory syntrophic consortia of proton-reducing acetogenic bacteria and hydrogen-consuming methanogenic archaea. Anaerobic microorganisms that use insoluble electron acceptors for growth, such as iron- and manganese-oxide as well as inert graphite electrodes in microbial fuel cells, also transfer electrons exocellularly. Soluble compounds, like humic substances, quinones, phenazines and riboflavin, can function as exocellular electron mediators enhancing this type of anaerobic respiration. However, direct electron transfer by cell-cell contact is important as well. This review addresses the mechanisms of exocellular electron transfer in anaerobic microbial communities. There are fundamental differences but also similarities between electron transfer to another microorganism or to an insoluble electron acceptor. The physical separation of the electron donor and electron acceptor metabolism allows energy conservation in compounds as methane and hydrogen or as electricity. Furthermore, this separation is essential in the donation or acceptance of electrons in some environmental technological processes, e.g. soil remediation, wastewater purification and corrosion.

Anaerobiosis↗

PubMed2001

Intrinsic errors in genome annotation.

Genome sequencing is usually followed by routine annotation of protein function based on the assumption that similar sequences will have similar functions. Here, we introduce a simple calculation to estimate the magnitude of any possible annotation errors. We counted the number of discrepancies in the annotation of well-established sets of similar proteins and extrapolated these values to the pairs of similar sequences used for the annotation of different microbial genomes. We conclude that the number of potential errors in the prediction of detailed functions is higher than is usually believed.

Binding Sites↗

PubMed1990

In vitro aggregation of bovine neonatal neutrophils. A comparative study with adult cattle.

Deficient in vitro functions of neonatal neutrophils have been reported in various species. They may be functionally related to the well-known susceptibility of newborn individuals to microbial infections. To evaluate an early step in the sequence of neutrophil activation, neutrophils from adult cows (A-PMN) and newborn calves (N-PMN) were stimulated with zymosan-activated plasma (ZAP) or with the lipid mediator platelet-activating factor (PAF): Aggregation was recorded kinetically in a standard aggregometer and measured quantitatively as the area under the aggregation curve (AUAC). The mean +/- SEM of the AUAC of the first 2.5 min of the reaction induced with ZAP was similar in N-PMN and A-PMN. However, N-PMN deaggregated only partially, whereas A-PMN deaggregated almost completely (P less than 0.05). This may indicate a mechanism of microvascular sequestration in vivo with the potential to inhibit chemotaxis. PAF (10(-5)-10(-10) M) aggregated N- and A-PMNs similarly and dose-dependently with a maximal reaction at 10(-6) M. Inhibition of aggregation induced by 10(-6) M PAF was evaluated by preincubation with four antiinflammatory drugs: dexamethasone (Dex: 5.1, 51.0, 510.0 microM), flumethasone (Flu: 12.2 and 122.0 microM), phenylbutazone (PB: 0.33 and 3.3 mM), and flunixin meglumine (Flxin: 51 and 510 microM). Dex and Flu each inhibited (P less than 0.05) PAF-induced N-PMN aggregation at the highest dose, and A-PMN aggregation at the two higher doses. PB and Flxin each inhibited aggregation of N- and A-PMNs at all doses used. We compared the inhibition rate in both age groups and could demonstrate that Dex, Flu, and Flxin each at the highest dose, and PB at all doses used, inhibited PAF-induced aggregation less (P less than 0.05) in N-PMNs than in A-PMNs. These functional differences indicate hyperirritability of N-PMNs, and they need further elucidation to help understand mechanisms of increased neonatal susceptibility.

Aging↗

PubMed1993

Structure-function relationships of lipoprotein lipase: mutation analysis and mutagenesis of the loop region.

The molecular models of two microbial lipases and human pancreatic lipase (PL) have suggested the existence of common structural motifs including a buried active site shielded by an amphipathic surface loop. In an effort to explore the role of residues comprising the loop of lipoprotein lipase (LPL), we have used site-directed mutagenesis to generate three new LPL variants. In variant LPLM1 we deleted 18 amino acids leaving a loop of only 4 residues which resulted in an LPL protein inactive against triolein substrates. In contrast, two other LPL variants with only partial deletions, involving the apical section of the loop [LPLM2 (-8 amino acids) and LPLM3 (-2 amino acids)] manifested normal lipolytic activity. These findings indicate a critical requirement for the maintenance of charge and periodicity in the proximal and distal segments of the LPL loop in normal catalytic function. This is further highlighted by the detection of a mutation in the proximal section of the loop in a patient with LPL deficiency at position 225 which results in a substitution of threonine for isoleucine. The intact catalytic activity of the partial deletion variants (LPLM2 and LPLM3) further suggests that the apical residues of the loop contribute minimally to the functional motifs of the active site. We support this postulate by showing that the conserved glycine in the apical turn section (G229) can be substituted by glutamine, lysine, proline, or threonine without significantly affecting catalytic activity.

Base Sequence↗

PubMed1984

[Microbial content of the air in poultry houses].

The industrial animal-breeding complex is characterized as an ecotechnical system the function of which is determined by the action of antropogenic factors. It has been demonstrated that up to now the stress of antropogenic activity has been laid on the optimization of the abiotic factors. The control and optimization of the biotic factors has constituted a problem for industrial poultry breeding, especially important being the microbial content of air. Investigations have shown that with the industrial raising of birds air microbism has assumed the importance of a factor that lowers the effectiveness of the technologies applied. The factors have been discovered that govern the extent of microbial contamination of air. Results of experiments in productional poultry houses and climatic chambers have led to the offer of measures aimed at limiting the microbial contamination of air in the industrial raising of birds.

Air Ionization↗

PubMed2002

Microbial communities and their interactions in soil and rhizosphere ecosystems.

Since the first estimate of prokaryotic abundance in soil was published, researchers have attempted to assess the abundance and distribution of species and relate this information on community structure to ecosystem function. Culture-based methods were found to be inadequate to the task, and as a consequence a number of culture-independent approaches have been applied to the study of microbial diversity in soil. Applications of various culture-independent methods to descriptions of soil and rhizosphere microbial communities are reviewed. Culture-independent analyses have been used to catalog the species present in various environmental samples and also to assess the impact of human activity and interactions with plants or other microbes on natural microbial communities. Recent work has investigated the linkage of specific organisms to ecosystem function. Prospects for increased understanding of the ecological significance of particular populations through the use of genomics and microarrays are discussed.

Archaea↗

PubMed1998

Characterization and functional analysis of the porcine lactoferrin gene promoter.

Lactoferrin, a ferric binding glycoprotein found in milk, can possibly prevent microbial infection of the mammary gland and gastrointestinal tract. To define the regulation of the porcine lactoferrin gene (pLTF), we cloned its 5'-flanking region from a porcine liver genomic library and analyzed the 5' upstream region of approx. 4kb, two exons, and an intron. The transcription start site was localized by primer extension to residue G, which is 41 nucleotides upstream from the ATG start codon. The pLTF 5'-flanking region possesses several putative cis-acting regulatory elements found in both housekeeping and inducible genes; to define their function, they were inserted into a chloramphenicol acetyltransferase reporter construct. The region up to -156 sufficed for basic promoter activity, whereas the region up to -780 was required for maximal promoter activity in porcine testis cells (STcells), kidney cells (PK15 cells) and human mammary epithelial cells (HBL-100 cells). Detailed analysis of this proximal region by DNase I footprinting and electrophoretic mobility shift assays reveals that the ubiquitous factors SP1, AP2 and the mammary gland-specific factor (MGF) might play significant roles in regulating the transcription of the pLTF gene.

Animals↗

PubMed2004

Development of joint application strategies for two microbial gene finders.

MOTIVATION: As a starting point in annotation of bacterial genomes, gene finding programs are used for the prediction of functional elements in the DNA sequence. Due to the faster pace and increasing number of genome projects currently underway, it is becoming especially important to have performant methods for this task. RESULTS: This study describes the development of joint application strategies that combine the strengths of two microbial gene finders to improve the overall gene finding performance. Critica is very specific in the detection of similarity-supported genes as it uses a comparative sequence analysis-based approach. Glimmer employs a very sophisticated model of genomic sequence properties and is sensitive also in the detection of organism-specific genes. Based on a data set of 113 microbial genome sequences, we optimized a combined application approach using different parameters with relevance to the gene finding problem. This results in a significant improvement in specificity while there is similarity in sensitivity to Glimmer. The improvement is especially pronounced for GC rich genomes. The method is currently being applied for the annotation of several microbial genomes. AVAILABILITY: The methods described have been implemented within the gene prediction component of the GenDB genome annotation system.

Algorithms↗

PubMed2004

Biased biological functions of horizontally transferred genes in prokaryotic genomes.

Horizontal gene transfer is one of the main mechanisms contributing to microbial genome diversification. To clarify the overall picture of interspecific gene flow among prokaryotes, we developed a new method for detecting horizontally transferred genes and their possible donors by Bayesian inference with training models for nucleotide composition. Our method gives the average posterior probability (horizontal transfer index) for each gene sequence, with a low horizontal transfer index indicating recent horizontal transfer. We found that 14% of open reading frames in 116 prokaryotic complete genomes were subjected to recent horizontal transfer. Based on this data set, we quantitatively determined that the biological functions of horizontally transferred genes, except mobile element genes, are biased to three categories: cell surface, DNA binding and pathogenicity-related functions. Thus, the transferability of genes seems to depend heavily on their functions.

Algorithms↗

PubMed2026

Genome-resolved analysis reveals disruption of gut microbial vitamin B and K2 biosynthesis during Toxoplasma gondii infection in mice.

UNLABELLED: Toxoplasma gondii infection remodels the gut microbiome, yet its impact on microbial vitamin biosynthetic potential and host redox metabolism remains unclear. Here, we integrated mouse gut metagenomes with publicly available metagenome-assembled genomes (MAGs) to construct a genome-resolved atlas of B-vitamin and vitamin K2 biosynthesis. From 45,697 MAGs, we curated 4,771 representative genomes, of which 2,682 met high-quality criteria (completeness ≥90%, contamination <5%). Functional annotation identified 229,717 vitamin-related genes corresponding to 177 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs across de novo pathways for eight B vitamins, thiamine (B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and vitamin K2. Among the high-quality genomes, 1,665 encoded complete de novo pathways for at least one vitamin, highlighting functional specialization and community-level complementarity. Transcripts per million-normalized metagenomic read counts revealed significant differences in KEGG ortholog abundances across six of the nine vitamin pathways. Reanalysis of metagenomic data from infected mice (acute, chronic, and control; n = 10 per group) revealed a stage-dependent reduction in α-diversity of vitamin biosynthesis pathways during acute infection, and a clear β-diversity separation from chronic and control groups. Core niacin biosynthesis genes (nadB, nadA, nadC) displayed phylum-specific redistribution, indicating selective remodeling of microbial NAD+ precursor production under infection-induced metabolic stress. These results suggest that T. gondii infection disrupts cooperative vitamin biosynthetic networks while specifically modulating niacin pathways linked to host NAD+ metabolism. IMPORTANCE: Gut microbes can synthesize essential vitamins, but how infection alters this function is poorly understood. By integrating mouse gut metagenomes with genome-resolved microbial data, we show that Toxoplasma gondii infection reshapes the vitamin biosynthetic potential of the gut microbiome in a stage-dependent manner. Acute infection reduces the diversity of vitamin biosynthesis pathways and shifts the taxonomic distribution of key niacin biosynthesis genes involved in microbial NAD+ precursor production. These findings identify vitamin metabolism, especially niacin-related pathways, as a sensitive functional axis of microbiome remodeling during infection. Our work links microbial taxonomic changes to functional metabolic consequences and suggests that microbiome-mediated regulation of NAD+-related metabolism may contribute to host redox adaptation during T. gondii infection.

B vitamins↗

PubMed2026

Decoding the spatiotemporal patterns of food spoilage microbial communities: Integrating multi-omics and artificial intelligence to enable precision preservation.

In the global food supply chain, food wastage caused by spoilage has resulted in significant economic losses, food shortages, and environmental pressure. This process is fundamentally driven by the spatiotemporal dynamics of microbial communities. However, traditional research methods struggle to elucidate the complex mechanisms of spatial heterogeneity, interspecies interactions, and functional succession. This limits the development of effective preservation strategies. This review systematically reviews the cutting-edge progress of integrating multi-omics technologies and artificial intelligence (AI) to study food spoilage microbial communities, breaking through this bottleneck. We propose an intelligent theoretical framework that could potentially analyze microbial metabolic activities and predict dynamic shelf life if implemented. The conceptual framework integrates multidimensional data, including spatial metabolomics, temporal metatranscriptomics, single-cell transcriptomics, and longitudinal metagenomics. It can also be combined with AI models, such as graph neural networks. The article elaborates on the principles and applications of spatio-temporal monitoring technologies, such as nano secondary ion mass spectrometry, hyperspectral imaging, and the Internet of Things sensing. Through illustrative cases of typical perishable foods, it also explores how such a multi-omics - AI system might be applied to spoilage warning and precise intervention. Additionally, the article addresses the current challenges in data coverage, model generalization, and federated learning implementation. Then the research further explores emerging areas such as engineered probiotics, edge AI, and microfluidic sensing. These areas are targeted at transforming food preservation from an empirical control approach to a data-driven, precise regulatory framework. This transformation provides theoretical support and technical approaches for developing a smart, sustainable food preservation system.

Multiomics↗

PubMed2026

Lesion-specific oral microbiome signatures and predicted carcinogenic pathways in oral squamous cell carcinoma: a paired-site study in Pakistan.

BACKGROUND: Oral squamous cell carcinoma accounts for over 90% of oral neoplasms. Despite therapeutic advances, the lack of reliable, non-invasive biomarkers and delayed diagnosis continues to impede effective clinical management. By combining paired lesion and non-lesion sampling with predictive metagenomics analysis, our study addresses this gap and advances the current understanding of microbiome‒tumor interactions. METHODS: We analyzed 92 buccal swab samples from 39 OSCC patients and 14 healthy controls using 16S rRNA gene (V3-V4) sequencing. Taxonomic profiling was conducted using QIIME2 and SILVA/eHOMD databases, functional pathways were predicted using PICRUSt2, and hub taxa were identified through co-abundance network analysis. RESULTS: Microbial community structure differed significantly across lesion, non-lesion, and healthy sites (PERMANOVA, p = 0.001). Lesions were enriched with Selenomonas infelix and Treponema vincentii, while healthy controls harbored Streptococcus oralis and Gemella haemolysans. Co-abundance network analysis revealed lesion-specific hub species, notably T. vincentii, strongly correlated with predicted activation of pyrimidine biosynthesis pathways (r = 0.69, q < 1E-6), suggesting predicted metabolic alterations in the tumor microenvironment. Non-lesion sites were also characterized by two hub species, Prevotella melaninogenica and Segatella oulorum. CONCLUSION: Our findings define a lesion-specific microbial signature of OSCC characterized by the depletion of health-associated taxa, enrichment of pro-inflammatory pathobionts, and predicted associations with metabolic pathways implicated in carcinogenesis. These alterations reflect a predicted functionally altered tumor microenvironment.

16S rRNA gene↗

PubMed2003

The concept of multiple-nutrient-limited growth of microorganisms and its application in biotechnological processes.

The "law of the minimum" (Liebig's law) states that usually one nutrient restricts the maximum quantity of biomass that can be produced within a system, whereas all other nutrients are in excess. This general rule has been applied also to the growth of microorganisms, e.g., by adjusting the relative concentrations of the individual nutrients in growth media such that one of them, in the case of heterotrophic microbes, usually the carbon source, determines the maximum cell density that can be obtained in a culture. However, experimental data demonstrated that growth of microbial cultures can be limited simultaneously by two or more nutrients. These authors reported that during growth of bacteria and yeasts at a constant dilution rate in the chemostat, three distinct growth regimes were recognised as a function of the C:N ratio in the inflowing medium: (1) a clearly carbon-limited regime with the nitrogen source in excess, (2) a transition ("double-nutrient-limited") growth regime where both the carbon and the nitrogen source were below the detection limit, and (3) a clearly nitrogen-limited growth regime with the carbon source in excess. Subsequent calculations suggested that the extension and position of this double-nutrient-limited zone should be strongly dependent on the imposed growth rate: Whereas it is very narrow at high growth rates it should become very broad during slow growth. This pattern as a function of growth rate has now been confirmed for a number of different organisms. In industrial processes, microbial growth is always in some way controlled by the limited availability of nutrients, and limitation of specific nutrients is frequently used to force microbial cultures into a productive physiological state. This article will discuss what the consequences of multiple-nutrient-limited growth are for industrial processes and how the concept might be applied. Specific examples will be given that demonstrate the advantages and the potential of multiple nutrient-limited growth conditions for industrial production processes.

Bacteria↗

PubMed2006

Virus or TLR agonists induce TRAIL-mediated cytotoxic activity of plasmacytoid dendritic cells.

Among dendritic cells, plasmacytoid dendritic cells (PDC) represent a functionally distinct lineage. Regarding innate immunity, PDC secrete large amounts of type I IFN upon viral exposure or stimulation by microbial products such as unmethylated CpG-motif containing oligo-DNA due to their selective expression of TLR7 and TLR9. We asked whether they could acquire cytotoxic functions during the early phases of infection or after activation with TLR7 or TLR9 agonists. In the present study, we describe a human PDC cell line called GEN2.2, derived from leukemic PDC, that shares most of the phenotypic and functional features of normal PDC. We show that after contact with the influenza virus, GEN2.2, as well as normal PDC, acquires TRAIL and killer activity against TRAIL-sensitive target cells. Moreover, we show that activation of GEN2.2 cells by CpG-motif containing oligo-DNA or R848 also induces TRAIL and endows them with the ability to kill melanoma cells. Therefore, PDC may represent a major component of innate immunity that could participate to the clearance of infected cells and tumor cells. This phenomenon could be relevant for the efficacy of TLR7 or TLR9 agonists in the therapy of infectious disease and cancer.

Animals↗

PubMed1989

Biologic and clinical rationale for second-stage surgery and maintenance.

Increased understanding of the biologic and functional demands of osseointegration procedures have enhanced predictability. Basic science and clinical research have added to our knowledge of the microbiologic, histologic, and functional requirements of what constitutes successful cases. It is evident that control of the microbial flora around abutments is vital in maintaining peri-implant health. It has also been shown that a potential pathogenic flora is more likely to occur in the partially edentulous patient. More predictable indicators of peri-implant disease must be established, as classic periodontal measurements do not correspond to the active disease state around implants. Second-stage surgery must create a peri-implant environment in which functional and biologic needs are met. The patient's esthetic and phonetic requirements must be fulfilled. Using procedures described in this article these standards can be achieved.

Dental Implantation, Endosseous↗