Oxygen exposure decreases the yield of high-molecular-weight DNA from some anaerobic bacteria and bacterial communities during DNA extraction.

OBJECTIVES: The central challenge in third-generation sequencing lies in meeting the requirements for DNA quality (integrity and purity) and quantity. Therefore, novel improvements in DNA extraction methods are needed to satisfy these requirements. We reasoned that in anaerobic microbial communities, the presence of certain strict anaerobes containing oxygen-activated DNase activity might contribute substantially to the poor integrity of extracted metagenomic DNA (or genomic DNA from some pure cultures) if exposed to air. METHODS: To test this hypothesis, we developed an enhanced genomic and metagenomic DNA isolation technique that we applied to a specifically chosen set of both strict and aerotolerant anaerobes, as well as to the hindgut microbiota of a herbivorous marine fish. RESULTS: Considering the quality (or degradation) of extracted DNA obtained under anaerobic versus aerobic conditions, we found that DNA extracted aerobically from cells of some strict anaerobes showed more degradation of high molecular weight DNA than analogous preparations under anaerobic conditions. In contrast, with the selected aerotolerant anaerobes, no discernible difference was found between the molecular sizes of DNA extracted aerobically and anaerobically. Metagenomic DNA extracted from the fish hindgut microbiota showed higher yields and better quality under anaerobic conditions compared to aerobic conditions. CONCLUSION: Our study effectively demonstrates the advantages of our improved extraction protocol in anaerobic conditions. This is evident through the improved quality of extracted DNA. Such findings may be valuable for studies, especially metagenomic studies, where the quality and quantity of DNA are crucial for downstream analysis.

Chakrabartyella piscis gen. nov., sp. nov., a member of the family Lachnospiraceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus.

A Gram-stain-negative, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP5GT, was isolated from the hindgut of a silver drummer (Kyphosus sydneyanus) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the family Lachnospiraceae in the phylum Bacillota and was most closely related to Anaerotignum propionicum with 94.06 % sequence identity. Isolate BP5GT grew on agar medium containing mannitol and fish gut fluid as carbon sources. Clear colonies of approximately 1 mm diameter of the isolate grew within a week at 20-28 °C (optimum, 28 °C) and pH 7.6-8.5 (optimum, pH 8.5). Strain BP5GT was very sensitive to NaCl and the optimal concentration for growth was 0.045 % (w/v). Acetate and propionate were the major fermentation products. The major cellular fatty acids were C12 : 0, C14 : 0, C15 : 0 and C16 : 0. The genome sequence of the isolate was determined. Its G+C content was 38.41 mol% and the 71.41 % average nucleotide identity of the BP5GT genome to its closest neighbour with a sequenced genome (A. propionicum DSM 1682T) indicated low genomic relatedness. Based on the phenotypic and taxonomic characteristics observed in this study, a novel genus and species named Chakrabartyella piscis gen. nov., sp. nov. is proposed for isolate BP5GT (=ICMP 24687T=JCM 35769T).

Tannockella kyphosi gen. nov., sp. nov., a member of the family Erysipelotrichaceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus.

A Gram-stain-positive, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP52GT, was isolated from the hindgut of a Silver Drummer (Kyphosus sydneyanus) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belonged to the family Erysipelotrichaceae in the phylum Firmicutes and was most closely related to Clostridium saccharogumia with 93.3 % sequence identity. Isolate BP52GT grew on agar medium containing mannitol as the sole carbon source. White, opaque and shiny colonies of the isolate measuring approximately 1 mm diameter grew within a week at 20-28 °C (optimum, 24 °C) and pH 6.9-8.5 (optimum, pH 7.8). BP52GT tolerated the addition of up to 1 % NaCl to the medium. Formate and acetate were the major fermentation products. The major cellular fatty acids were C16 : 0, C16:1n-7t and C18:1n-7t. The genome sequence of the isolate was determined. Its G+C content was 30.7 mol%, and the 72.65 % average nucleotide identity of the BP52GT genome to its closest neighbour with a completely sequenced genome (Erysipelatoclostridium ramosum JCM 1298T) indicated low genomic relatedness. Based on the phenotypic and taxonomic characteristics observed in this study, a novel genus and species Tannockella kyphosi gen. nov., sp. nov. is proposed for isolate BP52GT (=NZRM 4757T=JCM 34692T).

Fucoidan Extracted From Sporophyll of Undaria pinnatifida Grown in Weihai, China - Chemical Composition and Comparison of Antioxidant Activity of Different Molecular Weight Fractions.

Fucoidan is a multifunctional marine carbohydrate polymer that differs in its chemical composition and bioactivity both between seaweed species and within species from different locations across the globe. In this study, fucoidan was extracted from the sporophyll of Undaria pinnatifida grown in Weihai, Shandong Province, China. Fucoidan fractions with molecular weight cutoffs (MWCO) of >300 kDa and <10 kDa were obtained via dialysis. The fucoidan standard from Sigma (Fstd, ≥95, CAS: 9072-19-9), fucoidan crude extract (WH), >300 kDa fraction (300k) and <10 kDa fraction (10k) were compared in terms of chemical composition and antioxidant capacity. Based on Fourier transform infrared spectroscopy (FT-IR) analysis, Fstd, WH, and 300k all showed strong bands around 830 cm-1, corresponding to the sulfate substituent in the molecule. The results showed that compared with WH and 300 k, the degree of sulfation at 10k was the lowest. From Nuclear magnetic resonance spectroscopy (NMR) result, the four fucoidan samples all contain α-L-fucose. The primary antioxidant ability of the 10k is significantly higher than that of the 300k, WH, and Fstd, but the secondary antioxidant capabilities of the 10k and 300k were similar, and both were higher than that of the butylated hydroxyanisole (BHA). The ferric reducing antioxidant ability was higher in the 300k and WH fractions. This demonstrates that fucoidan extracted from U. pinnatifida grown in Weihai, China should be a useful nutraceutical resource.

Effects of Different Doses of Eucalyptus Oil From Eucalyptus globulus Labill on Respiratory Tract Immunity and Immune Function in Healthy Rats.

Eucalyptol (1,8-cineole), the major constituent of eucalyptus oil (EO), was used in traditional medicine as a remedy for colds and bronchitis. This study aimed at clarifying the effect of eucalyptol on respiratory immune function of CD8 and CD4 cells, and alveolar macrophages (AM). Thirty male Sprague-Dawley rats were divided into experimental and control groups. The drug was given once a day for 3 weeks and the experimental group was divided according to the eucalyptol dose into: 30, 100, and 300 mg·kg-1 groups. Flow cytometry was used to detect the phagocytic function of CD4, CD8 cells, and AM in the bronchopulmonary lavage fluid. The 30 and 100 mg·kg-1 groups had an up-regulation effect on CD8 (p < 0.05), with no significant effect on macrophage phagocytosis. The 300 mg·kg-1 group had an inhibitory effect on CD8 and macrophage phagocytosis (p < 0.05), with no significant difference in CD4 between groups. Further investigation was conducted to evaluate the effect of EO on immune function in rats by detecting blood T, B, and NK cells using flow cytometry, and blood IgA, IgG, IgM, and IFN-γ levels by ELISA. High dosage of eucalyptol significantly reduced the proportion of blood B and NK cells (p < 0.05). IgA was decreased in the 100 and 300 mg·kg-1 groups (p < 0.05). There are no significant differences between the number of T cells and the IgG, IgM, and IFN-γ levels between experimental and control groups. Rational use of EO containing eucalyptol can improve the immune function of the respiratory tract and the body immunity, while high dose could have damaging effects, through modifying the phagocytic function of CD8 cells and reducing the proportion of blood B cells, NK cells, and IgA.

Effects of preparation method on the biochemical characterization and cytotoxic activity of New Zealand surf clam extracts.

Molluscan extracts confer a wide range of health promoting properties, one of them is cytotoxicity. Extraction and processing can affect the efficacy and properties of bioactive molecules. New Zealand (NZ) surf clams have never been thoroughly studied for bioactives until recently. However, the effect of cold and heat extraction procedure on biochemical composition and cytotoxic activities of NZ surf clam remains unanswered. The objective is to compare the effects on cytotoxicity of three NZ surf clams (Diamond shell, Crassula aequilatera; Storm shell, Mactra murchisoni; and Deepwater Tua tua, Paphies donacina) extracts via cold or heat process across cancer cell lines to find out which process can preserve bioactivity better. Fractions of extracts prepared via cold or heat procedures were tested for cell growth inhibition, apoptosis induction and cell cycle arrest in seven cancer cell lines. Apoptosis was induced through all cell lines, as further evidenced in Caspase-3/7 activities. Cell cycle arrest was focused on G2/M- and S- phases. Petroleum ether and ethyl acetate fractions, with the greatest bioactivity in this study, are rich in lipids and proteins, indicating likely bioactive sources. Cold preparation was responsible for the lowest cancer cell viability and induced greater apoptosis. Cold process retained better bioactivity/cytotoxicity than that of heat-processed extracts. This information may guide future health/nutraceutical clam product development.

Cytotoxicity of Extracts from New Zealand Surf Clams Against Organ Cancer Cell Lines.

In this study, we examined the cytotoxic effects of four fractions from three species of New Zealand (NZ) surf clam on four common organ cancer cells. In most cases, a dose- and time-dependent inhibition on the proliferation of the cancer cells was observed. This was most significant in WiDr (colon) cells, where the percentages of viability reduced to as low as 6%, 5%, and 17% (at 1000 µg 72 h) by extracts from Diamond shell, Storm shell, and Tua tua species, respectively. A549 (lung) cells were the least susceptible to the treatment, with viability percentages at 82%, 15%, and 45%, under the same conditions. Induction of caspase-dependent apoptosis and alterations to the cell cycle further supported the observed morphological analysis. The ethanol, petroleum ether, and ethyl acetate fractions of NZ surf clam, rich in lipids and proteins, were more potent than their water-based counterpart. This is the first demonstration where extracts from NZ surf clams show the ability to inhibit the growth and proliferation of cancer cell lines. We suggest that NZ surf clam extracts have the potential to be further studied and developed as candidates for cancer supplementary management/treatment.

Extraction techniques and potential health benefits of bioactive compounds from marine molluscs: a review.

Marine molluscs and their bioactive compounds are of particular relevance to the growing pool of nutraceutical resources under global investigation. A number of extraction techniques have been developed to isolate bioactive compounds according to their chemical characterization, such as proteins, carbohydrates and lipids. We briefly reviewed those methods in general. Bioactive molecules are 'concealed' in the primary structures of tissue samples of molluscs as amino acids, lipids or carbohydrates which are released by mechanical and chemical processes. The major health benefits of extracts of molluscs include antioxidant, anticancer, and anti-infectious disease activities and cardiovascular protection, which have been reviewed in detail. This review provides a novel view into the efficacy of isolation techniques and subsequent bioactivity analysis of compounds under investigation. Future development in extraction-bioactivity has also been discussed.

Fucoidan Extracted from the New Zealand Undaria pinnatifida-Physicochemical Comparison against Five Other Fucoidans: Unique Low Molecular Weight Fraction Bioactivity in Breast Cancer Cell Lines.

Fucoidan, the complex fucose-containing sulphated polysaccharide varies considerably in structure, composition, and bioactivity, depending on the source, species, seasonality, and extraction method. In this study, we examined five fucoidans extracted from the same seaweed species Undaria pinnatifida but from different geological locations, and compared them to the laboratory-grade fucoidan from Sigma (S). The five products differed in molecular composition. The amount of over 2 kDa low molecular weight fraction (LMWF) of the New Zealand crude fucoidan (S1) was larger than that of S, and this fraction was unique, compared to the other four fucoidans. The difference of molecular compositions between S and S1 explained our previous observation that S1 exhibited different anticancer profile in some cancer cell lines, compared with S. Since we observed this unique LMWF, we compared the cytotoxic effects of a LMWF and a high molecular weight fucoidan (HMWF) in two breast cancer cell lines-MCF-7 and MDA-MB-231. Results indicated that the molecular weight is a critical factor in determining the anti-cancer potential of fucoidan, from the New Zealand U. pinnatifida, as the LMWF exhibited a dose-dependent inhibition on the proliferation of breast cancer cells, significantly better than the HMWF, in both cell lines. A time-dependent inhibition was only observed in the MCF-7. Induction of caspase-dependent apoptosis was observed in the MDA-MB-231 cells, through the intrinsic apoptosis pathway alone, or with the extrinsic pathway. LMWF stimulated a dose-dependent NOS activation in the MDA-MB-231 cells. In conclusion, the fucoidan extracted from the New Zealand U. pinnatifida contains a unique LMWF, which could effectively inhibit the growth of breast cancer cell lines. Therefore, the LMWF from New Zealand U. pinnatifida could be used as a supplement cancer treatment.

Investigation of Different Molecular Weight Fucoidan Fractions Derived from New Zealand Undaria pinnatifida in Combination with GroA Therapy in Prostate Cancer Cell Lines.

Fucoidan, a sulfated polysaccharide extracted from brown seaweeds, has been shown to possess various antioxidant, anticoagulant, antiviral, and anticancer functions. In this study, we focused on low molecular weight fucoidan (LMWF) which was extracted from New Zealand Undaria pinnatifida, and investigated its anti-proliferative effects, combined with a quadruplex-forming oligonucleotide aptamer (GroA, AS1411), a powerful cell surface Nucleolin inhibitor, in prostate cancer cells. We examined LMWF (<10 kDa) and compared it with laboratory grade Fucoidan purchased from Sigma (FS), all extracted from the same seaweed species U. pinnatifida. We found that LMWF significantly improved the anti-proliferative effect of GroA, as it decreased cancer cell growth and viability and increased cell death. This research may provide the foundation for LMWF to be used against prostate cancers as a supplement therapy in combination with other therapeutic agents.

Fucoidan Extracted from Undaria pinnatifida: Source for Nutraceuticals/Functional Foods.

The importance of fucoidan as a functional ingredient in food, health products, and pharmaceutics is well-recognized due to its beneficial biological effects. Fucoidan is usually extracted from brown seaweeds, including Undaria pinnatifida. Fucoidan exhibits beneficial bio-activity and has antioxidant, anticancer, and anticoagulant properties. This review focuses on the biological activity of U. pinnatifida-derived fucoidan and investigates its structure⁻activity or fraction⁻activity relationship. It also describes several fucoidan extracts, along with their claimed anticancer effects. It aims to provide information and thoughts for future research such as the development of fucoidan into functional foods or nutraceuticals.

Immune Activation of RAW264.7 Macrophages by Low Molecular Weight Fucoidan Extracted from New Zealand Undaria pinnatifida.

Fucoidan, a sulfated polysaccharide extracted from brown seaweeds, has been shown to possess various bioactivities. In particular, low molecular weight fucoidan (LMWF) has been shown to have better bioactivities. In this study, a LMWF (<10 kDa) was extracted from New Zealand Undaria pinnatifida and investigated for its immune modulation effects. LMWF at a concentration range from 1 to 50 µg/mL exerted an effective immune activation in RAW264.7 macrophages. LMWF treatment promoted significant NO release, iNOS expression, and TNF-α and IL-6 secretion in a concentration-dependent manner. It also significantly stimulated the activation of NF-κB and MAPK signaling pathways, and specific inhibitors of NF-κB and MAPK pathways diminished the stimulation, confirming the activation pathways. These results indicate that LMWF possesses potential health benefits through immune-stimulation, which may lead to future pharmaceutical development.

The natural compound fucoidan from New Zealand Undaria pinnatifida synergizes with the ERBB inhibitor lapatinib enhancing melanoma growth inhibition.

Melanoma remains one of the most aggressive and therapy-resistant cancers. Finding new treatments to improve patient outcomes is an ongoing effort. We previously demonstrated that melanoma relies on the activation of ERBB signaling, specifically of the ERBB3/ERBB2 cascade. Here we show that melanoma tumor growth is inhibited by 60% over controls when treated with lapatinib, a clinically approved inhibitor of ERBB2/EGFR. Importantly, tumor growth is further inhibited to 85% when the natural compound fucoidan from New Zealand U. pinnatifida is integrated into the treatment regimen. Fucoidan not only enhances tumor growth inhibition, it counteracts the morbidity associated with prolonged lapatinib treatment. Fucoidan doubles the cell killing capacity of lapatinib. These effects are associated with a further decrease in AKT and NFκB signaling, two key pathways involved in melanoma cell survival. Importantly, the enhancing cell killing effects of fucoidan can be recapitulated by inhibiting ERBB3 by either a specific shRNA or a novel, selective ERBB3 neutralizing antibody, reiterating the key roles played by this receptor in melanoma. We therefore propose the use of lapatinib or specific ERBB inhibitors, in combination with fucoidan as a new treatment of melanoma that potentiates the effects of the inhibitors while protecting from their potential side effects.

The antioxidant potential of the New Zealand surf clams.

The antioxidant action of three New Zealand surf clams was evaluated for the first time. Aqueous (cd) and ethanolic extracts from Diamond shell - Crassula aequilatera, Storm shell - Mactra murchisoni, and Tua tua - Paphies donacina were studied for their antioxidant potentials using two in vitro assays. The ethanolic extracts were further fractioned into four parts; petroleum ether (pe), ethyl acetate (ea), n-butanol (nb), and the final aqueous fraction (w). Comparing among all fractions tested, the ea fraction of P. donacina showed the strongest free radical scavenging power, with a radical scavenging activity of 76.14% at 20µg/mL. The ea fraction of C. aequilatera had the highest copper reducing activity with an absorbance of 1.596 at 20µg/mL. Results from this study suggest that some bioactive compounds with significant antioxidant effects may exist in the New Zealand surf clams, and could potentially reduce oxidative stress to deliver health benefits or to produce functional foods.

Comparison of physicochemical characteristics, sensory properties and volatile composition between commercial and New Zealand made wakame from Undaria pinnatifida.

This study aims to obtain chemical and sensory profiles of the New Zealand wakame from Undaria pinnatifida for the first time since the lift of its commercial harvest in May 2010. We compared mannitol content, sensory quality and volatile profiles of wakame produced from New Zealand U. pinnatifida with Japanese and Korean commercial samples. Sensory analysis showed that New Zealand wakame processed in August was different from commercially available wakame in texture only. A total of 10 alkanes, 5 ester, 3 alcohol, 13 aldehyde, 8 ketone and 2 alkyne were detected in the two New Zealand processed wakame samples. Mannitol content in freeze-dried U. pinnatifida was also measured and result showed that mannitol was the only free carbohydrate in U. pinnatifida.

Extracts from New Zealand Undaria pinnatifida Containing Fucoxanthin as Potential Functional Biomaterials against Cancer in Vitro.

This study tested extracts from New Zealand seaweed Undaria pinnatifida containing fucoxanthin, in parallel with pure fucoxanthin, in nine human cancer cell lines, for anticancer activity. Growth inhibition effects of extracts from Undaria pinnatifida were found in all types of cancer cell lines in dose- and time- dependent manners. Cytotoxicity of fucoxanthin in three human non-cancer cell lines was also tested. Compared with pure fucoxanthin, our extracts containing low level of fucoxanthin were found to be more effective in inhibiting the growth of lung carcinoma, colon adenocarcinoma and neuroblastoma. Our results suggest that fucoxanthin is a functional biomaterial that may be used as a chemopreventive phytochemical or in combination chemotherapy. Furthermore, we show for the first time that some unknown compounds with potential selective anti-cancer effects may exist in extracts of New Zealand Undaria pinnatifida, and New Zealand Undaria pinnatifida could be used as a source for either functional biomaterial extraction or production of functional food.

Anti-Proliferation Potential and Content of Fucoidan Extracted from Sporophyll of New Zealand Undaria pinnatifida.

Undaria pinnatifida is a species of brown seaweed known to contain rich amounts of fucoidan, a sulfated polysaccharide known to possess various biological activities. We isolated crude fucoidan (F0) from the sporophylls of U. pinnatifida grown in the Marlborough Sounds, New Zealand. Sulfate content, uronic acid content, and molecular weight of F0 were 15.02, 1.24, and >150 kDa, respectively. F0 was fractionated to yield three further fractions: F1, F2, and F3. Cytotoxicity of two major fractions was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The algal fucoidans specifically suppressed the proliferation of three cancer cell lines with less cytotoxicity against the normal cells. Selective cytotoxicity could relate to the distinctive structures of each fucoidan fraction. Results from this study provide evidence that fucoidan, especially from U. pinnatifida grown in New Zealand, possesses great potential to be used as a functional food to reduce cancer risk or supplement cancer treatment.