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PubMed2005

Bioremediation of polynitrated aromatic compounds: plants and microbes put up a fight.

Industrialization and the quest for a more comfortable lifestyle have led to increasing amounts of pollution in the environment. To address this problem, several biotechnological applications aimed at removing this pollution have been investigated. Among these pollutants are xenobiotic compounds such as polynitroaromatic compounds--recalcitrant chemicals that are degraded slowly. Whereas 2,4,6-trinitrophenol (TNP) can be mineralized and converted into carbon dioxide, nitrite and water, 2,4,6-trinitrotoluene (TNT) is more recalcitrant--although several microbes can use it as a nitrogen source. The most effective in situ biotreatments for TNT are the use of bioslurry (which can be preceded by an abiotic step) and phytoremediation. Phytoremediation can be enhanced by using transgenic plants alone or together with microbes.

Bacteria↗

PubMed2005

Perisinusoidal B cells in the bone marrow participate in T-independent responses to blood-borne microbes.

Mature recirculating B cells are generally assumed to exist in follicular niches in secondary lymphoid organs, and these cells mediate T-dependent humoral immune responses. We show here that a large proportion of mature B lymphocytes occupy an anatomically and functionally distinct perisinusoidal niche in the bone marrow. Perisinusoidal B cells circulate freely, as revealed by parabiosis studies. However, unlike their counterparts in the follicular niche, these cells are capable of being activated in situ by blood-borne microbes in a T-independent manner to generate specific IgM antibodies. The bone marrow represents a unique type of secondary lymphoid organ in which mature B cells are strategically positioned in the path of circulating microbes.

Animals↗

PubMed2005

Change in IFN-gamma-producing capacity in early life and exposure to environmental microbes.

BACKGROUND: Exposure to environmental microbes in early life might lead to type 1-skewed T cell responses and therefore reduce the risk of allergic diseases. OBJECTIVE: To investigate whether the cytokine responses at birth and at age 3 months are associated with environmental factors, especially exposure to microbes. Living in a farm, level of house dust endotoxin, cleanliness of the home, and presence of cats and dogs in the household were studied as possible determinants of cytokine production. METHODS: Twelve farmers' and 17 nonfarmers' children were studied. Production of IL-4, IL-6, TNF-alpha, and IFN-gamma in cord blood and in peripheral blood at 3 months was measured after 8-hour and 24-hour stimulation with phorbol ester plus concanavalin A. RESULTS: IFN-gamma responses at age 3 months were associated with farming (median, 53 vs 17 pg/mL; P = .019) and cats and dogs (49 vs 14 pg/mL; P = .014) (8 hours). Change in IFN-gamma-producing capacity from birth to 3 months was larger in children with higher than median endotoxin concentration in bed dust (P = .038) and in children with a cat or dog (P = .005) (8 hours). Increased IL-6 responses at birth were associated with cat or dog exposure (P = .004; 8 hours) and endotoxin level in settled dust (P = .039; 24 hours). CONCLUSION: The development of IFN-gamma-producing capacity during the first 3 months of life is associated with farming, endotoxin in house dust, and cat and dog exposure. These environmental characteristics may indicate some microbial exposure capable of driving developing immune system toward T(H)1 responses.

Aging↗

PubMed2024

Dissecting host-microbe interactions with modern functional genomics.

Interrogation of host-microbe interactions has long been a source of both basic discoveries and benefits to human health. Here, we review the role that functional genomics approaches have played in such efforts, with an emphasis on recent examples that have harnessed technological advances to provide mechanistic insight at increased scale and resolution. Finally, we discuss how concurrent innovations in model systems and genetic tools have afforded opportunities to interrogate additional types of host-microbe relationships, such as those in the mammalian gut. Bringing these innovations together promises many exciting discoveries ahead.

Genomics↗

PubMed2005

Geomicrobiology in oceanography: microbe-mineral interactions at and below the seafloor.

Oceanography is inherently interdisciplinary and, since its inception, has included the study of microbe-mineral interactions. From early studies of manganese nodules, to the discovery of hydrothermal vents, it has been recognized that microorganisms are involved at various levels in the transformation of rocks and minerals at and below the seafloor. Recent studies include mineral weathering at low temperatures and microbe-mineral interactions in the subseafloor "deep biosphere". A common characteristic of seafloor and subseafloor geomicrobiological processes that distinguishes them from terrestrial or near-surface processes is that they occur in the dark, one or more steps removed from the sunlight that fuels the near-surface biosphere on Earth. This review focuses on geomicrobiological studies and energy flow in dark, deep-ocean and subseafloor rock habitats.

Bacteria↗

PubMed1986

Sperm washing and swim-up technique using antibiotics removes microbes from human semen.

Pelvic infections may follow intrauterine or intratubal insemination with washed semen. In this study, we determined whether sperm washing removes microorganisms from human semen. Before and after semen wash, we cultured 15 ejaculates for aerobic and anaerobic bacteria, genital mycoplasma, and chlamydia. All semen samples had from one to five organisms isolated (total, 40 isolates) before the semen wash preparation. The mean number (+/- standard deviation) of isolates per sample was 2.67 +/- 1.35. After the semen were prepared, none of the samples showed a positive culture. The decrease in the number of samples with positive cultures and the decrease in the number of isolates is significant (P less than 0.0001). After sperm washing, electronmicroscopic studies did not show any microbes attached to any portion of the spermatozoa. We conclude that the method of sperm wash preparation used is effective in removing microbes present in human semen.

Anti-Bacterial Agents↗

PubMed2002

Role of microbes in controlling the speciation of arsenic and production of arsines in contaminated soils.

The influence of microbes on the speciation of arsenic and production of arsines in contaminated soils was investigated under laboratory conditions. Microbes were able to carry out reactions that resulted in changes in the speciation of arsenic in soil. The transformation of soil dominating species, arsenate [As(V)], under both aerobic and anaerobic conditions to arsenite [As(III)], monomethylarsonic acid [MMAA], dimethylarsinic acid [DMAA] and to volatile trimethylarsine [TMA] was, however, less than 0.5%, of which the production of TMA represented 0.02-0.3%. The volatilization process was also verified in the field, in the soil of a dumping area. The 'life-time' of arsines in air was, however, short and they were rapidly converted back to water soluble species, As(V) and trimethyl arsine oxide (TMAO).

Arsenic↗

PubMed2003

Effects of different plant protection programs on soil microbes.

The aim of this study was to assess the effects of two pesticide regimens (conventional full insurance compared with supervised and reduced pesticide use) and two cultivation techniques (conventional tillage and fertilization compared with no tillage and lower fertilization) on soil microbes in a field study, and to evaluate the results with laboratory tests. The herbicides used were chlorsulfuron, MCPA, and bentazone; the fungicides carboxin-imazalin and propiconazole; and the insecticides dimethoate and pirimicarb. In the field studies, the effects on microbial biota were assessed by measuring biomass (ATP content) and microbial activities related to carbon and nitrogen metabolism (soil respiration, nitrification potential). Potential harmful effects of commercial formulations of the same pesticides on microbes were studied in the laboratory with two bacterial toxicity tests (Pseudomonas putida growth inhibition and Vibrio fischeri luminescence inhibition tests) and with a soil respiration inhibition test. Bioavailability of the pesticides in the soil was assessed by a solid-phase modification of the luminescent bacteria test. In the field studies the microbial activities and biomass followed the weather conditions during the growing season, and significant effects of pesticide treatments on microbial processes were not observed. In the laboratory studies the toxicity of certain pesticides was clearly detected by bacterial toxicity tests. However, in the soil respiration inhibition assessment with soil similar to that used in the field trial, inhibition was observed only at unrealistically high concentrations. This could be due to the limited bioavailability of the pesticides in soil of high clay and organic carbon content.

Adenosine Triphosphate↗

PubMed1998

Clinical significance of alimentary tract microbes in bone marrow transplant recipients.

A prospective study on the microbes isolated from the alimentary tract in 120 bone marrow transplant (BMT) recipients (1991-1993) was undertaken to define the spectrum of organisms isolated under antimicrobial prophylaxis, their temporal sequence of emergence, and the associated morbidity and mortality. Clostridium difficile (n = 20), isolated in the pre-engraftment and early post-engraftment periods (day 2-45 post-BMT), was the most common microbe recovered from stool of patients with diarrhea. In contrast to previous reports, no significant difference in mortality was observed between patients with and without C. difficile isolated in stool. Two patients had neutropenic ileocecitis with concomitant bacteremia due to Escherichia coli and Klebsiella pneumoniae. One patient was found to have astrovirus gastroenteritis (day 7), and Giardia lamblia was recovered from the stool of another (day -7). Heavy growth of Staphylococcus aureus from direct smear-positive specimens was found from the upper airway of two patients with severe mucositis and complete dysphagia (day 12 and 23). Salmonella spp. of groups B and E were found in the stool of five asymptomatic patients at the time of conditioning. No specific organisms was recovered from the endoscopic brushing of two patients with lower end esophagitis, three patients with upper gastrointestinal bleeding, and three patients with perirectal cellulitis. During the post-engraftment period, five patients had documented cytomegalovirus gastroenterocolitis (days 34-97), one had Mycobacterium chelonae colitis (day 70), and another had nodular gastritis due to Acremonium falciforme (day 270). Overall, only 28% of patients with alimentary tract symptoms/syndrome had specific pathogens isolated from clinical specimens. Differentiation of the causation of alimentary tract symptoms was often difficult because noninfectious complications such as conditioning toxicity, graft-versus-host disease, and its treatment often caused alimentary tract symptoms in addition to predisposed BMT patient to infection. The reluctance of obtaining tissue biopsy for ascertaining the importance of those potential alimentary tract pathogens often dictate the use of empirical treatment.

Adolescent↗

PubMed1999

Engineering of improved microbes and enzymes for bioremediation.

Bioremediation with microorganisms is an attractive alternative to conventional techniques, such as incineration and chemical treatment, for disposing of pollutants. Recent progress in molecular biology, microbiology, and genetics is providing the driving force towards engineering improved microbes and enzymes for bioremediation. A number of genetic engineering approaches have been developed in the past several years that have proven useful in introducing/evolving the desired properties for different biodegradative pathways or enzymes. The initial excitement generated in this area should continue to pave the way for rational or irrational design of microbes or enzymes with novel remedial properties.

Amino Acid Sequence↗

PubMed2002

Production of short-chain fatty acids and gas from various oligosaccharides by gut microbes of carp (Cyprinus carpio L.) in micro-scale batch culture.

We studied the metabolism of various oligosaccharides by carp (Cyprinus carpio) hindgut microbes by measuring gas productivity and organic acid production in gut contents using a 50-microl-scale batch culture system. Carp hindgut contents were incubated with 500 microg each of raffinose, lactosucrose, kestose, lactulose, gentiobiose, 4'-galactosyllactose and 6'-galactosyllactose and soybean-, xylo-, and isomalto-oligosaccharides or none (blank culture) at 25 degrees C for 6 h. The time-course of gas release from the culture (Y microl/culture) was expressed as an exponential function of incubation time (t) [Y=A+Bx(1-e(-kt))]; A, B and k are constants). Potential production of gas (A+B) from soybean-oligosaccharide and raffinose was larger than for the other saccharides except for kestose, and blank culture. The rate constant of gas (k) for lactosucrose was larger than that for isomalto- and xylo-oligosaccharide, lactulose, kestose or blank culture. Net production of total SCFA (sum of acetic, propionic and n-butyric acid weights) from cultures with soybean- and isomalto-oligosaccharides, raffinose, gentiobiose and lactosucrose was greater than that from blank culture. These results suggested that soybean-oligosaccharide and raffinose were potentially highly fermentable oligosaccharides for carp hindgut microbes. Chemical structures of oligosaccharides seem to play an important role in the fermentability. It is also likely that oligosaccharide utilization differs between mammals and teleosts.

Animals↗

PubMed2001

Caveolae as portals of entry for microbes.

Many pathogens, including many traditionally extracellular microbes, now appear capable of entry into host cells with limited loss of viability. A portal of entry shared by some bacteria, bacterial toxins, viruses and parasites are caveolae (or lipid rafts), which are involved in the import and intracellular translocation of macromolecules in host cells. A requirement for caveolae-mediated endocytosis of microbes appears to be that the respective receptor is a constituent of caveolae or must move to caveolae following ligation.

Animals↗

PubMed2003

Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory.

Any talk of the demise of in vitro cultivation as a useful mechanism for revealing many of nature's past and present secrets appears to be unfounded and premature. The first years of this century have been as productive in the cultivation of physiologically novel, environmentally abundant and phylogenetically distinct microbes as were the first years of the 20th century. The diversity of organic and inorganic electron donors and acceptors known to be used during microbial energy metabolisms continues to grow, expanding our appreciation for the niches that may be, or historically may have been, filled by microbes in the biosphere. Either guided and instigated by, or independent of, the results of gene inventories representing diverse environmental settings, significant advances are constantly being made in the isolation of bacteria and archaea, demonstrating either strikingly rich phylogenetic diversity or significant activity and abundance in their respective environments. The potential synergisms between molecular ecological analyses and innovative in vitro growth studies are real and should be embraced, rather than treated as dueling agents in some zero-sum game.

Bacteria↗

PubMed2006

Terrestrial biotic ligand model. 2. Application to Ni and Cu toxicities to plants, invertebrates, and microbes in soil.

The Terrestrial Biotic Ligand Model (TBLM) is applied to a number of noncalcareous soils of the European Union for Cu and Ni toxicities using organisms and endpoints representing three levels of terrestrial organisms: higher plants, invertebrates, and microbes. A comparison of the TBLM predictions to soil metal concentration or free metal ion activity in the soil solution shows that the TBLM is able to achieve a better normalization of the wide variation in toxicological endpoints among soils of disparate properties considered in this study. The TBLM predictions of the EC50s were generally within a factor of 2 of the observed values. To our knowledge, this is the first study that incorporates Cu and Ni toxicities to multiple endpoints associated with higher plants, invertebrates, and microbes for up to eleven noncalcareous soils of disparate properties, into a single theoretical framework. The results of this study clearly demonstrate that the TBLM can provide a general framework for modeling metals ecotoxicity in soils.

Animals↗

PubMed2003

In vitro kinetics of allergen- and microbe-induced IL-4 and IFN-gamma mRNA expression in PBMC of pollen-allergic patients.

BACKGROUND: According to a hypothesis allergens induce Th2 responses in allergic patients, and microbes induce Th1 responses. We studied the kinetics of in vitro allergen-, tuberculin (PPD)- and tetanus toxin (TT)-induced IFN-gamma and IL-4 mRNA expression in peripheral blood mononuclear cell (PBMC) cultures of pollen-allergic patients and healthy controls. METHODS: PBMC of 10 birch or timothy pollen-allergic patients and of 13 healthy controls were stimulated in vitro with allergen (birch or timothy), PPD or TT. Pellets and supernatants were collected at 24, 48, 72 and 96 h after stimulation. IFN-gamma and IL-4 production was measured by enzyme linked immunosorbent assay and mRNA expression using RT-PCR and time-resolved fluorometry. RESULTS: Allergen induced IFN-gamma production and mRNA expression in PBMC more in allergic patients than in healthy controls. Also allergen induced IL-4 mRNA expression more in allergic patients than in healthy controls. PPD induced IFN-gamma mRNA expression both in allergic patients and healthy controls, whereas IFN-gamma production was induced only in healthy controls and IL-4 was not induced at all. TT induced IFN-gamma mRNA expression in both groups, IFN-gamma production in allergic patients, and IL-4 mRNA expression in both allergic patients and healthy controls. CONCLUSIONS: In vitro stimulation with allergen induced both IFN-gamma and IL-4 mRNA expression of PBMC in allergic patients. These observations challenge the clearcut division of microbe-specific Th1 and allergen-specific Th2 responses in peripheral blood.

Adult↗

PubMed2002

Immunoglobulin G antibodies against indoor dampness-related microbes and adult-onset asthma: a population-based incident case-control study.

Immunoglobulin G (IgG) antibodies against microbes related to indoor dampness problems have been used as potential biomarkers of fungal exposure in clinical investigations. There is limited information on their relation to asthma. We conducted a population-based incident case-control study to assess the risk of asthma in relation to specific IgG antibodies to eight dampness-related microbes: Aspergillus fumigatus, A. versicolor, Cladosporium cladosporioides, Fusarium oxysporum, Sporobolomyces salmonicolor, Stachybotrys chartarum, Streptomyces albus and Trichoderma citrinoviride. We recruited systematically all new cases of asthma during a 2.5-year study period and randomly selected controls from a source population of adults 21-63 years of age living in the Pirkanmaa Hospital District, South Finland. The clinically diagnosed case series consisted of 521 adults with newly diagnosed asthma and the control series of 932 controls selected randomly from the source population. IgG antibodies were analysed with ELISA. An increased risk of developing asthma in adulthood was significantly related to IgG antibodies to T. citrinoviride, but not to the other moulds. There was no evidence of a dose-response relation between the IgG antibody level and the risk of asthma. T. citrinoviride may play a role in the aetiology of adult-onset asthma or serve as an indicator of other causal factors.

Adult↗

PubMed1995

Reassessing the manipulation of protein synthesis by rumen microbes.

Protein synthesis by rumen microbes plays an important role in ruminant nutrition. Microbial proteins that are not recycled flow out of the rumen and account for more than 50% of the total proteins entering the intestines. Determination of microbial nitrogen in digesta is based on the isolation of a representative sample of rumen microbes and on the use of specific markers (purine bases, RNA, 15N incorporation). This review discusses the reliability of microbial markers and examines current methods for assessing differences in turnover rate and microbial composition among liquid and particulate compartments. Four groups of factors acting on microbial synthesis, which are also adaptable to farm conditions, are considered: I) modification of protozoal population; II) modification of liquid and solid phase kinetics in the rumen; III) balance in the components of the diet; and IV) probiotics. The effects of these factors are discussed, considering their feasibility and their usefulness for the host.

Animal Nutritional Physiological Phenomena↗

PubMed2005

Microbes on the human vaginal epithelium.

Using solely a gene-based procedure, PCR amplification of the 16S ribosomal RNA gene coupled with very deep sequencing of the amplified products, the microbes on 20 human vaginal epithelia of healthy women have been identified and quantitated. The Lactobacillus content on these 20 healthy vaginal epithelia was highly variable, ranging from 0% to 100%. For four subjects, Lactobacillus was (virtually) the only bacterium detected. However, that Lactobacillus was far from clonal and was a mixture of species and strains. Eight subjects presented complex mixtures of Lactobacillus and other microbes. The remaining eight subjects had no Lactobacillus. Instead, Bifidobacterium, Gardnerella, Prevotella, Pseudomonas, or Streptococcus predominated.

Adult↗