16S RNA Research Articles

Archaeal SRP RNA and SRP19 facilitate the assembly of SRP54-FtsY targeting complex

The signal recognition particle (SRP) plays an essential role in protein translocation across biological membranes. Stable complexation of two GTPases in the signal recognition particle (SRP) and its receptor (SR) control the delivery of nascent polypeptide to the membrane translocon. In archaea, protein targeting is mediated by the SRP54/SRP19/7S RNA ribonucleoprotein complex (SRP) and the FtsY protein (SR). In the present study, using fluorescence resonance energy transfer (FRET), we demonstrate that archaeal 7S RNA stabilizes the SRP54·FtsY targeting complex (TC). Moreover, we show that archaeal SRP19 further assists 7S RNA in stabilizing the targeting complex (TC). These results suggest that archaeal 7S RNA and SRP19 modulate the conformation of the targeting complex and thereby reinforce TC to execute protein translocation via concomitant GTP hydrolysis.

Identification of a predictive metabolic signature of response to immune checkpoint inhibitors in non-small cell lung cancer: METABO-ICI clinical study protocol

BackgroundImmune checkpoints inhibitors (ICI) are becoming new standards of care for the treatment of non-small cell lung cancer (NSCLC), both as first (alone or in association with chemotherapy) and second line. However, no powerful predictive biomarker of therapeutic response to ICI has been found to date. It has been recently shown that microbiota composition could influence the ability of patients to respond to ICI. Indeed, the microbiota produces circulating metabolites that will subsequently act on immune system, the investigators hypothesized that plasma metabolic signature, reflecting a global microbiota function, could represent a predictive biomarker of response to ICI. MethodsMonocentric prospective study. Primary objective is to identify baseline metabolic signature (metabolomics analysis by mass spectrometry) associated to ICI response. Secondary objectives are to link metabolic signature with microbiota composition (metagenomics analysis RNA 16S) and immune profile, and altogether with clinic response to ICI. The study will include 60 NSCLC patients treated by ICI in 1st, 2nd or 3rd line of treatment at the Grenoble Alpes University hospital (CHUGA) in 18 months. Patients that have received antibiotic or steroid treatment, 2 or 4 weeks before ICI initiation, respectively, will be excluded. Blood and feces will be collected prior to, at 2 months after ICI treatment initiation, and at 6 months or at progression. Expected resultsWe expect to highlight a metabolic profile predictive of response to ICI. By identifying factors associated with early progression, we could avoid to treat potential non-responding patients. Moreover, by restoring a favorable microbiota, patients’ ability to respond to these treatments might be restored.

Nutrient pollution alters the gut microbiome of a territorial reef fish

Human-induced nutrient pollution threatens coral reefs worldwide. Although eutrophication disrupts coral microbiomes, often leading to coral mortality, it is unknown whether eutrophication impacts the microbiomes of other coral reef organisms. Of particular interest are herbivorous fishes, whose algae consumption is critical in maintaining healthy corals. To examine the effects of eutrophication on fish gut microbiomes, we experimentally enriched territories of Stegastes nigricans, a predominantly herbivorous damselfish that farms turf algae. Using 16S RNA sequencing, we demonstrate that hindgut and foregut microbiomes have significantly higher alpha diversity in nutrient-enriched territories as compared to unenriched controls. S. nigricans gut microbiomes also exhibited significantly different compositions across treatments. In contrast, these changes were not observed in the microbiomes of the turf algae consumed by S. nigricans, indicating that the gut microbiome changes were autochthonous. Combined, our results provide a novel example of endogenous microbial shifts in wild vertebrates caused by simulated anthropogenic stress.

Metformin Reverses Hashimoto's Thyroiditis by Regulating Key Immune Events.

BackgroundHashimoto’s thyroiditis (HT) is a common autoimmune disease characterized by high levels of thyroid peroxidase antibody (TPOAb) and thyroid globulin antibody (TgAb) as well as infiltration of lymphocytes in thyroid. In recent years, metformin has been proven to be effective in a variety of autoimmune diseases, such as systemic lupus erythematosus, rheumatoid arthritis and multiple sclerosis.MethodsThis study systematically explored the therapeutic effect of metformin on HT and its underlying mechanism by comprehensively utilizing methods including animal model, in vitro cell culture and differentiation, mRNA sequencing and 16S rRNA sequencing.FindingsWe found that metformin indeed had a therapeutic effect on mice with HT mainly by reducing TgAb and lymphocyte infiltration in thyroid tissue. In addition, metformin also significantly suppressed the number and function of Th17 cells and M1 macrophages polarization in HT mice. Furthermore, metformin can inhibit the differentiation and function of Th17 in vitro. The results of mRNA sequencing of thyroid tissue illustrated that the therapeutic effect of metformin on HT was mainly achieved by regulating immune pathways. 16S RNA sequencing of the intestinal flora found that the intestinal flora of HT mice differs significantly from that of the normal mice and also were altered by metformin treatment.InterpretationThese experiments provided a preliminary theoretical basis for the clinical application of metformin in the treatment of HT.

Macroalgae degradation promotes microbial iron reduction via electron shuttling in coastal Antarctic sediments.

Colonization of newly ice-free areas by marine benthic organisms intensifies burial of macroalgae detritus in Potter Cove coastal surface sediments (Western Antarctic Peninsula). Thus, fresh and labile macroalgal detritus serves as primary organic matter (OM) source for microbial degradation. Here, we investigated the effects on post-depositional microbial iron reduction in Potter Cove using sediment incubations amended with pulverized macroalgal detritus as OM source, acetate as primary product of OM degradation and lepidocrocite as reactive iron oxide to mimic in situ conditions. Humic substances analogue anthraquinone-2,6-disulfonic acid (AQDS) was also added to some treatments to simulate potential for electron shuttling. Microbial iron reduction was promoted by macroalgae and further enhanced by up to 30-folds with AQDS. Notably, while acetate amendment alone did not stimulate iron reduction, adding macroalgae alone did. Acetate, formate, lactate, butyrate and propionate were detected as fermentation products from macroalgae degradation. By combining 16S rRNA gene sequencing and RNA stable isotope probing, we reconstructed the potential microbial food chain from macroalgae degraders to iron reducers. Psychromonas, Marinifilum, Moritella, and Colwellia were detected as potential fermenters of macroalgae and fermentation products such as lactate. Members of class deltaproteobacteria including Sva1033, Desulfuromonas, and Desulfuromusa together with Arcobacter (former phylum Epsilonbacteraeota, now Campylobacterota) acted as dissimilatory iron reducers. Our findings demonstrate that increasing burial of macroalgal detritus in an Antarctic fjord affected by glacier retreat intensifies early diagenetic processes such as iron reduction. Under scenarios of global warming, the active microbial populations identified above will expand their environmental function, facilitate OM remineralisation, and contribute to an increased release of iron and CO2 from sediments. Such indirect consequences of glacial retreat are often overlooked but might, on a regional scale, be relevant for the assessment of future nutrient and carbon fluxes.

BIO-FLOCCULATION AND ANTIMICROBIAL ACTIVITIES OF POWDERED MORINGA OLEIFERA (LAM) SEEDS AND ALUM ON DOMESTIC WASTEWATER MICROBIAL CONSORTIA

Introduction: Moringa oleifera seed is a bio-flocculant liable to purify water and verified to be one of the generally efficient prime coagulants for water treatment. M. oleifera seeds also have the potentials to eliminate a broad variety of bacteria, including Escherichia coli, Bacillus subtilis, B. cereus, Pseudomonas aeruginosa and Enterobacter ludwigii, from domestic wastewater. Objective: The comparative bio-flocculating ability and antimicrobial activities of powdered Moringa oleifera seeds and alum for the treatment of domestic wastewater from a university student’ hostels were explored. Methods: Collection of wastewater samples, physicochemical analysis of wastewater samples and treatment of the wastewater samples with powdered M. oleifera seeds and alum were conducted using standard techniques. Enumeration and identification of bacteria using biochemical depiction and (16S RNA) with fungi after treatment were employed via standard protocols. Results: The optimum pH obtained using powdered M. oleifera seeds was 6.00 – 7.38 and in line with the recommended WHO standard. This study revealed that the bacterial count in wastewater samples of Jibowu and Abiola hostels after treatment with 2g of powdered M. oleifera seeds and 6g of alum was high (199.67±0.89 CFU/ml); low (26.00±0.57 CFU/ml) for powdered M. oleifera seeds and high (87.00±0.57 CFU/ml); low (6.33±0.57 CFU/ml) for alum respectively. The fungal count of the wastewater samples for Akindeko and Jibowu hostels after treatment with 2g of powdered M. oleifera seeds and 6g of alum was high (26.00±0.57 Sfu/ml); low (5.00±0.57 Sfu/ml) for powdered M. oleifera seeds and high (19.00±0.58 Sfu/ml); low (2.00±0.57 Sfu/ml) for alum respectively. Escherichia coli, Bacillus subtilis with NCBI-certified B. cereus mkbk1, Pseudomonas aeruginosa mkbk 2 and Enterobacter ludwigii mkbk 3 were isolated from the wastewater samples. Conclusion: The findings of this study suggest that the bio-flocculating ability of powdered M. oleifera seeds accentuated better antimicrobial efficacy of M. oleifera over alum as a proviso to the blend of powdered M. oleifera seeds and alum for the treatment of domestic wastewaters.

The complete mitochondrial genome of the Thick-billed Flowerpecker (Dicaeum agile)

The Thick-billed Flowerpecker (Dicaeum agile), a small member of the flowerpecker family, inhabits tropical Southern Asia, and is widely distributed from India east to Indonesia and Timor. In this study, next generation sequencing (NGS) was used to obtain a mitochondrial genome sequence for D. agile. The complete mitogenome was 16,809bp in length, with a GC content of 46.40%. The genome sequence contained thirteen protein-coding genes, one 12S RNA gene, one 16S RNA gene, and 22 tRNA genes. A phylogenetic tree constructed for the family confirmed that D. agile is closely related to another species of Dicaeum (Dicaeum eximium). The mitochondrial genome of the Thick-billed Flowerpecker will be useful for future phylogeographic studies of this species.

Long-term dual antiplatelet-induced intestinal injury resulting in translocation of intestinal bacteria into blood circulation increased the incidence of adverse events after PCI in patients with coronary artery disease

Background and aimsThe present study aimed to investigate the efficacy and safety of long-term (>18 months) dual antiplatelet therapy (DAPT) after percutaneous coronary intervention (PCI). MethodsA total of 3205 coronary artery disease (CAD) patients after PCI from CORFCHD-PCI, a retrospective cohort study (Identifier: ChiCTR-ORC-16010153), were divided into two groups: monotherapy of aspirin or clopidogrel group (SAPT group, n = 2188 and DAPT group, n = 1017) according to whether to discontinue DAPT 18 months after PCI. After propensity matching analysis (PSM), we included 1017 patients in the DAPT group and 1017 patients in the SAPT group. All the patients were followed-up for at least 18 months and the longest follow-up time is 120 months. The primary endpoint was the incidence of major adverse cardiac events (MACEs). The secondary endpoints were the incidence of major adverse cardiovascular and cerebrovascular events (MACEEs) and bleeding events. We also selected 178 patients for detection of claudin-3 and intestinal fatty acid-binding protein and 58 patients for 16s RNA sequencing of whole blood. ResultsThe incidences of MACEs (13.9% vs. 9.0%, p = 0.001) and MACCEs (16.3% vs.10.0%, p < 0.001) were significantly increased in the DAPT group compared to the SAPT group. We also found DAPT increased the bleeding events compared to SAPT (4.6% vs. 2.9%, p = 0.048). Multivariate Cox regression analyses showed that in the DAPT group, cumulative risk of MACCEs increased 1.797 times (HR = 1.797, 95%CI: 1.429–2.226, p < 0.001), MACEs increased 1.737 times (HR = 1.737, 95%CI: 1.360–2.218, p < 0.001) and the bleeding events increased 2.129 times (HR = 2.129, 95%CI: 1.388–3.266, p = 0.001) compared to the SAPT group. We also found the plasma concentrations of claudin-3 and intestinal fatty acid-binding protein (I-FABP) were significantly higher in patients in the DAPT group compared with patients in the SAPT group (both p < 0.001). Correspondingly, the abundance of blood intestinal bacteria in the DAPT group was significantly increased compared to that in the SAPT group (p < 0.001). Furthermore, high-throughput metabolomics analysis suggested that serum level of ceramide (d18:1/16:0) and Neu5Ac was significantly increased in the DAPT group compared to the SAPT group (both p < 0.001). ConclusionsThe present study suggests that long-term dual antiplatelet therapy longer than 18 months significantly increases the incidence of both ischemic events and bleeding events after PCI. This preliminary study also indicates that long-term DAPT causes intestinal injury, which induces translocation of intestinal bacteria into the bloodstream.

Probiotic research as highest antimicrobial Listeria monocytogenes from virgin coconut oil [VCO] Padang West Sumatra

Virgin Coconut Oil [VCO] is a natural oil, made from fresh coconut milk fermentation without adding chemicals and other additives. Several Lactic acids Bacteria [LAB], have been isolate and characterization as probiotic. Several 5 different VCO sample products in local Padang Market have been determined. Specifics MRS medium has been used for LAB isolation and morphological characterization. The samples code are A, B, C, D, and E for 5 VCO samples. The highest total colony of LAB is from Samples A, which is about 1377 ×107 CFU/mL. 18 isolates have been identified as Gram-positive bacteria while 8 bacteria’s are coccus and others form basil. All 18 LAB were grown at pH 2, and showing a resistance of about 49 %. Only 50 % of LAB resistant 0,3% oxgall for 4 hours. 3 isolate namely isolate A-1, A-3, and D-1 were showed the highest antimicrobial activities against Listeria monocytogenes with holozone averages of 26 mm. The hydrophobicity against xylene was also determined. The potential A-3 colonies are the highest percentages grown about 19% and resistant to several antibiotics such as Ampicillin, Chloramphenicol, Erythromycin, and Tetracycline. Molecular identification for potential A-3 using 16S RNA, showing phylogenetics species as Lactobacillus fermentum strain KF7.

I ncreased Host Energy Metabolism in the Proximal Colon‐Microbiota Interface Elevates Blood Pressure

Introduction : Hypertensive subjects present with alterations in gut microbiota and short chain fatty acids (SCFAs). SCFAs are the major metabolic products of bacterial fermentation in the intestine. While acetate and propionate are energy sources for peripheral tissues, butyrate is the primary energy source for the host colonic epithelium via β-oxidation or glycolysis. Since butyrate is known to elevate blood pressure (BP), we hypothesized that the mechanism of gut microbial butyrate-mediated elevation in BP is linked with an increased energy metabolism in the proximal colon. Methods : To test this hypothesis, 7 weeks old concomitantly raised male germ-free Sprague Dawley rats (GF, n=5-6) were compared with GF acquiring microbiota acutely for 10 days (germ-free conventionalized rats, GFC, n=6) for (1) BP, (2) cecal butyrate by proton nuclear magnetic resonance (1-H NMR), (3) microbial profiling by 16S RNA sequencing and (4) proximal colonic transcriptomic signatures for energy metabolism by real time qRT-PCR. Results : GFC rats acquired microbiota successfully (Figure 1 C and D) and represented an energy-repleted state with a marked increase of the colonic energy substrate, butyrate (Figure 1E). Interestingly, GFC rats had a significant increase in systolic and diastolic BP compared to GF rats (Figure 1 A and B, p<0.05). This increase in BP was associated with a significant upregulation of all 11 genes tested by qRT-PCR for energy metabolism pathways for β-oxidation and glycolysis in the colon of the GFC rats compared to GF rats (Figure 1F). These genes are: peroxisome proliferator activated receptor γ (Pparγ), free fatty acid receptor 2 (Ffar2), acyl-CoA synthetase short chain family member 1(Acss1), acyl-CoA dehydrogenase long chain(Acadl), carnitine palmitoyltransferase 2(Cpt2), hexokinase 2(Hk2), phosphofructokinase, platelet(Pfkp), phosphoglycerate mutase 1(Pgam1), glycerol-3-phosphate dehydrogenase 2(Gpd2), sirtuin 3(Sirt3)and carnitine O-acetyltransferase(Crat). Conclusion : Collectively our data reported here is the first to provide evidence for a direct relationship between host energy metabolism at the proximal gut-microbiota interface and BP regulation. Further, our studies suggest that butyrate, which is a predominant colonic energy metabolite, contributes to the mechanism governing this relationship between energy metabolism in the proximal colon with BP regulation.

Gut Microbiota Modulate the Efficacy of Angiotensin‐converting Enzyme Inhibitor Captopril

Introduction: About 15-20% of the hypertensive population are resistant to antihypertensive drugs for reasons that remain unknown. Recent knowledge regarding the ability of gut microbiota to metabolize a variety of drugs led us to hypothesize that antihypertensive medications, such as the angiotensin-converting enzyme (ACE) inhibitor Captopril (CAP), are degraded by gut microbiota resulting in a loss of efficacy to lower blood pressure (BP). The goal of our study was to test this hypothesis and identify the bacteria involved. Methods: Once per day for 5 consecutive days, 16-week-old male spontaneously hypertensive rats (SHR) were administered with or without antibiotics (SHR±ABX) via oral gavage. Two days after the final ABX oral gavage, all SHR were provided CAP-containing drinking water (250 mg/day/kg) for the following 11 days. Systolic BP, diastolic BP, and mean arterial pressure (MAP) were periodically recorded during the 11 days via radio-telemetry. Fecal microbiota was profiled by 16S RNA sequencing at the beginning and end of the study. Results: Upon CAP treatment, there was a significantly greater reduction in systolic BP in the SHR+ABX, compared with SHR, on day 3 (SHR -10.92 mmHg vs SHR+ABX -23.05 mmHg, p=0.039, Fig. A) and day 4 (SHR -13.83 mmHg vs SHR+ABX -27.54 mmHg, p=0.05, Fig. A). Two-way ANOVA analysis demonstrated that CAP significantly contributed to the differences in systolic BP (Fig. A), diastolic BP (Fig. B) and MAP (Fig. C) between the groups (p<0.0001). Upon CAP treatment, gut microbiota of SHR+ABX showed a significantly increased diversity (SHR 5.11 vs SHR+ABX 6.18, p=0.006, Fig. D) and evenness (SHR 0.59 vs SHR+ABX 0.71, p=0.008, Fig. E). The gut microbiota of SHR+ABX upon CAP treatment showed a significantly reduced relative abundance of the Allobaculum genus (SHR 40.8% vs SHR+ABX 15.5%, p=0.001, Fig. F) of the Erysipelotrichaceae family. Conclusion: A significantly greater BP-lowering effect by CAP in the SHR+ABX group, in comparison to the SHR group, provides clear evidence for the involvement of gut microbiota in the modulation of antihypertensive drug efficacy. Further, the BP-lowering effect by CAP was negatively linked to the abundance of the genus Allobaculum, indicating that bacteria belonging to this genus contribute to the catabolism of CAP. Our study lends support to the potential for improved maintenance of blood pressure homeostasis and reduction of the prevalence of resistant hypertension via manipulation of gut microbiota.

Molecular characterization of two Australian temnocephalans (Temnocephalida, Platyhelminthes) introduced with alien crayfish (Parastacidae, Decapoda) into South Africa

In our previous research on a natural waterbody in South Africa, introduced Australian redclaw crayfish, Cherax quadricarinatus, were found to harbour two species of temnocephalans on their body surfaces and branchial chambers. The temnocephalans were morphologically consistent with Craspedella pedum and Diceratocephala boschmai, both known from this host species and native originally to Australia. In the current study, we report molecular data from the same material. DNA sequences from portions of the gene encoding the nuclear ribosomal 28S RNA indicated a close relationship of these worms with those from Australia. It is highly likely that the worms we found were introduced into South Africa along with the crayfish, following a similar trend elsewhere in the world. There is no evidence that they have been able to establish on native South African hosts.

Degradation of low-concentration perfluorooctanoic acid via a microbial-based synergistic method: assessment of the feasibility and functional microorganisms

Perfluorooctanoic acid (PFOA) is persistent in the environment. The activities of microorganisms alone are insufficient for the decomposition of PFOA, but microorganisms can contribute positively to the degradation of PFOA in synergistic systems. Herein, a synergistic system combining photocatalytic decay with microbial degradation of the transformation products was applied to degrade 500.0 μg L−1 PFOA. The microorganisms increased the total removed percentage by 30.7% to a final percentage of 79.7 ± 9.4% in comparison with the photocatalytic method alone. Moreover, an additional 44.2% of removed total organic carbon and additional defluorination percentage of 24.5% were obtained after the synergistic tests. The 16S RNA sequencing analysis indicated that Stenotrophomonas, Bacillus, Pseudomonas, and Brevundimonas were highly enriched in the functional microbial community, which was simultaneously shaped by photocatalysis and substances. This study found it would be feasible to use a synergistic method containing photocatalysis and a microbial community for the degradation of low-concentrations of PFOA, and the results provided a reference to modified the removal efficiency of the synergistic system by looking insight into the relationship between the functional microbial community and PFOA.

Molecular confirmation of metacercaria of Clinostomum complanatum recovered from one‐stripe spiny eel Macrognathus aral

The one-stripe spiny eel (Macrognathus aral, Bloch & Schneider, 1801) under the family Mastacembelidae, a native ornamental fish, were collected from the freshwater ponds and canals of West Bengal, with a purpose to raise the colony as ornamental fish broodstock. During acclimatization, fish were found to be lethargic and reluctant to consume feed followed by the appearance of deep wounds and red patches on the ventral part of the body surface. There was a mortality of 40.49% of affected fish within the next 48 hours. Post-mortem examinations revealed the presence of metacercariae inside the body cavity and on internal organs, spreading up to the buccal cavity. The abundance of the parasite was 15 to 36 numbers per fish. The length of the metacercaria varied from 5.2 mm to 9.8 mm. The metacercariae were identified as Clinostomum complanatum by light microscopy. Further, molecular confirmation of identification was done using PCR amplification and sequencing of the 18S RNA gene. This is the first report of metacercarial infestation of Clinostomum complanatum with molecular confirmation in indigenous M. aral with high ornamental value.

Autism-Associated Variant in the SLC6A3 Gene Alters the Oral Microbiome and Metabolism in a Murine Model.

Background: Altered dopamine (DA) signaling has been associated with autism spectrum disorder (ASD), a neurodevelopmental condition estimated to impact 1 in 54 children in the United States. There is growing evidence for alterations in both gastrointestinal function and oral microbiome composition in ASD. Recent work suggests that rare variants of the SLC6A3 gene encoding the DA transporter (DAT) identified in individuals with ASD result in structural and functional changes to the DAT. One such recently identified de novo mutation is a threonine to methionine substitution at position 356 of the DAT (DAT T356M). The DAT T356M variant is associated with ASD-like phenotypes in mice homozygous for the mutation (DAT T356M+/+), including social deficits, hyperactivity, and impaired DA signaling. Here, we determine the impact of this altered DA signaling as it relates to altered oral microbiota, and metabolic and gastrointestinal dysfunction.Methods: In the DAT T356M+/+ mouse, we determine the oral microbiota composition, metabolic function, and gastrointestinal (GI) function. We examined oral microbiota by 16S RNA sequencing. We measured metabolic function by examining glucose tolerance and we probed gastrointestinal parameters by measuring fecal dimensions and weight.Results: In the DAT T356M+/+ mouse, we evaluate how altered DA signaling relates to metabolic dysfunction and altered oral microbiota. We demonstrate that male DAT T356M+/+ mice weigh less (Wild type (WT) = 26.48 ± 0.6405 g, DAT T356M+/+ = 24.14 ± 0.4083 g) and have decreased body fat (WT = 14.89 ± 0.6206%, DAT T356M+/+ = 12.72 ± 0.4160%). These mice display improved glucose handling (WT = 32.60 ± 0.3298 kcal/g, DAT T356M+/+ = 36.97 ± 0.4910 kcal/g), and an altered oral microbiota. We found a significant decrease in Fusobacterium abundance. The abundance of Fusobacterium was associated with improved glucose handling and decreased body fat.Conclusions: Our findings provide new insights into how DAT dysfunction may alter gastrointestinal function, composition of the oral microbiota, and metabolism. Our data suggest that impaired DA signaling in ASD is associated with a number of metabolic and gastrointestinal changes which are common in individuals with ASD.

Detection Moleculer Of Putative 18S rRNA Gen Protozoa Trichodina sp. Infected Larvae Gurami (Osphronemus gouramy L) in Balai Benih Ikan Kutasari Purbalingga Central Java

Trichodina spp. are ectoparasitic pathogens of ciliata group that commonly infect both freshwater and marine fish, including gouramy fish. As a result of infection of Trichodina spp. this will lead to inhibition of fish growth and decreased fish production, resulting in low fish selling value. The rate of occurrence of Trichodina spp. that infects gurami can reach 100%. Research has been conducted to determine which one Trichodina spp. Protozoa that infects the gouramy seeds of BBI (Fish Seed Center) Kutasari Purbalingga following detection of 18S RNA gene. Gene detection method used in this research is Polymerase Chain Reaction (PCR) is a technique of DNA synthesis and amplification in vitro. This research is done following these methodes: (1) sampling of Gurami fish with purposive sampling which obtained from BBI Kutasari Purbalingga, (2) isolation of Trichodina spp., (3). Preparation of Trichodina spp. sample and its identification, and (4). Molecular character obervation following detection of 18S rRNA gene. This study obtained 10% percentage of detection of 18S rRNA genes of the species of Trichodina paraheterodentata that infect on the gouramy fish of Purbalingga. The percentage rate of detection of these genes is low when compared with the results of the detection of 18S rRNA Trichodina paraheterodentata gene that infects gouramy fish in Banjarnegara.

Metformin Modifies the Gut Microbiota of Mice Infected with Helicobacter pylori.

Metformin is widely prescribed to treat type 2 diabetes. Diabetes patients treated with metformin have a decreased risk of cancers, including gastric cancer. Among the factors influencing digestive carcinogenesis, gut microbiota interactions have been intensively studied. Metformin exhibits direct antimicrobial activity toward Helicobacter pylori, which plays a crucial role in gastric carcinogenesis. Mice were infected with H. pylori and treated for 12 days with either metformin or phosphate-buffered saline (PBS) as a control. At the end of the treatment period, the mice were euthanized and cecal and intestinal contents and stool were collected. The gut microbiota of the three different digestive sites (stool, cecal, and intestinal contents) were characterized through 16S RNA gene sequencing. In mice infected with H. pylori, metformin significantly decreased alpha diversity indices and led to significant variation in the relative abundance of some bacterial taxa including Clostridium and Lactobacillus, which were directly inhibited by metformin in vitro. PICRUSt analysis suggested that metformin modifies functional pathway expression, including a decrease in nitrate reducing bacteria in the intestine. Metformin significantly changed the composition and predicted function of the gut microbiota of mice infected with H. pylori; these modifications could be implicated in digestive cancer prevention.

The Association of Gut Microbiota 16s RNA Target Region with Obesity

Background: Gut dysbiosis is strongly associated with obesity and T2DM pathogenesis. Objective:To study the possible associations of gut microbiota 16s RNA target region with obesity. Patients and Methods:A case-control study that was done on 60 subjects (20 obese subjects without diabetes, 20 obese diabetic patients, and 20 control normal subjects). This study was based on gut microbiota 16s rRNA detection by DNA extraction from fresh frozen stool samples of study groups. Gene amplification was done by PCR. Using gene sequencing to identify the gut microbiota species. Results: 2 cases were positive for 16s RNA gene in control group, the sequence of this gene was belonging to Succinivibrio dextrinosolvens. 3 cases were positive for 16s RNA gene in obese without diabetes group; all were belonging to Prevotella copri. 5 cases were positive for 16s RNA gene in obese with diabetes group; 3 cases were belonging to Prevotella copri and 2 cases were belonging to Succinivibrio dextrinosolvens. Statistically there was no significant difference among the three study groups regarding the 16s RNA gene, nor abundant organism.Although there was a significant difference between obese without DM group & lean group regarding type of organism as 100% of obese without DM group had Prevotella copri compared to 0% in group A (P = 0.04). However, there was no statistical difference between lean group and obese with DM group as (p = 0.20). In addition, there was no difference between obese group and obese with DM group (P= 0.27) regarding type of organisms. Conclusion: Obesity is associated with microbial composition alteration using 16s rRNA sequences method.

Mitochondria and the Frozen Frog.

The wood frog, Rana sylvatica, is the best-studied of a small group of amphibian species that survive whole body freezing during the winter months. These frogs endure the freezing of 65–70% of their total body water in extracellular ice masses. They have implemented multiple adaptations that manage ice formation, deal with freeze-induced ischemia/reperfusion stress, limit cell volume reduction with the production of small molecule cryoprotectants (glucose, urea) and adjust a wide variety of metabolic pathways for prolonged life in a frozen state. All organs, tissues, cells and intracellular organelles are affected by freeze/thaw and its consequences. This article explores mitochondria in the frozen frog with a focus on both the consequences of freezing (e.g., anoxia/ischemia, cell volume reduction) and mitigating defenses (e.g., antioxidants, chaperone proteins, upregulation of mitochondria-encoded genes, enzyme regulation, etc.) in order to identify adaptive strategies that defend and adapt mitochondria in animals that can be frozen for six months or more every year. A particular focus is placed on freeze-responsive genes in wood frogs that are encoded on the mitochondrial genome including ATP6/8, ND4 and 16S RNA. These were strongly up-regulated during whole body freezing (24 h at −2.5 °C) in the liver and brain but showed opposing responses to two component stresses: strong upregulation in response to anoxia but no response to dehydration stress. This indicates that freeze-responsive upregulation of mitochondria-encoded genes is triggered by declining oxygen and likely has an adaptive function in supporting cellular energetics under indeterminate lengths of whole body freezing.

Effects of polyethylene microplastics on the microbiome and metabolism in larval zebrafish

Various microplastics (MPs) are found in the environment and organisms. MP residues in organisms can affect health; however, their impacts on metabolism in aquatic organisms remain unclear. In this study, zebrafish embryos were exposed to polyethylene MPs with sizes ranging from 1 to 4 μm at concentrations of 0, 10, 100, and 1000 μg/L for 7 days. Through qPCR technology, the results indicated that zebrafish exposed to polyethylene MPs exhibited significant change in microbes of the phyla Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia, etc. Moreover, 16S RNA gene sequencing revealed that there was a significant difference in alpha diversity between the control and 1000 μg/L MP-treated groups. At the genus level, the abundance of Aeromonas, Shewanella, Microbacterium, Nevskia and Methyloversatilis have increased remarkably. Conversely, the abundance of Pseudomonas, Ralstonia and Stenotrophomonas were significant reduction after MPs exposure. In addition, the levels of TG (triglyceride), TCHO (total cholesterol), NEFA (nonesterified fatty acid), TBA (total bile acid), GLU (glucose) and pyruvic acid significantly changed in MP-treated larval zebrafish, indicating that their metabolism was disturbed by MPs. Transcriptional levels of glucose and lipid metabolism-related genes showed a decreasing trend. Furthermore, LC/MS-based nontargeted metabolomics analysis demonstrated that a total of 59 phospholipid-related substances exhibited significant changes in larval fish treated with 1000 μg/L MPs. The mRNA levels of phospholipid metabolism-related genes were also obviously changed. Pearson correlation analysis indicated that the abundance of Aeromonas, Shewanella and Chitinibacter bacteria showed a negative correlation with most phospholipids, while Nevskia, Parvibacter and Lysobacter showed a positive correlation with most phospholipids. Based on these results, it is suggested that 1–4 μm PE-MPs could impact the microbiome and metabolism of larval zebrafish. All of these results indicated that the health risk of MPs cannot be ignored.