Deterministic and stochastic processes generating alternative states of microbiomes

微生物叢のゆらぎと安定性 --多種細菌群集の「代替状態」と制御可能性--. 京都大学プレスリリース. 2024-02-29.The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating the mechanisms that generate such “alternative states” of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the “stability landscapes” of ecological community compositions

Low-Waterway Variation Due to Change of Water and Sediment Supply Conditions

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv

Synergistic and Offset Effects of Fungal Species Combinations on Plant Performance

「1+1=2」じゃない共生の世界 --2種の菌が植物にもたらす相乗効果と相殺効果--. 京都大学プレスリリース. 2021-09-17.In natural and agricultural ecosystems, survival and growth of plants depend substantially on residing microbes in the endosphere and rhizosphere. Although numerous studies have reported the presence of plant-growth promoting bacteria and fungi in below-ground biomes, it remains a major challenge to understand how sets of microbial species positively or negatively affect plants’ performance. By conducting a series of single- and dual-inoculation experiments of 13 plant-associated fungi targeting a Brassicaceae plant species (Brassica rapa var. perviridis), we here systematically evaluated how microbial effects on plants depend on presence/absence of co-occurring microbes. The comparison of single- and dual-inoculation experiments showed that combinations of the fungal isolates with the highest plant-growth promoting effects in single inoculations did not have highly positive impacts on plant performance traits (e.g., shoot dry weight). In contrast, pairs of fungi with small/moderate contributions to plant growth in single-inoculation contexts showed the greatest effects on plants among the 78 fungal pairs examined. These results on the offset and synergistic effects of pairs of microbes suggest that inoculation experiments of single microbial species/isolates can result in the overestimation or underestimation of microbial functions in multi-species contexts. Because keeping single-microbe systems under outdoor conditions is impractical, designing sets of microbes that can maximize performance of crop plants is an important step for the use of microbial functions in sustainable agriculture

Core species and interactions prominent in fish-associated microbiome dynamics

魚の健康において鍵となる「コア微生物叢」 --ウナギ養殖水槽内の細菌叢動態--. 京都大学プレスリリース. 2023-03-30.[Background] In aquatic ecosystems, the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment. Nonetheless, finding microbes with profound impacts on fish’s performance out of thousands of candidate species remains a major challenge. [Methods] We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background (environmental) water. By targeting eel-aquaculture-tank microbiomes as model systems, we reconstructed the population dynamics of the 9605 bacterial and 303 archaeal species/strains across 128 days. [Results] Due to the remarkable increase/decrease of constituent microbial population densities, the taxonomic compositions of the microbiome changed drastically through time. We then found that some specific microbial taxa showed a positive relationship with eels’ activity levels even after excluding confounding effects of environmental parameters (pH and dissolved oxygen level) on population dynamics. In particular, a vitamin-B12-producing bacteria, Cetobacterium somerae, consistently showed strong positive associations with eels’ activity levels across the replicate time series of the five aquaculture tanks analyzed. Network theoretical and metabolic modeling analyses further suggested that the highlighted bacterium and some other closely-associated bacteria formed “core microbiomes” with potentially positive impacts on eels. [Conclusions] Overall, these results suggest that the integration of microbiology, ecological theory, and network science allows us to explore core species and interactions embedded within complex dynamics of fish-associated microbiomes

The Stretcher Operation of KSR (NUCLEAR SCIENCE RESEARCH FACILITY-Particle and Photon Beams)

The electron ring KSR has been utilized as a pulse stretcher of the 100 MeV S-band electron linac. The duty factor of the electron beam has been increased drastically more than 90% from 2 10-5

744-3 Inhibition of Nitric Oxide Synthesis does not Increase Cardiac Contractile Response but Reduces Coronary Blood Flow Response to β-Adrenergic Stimulation in Normal Dogs

Although the induction of nitric oxide (NO) synthesis has been implicated as a cause of cytokine-induced depression of cardiac β-adrenergic responsiveness. whether the NO system constitutively present in the normal myocardium plays a role in its physiologic response to β-adrenergic stimulation in vivoremains controversial. Accordingly, we examined the effects of low and high doses of NW-nitro-L-arginine methyl ester (L-NAME)(10 and 100 μg/kg/min for 10 min), an NO synthase inhibitor, administered into left circumflex coronary artery (LCX) on responses of peak left ventricular (LV) dP/dt, regional wall thickening in LCX region and LCX blood flow to graded intracoronary (IC) doses of isoproterenol (ISO:0.002 to 0.016 μg/kg/min) in 7 anesthetized dogs. IC L-NAME was associated with dose-related reductions in IC acetylcholine-induced coronary vasodilation. Effects of L-NAME on ISO-induced changes are shown:baselineISO:0.0020.0040.008.0016Peak LV dP/dt (mmHg/sec) (n=7)control2029±1362586±1922820±2003309±2554120±419*low L-NAME2171±1492566±1762894±2063214±2233707±250*high L-NAME2114±1662326±1932560±1523014±1403354±171*Wall thickening (%) (n=2)control22±725±629±533±735±9low L-NAME25±1125±1528±1931±1836±21high L-NAME28±1725±1525±1531±1934±15LCX blood flow (ml/min)(n=7)control33±648±752±661±870±9*low L-NAME36±741±844±947±852±9*high L-NAME33±736±838±740±748±8*mean ± SEM*p<0.05Thus, inhibition of NO synthesis by L-NAME did not change baseline contractility nor did it increase its response to ISO. It also did not alter baseline blood flow, but reduced significantly its response to ISO. These data strongly suggest that the NO system in the normal myocardium does not modulate contractility, but NO formation in the vasculature contributes to the β-adrenergic coronary vasodilation

Medical Treatment of Echinococcus multilocularis and New Horizons for Drug Discovery: Characterization of Mitochondrial Complex II as a Potential Drug Target

As an efficient drug for alveolar echinococcosis (AE) is still not available, new chemotherapy targets are necessary. The mitochondrial respiratory chain may be a good drug candidate because parasite respiratory chains are quite different from those of mammalian hosts. For example, Ascaris suum possesses an NADH‐fumarate reductase system (fumarate respiration) that is highly adapted to anaerobic environments such as the small intestine. It is composed of mitochondrial complex I (NADH‐ubiquinone reductase), complex II (succinate‐ubiquinone reductase), and rhodoquinone. We previously demonstrated that fumarate respiration is also essential in E. multilocularis. Quinazoline, a complex I inhibitor, inhibited growth of E. multilocularis larvae in vitro. These results indicate that fumarate respiration could be a target for E. multilocularis therapy. In the current chapter, we focused on complex II, which is another component of this system, because quinazoline exhibited strong toxicity to mammalian mitochondria. We evaluated the molecular and biochemical characterization of E. multilocularis complex II as a potential drug target. In addition, we found that ascofuranone, a trypanosome cyanide‐insensitive alternative oxidase inhibitor, inhibited E. multilocularis complex II at the nanomolar order. Our findings demonstrate the potential development of targeted therapy against Echinococcus complex II

Penetration of the sigmoid colon to the posterior uterine wall secondary to diverticulitis: a case report

<p>Abstract</p> <p>Introduction</p> <p>Penetration of the colon to the posterior uterine wall secondary to diverticulitis is unusual, with diagnostic methods not yet established. Non-invasive imaging, such as computed tomography and magnetic resonance imaging may help to establish a proper diagnosis, but confirmation may be reached only after surgical exploration.</p> <p>Case presentation</p> <p>We report the case of a 78-year-old Japanese woman who presented with a low grade fever and mild diarrhea which occurred two or three times a week. Computed tomography and magnetic resonance imaging demonstrated a capsular lesion including an air structure with a diameter of 5 cm, between the posterior aspect of the uterine body and the sigmoid colon. A gastrograffin enema and colonoscopy demonstrated a giant diverticulum of the sigmoid colon with no evidence of malignancy. These data confirmed the diagnosis of diverticulitis complicated by a giant diverticulum. Because of a relapsing fever after therapy with antibiotics, the patient had en bloc surgical treatment of the uterus, fallopian tubes, ovaries and sigmoid colon, the organs involved in the diverticulitis, followed by an uneventful recovery.</p> <p>Conclusion</p> <p>This is a rare case report of penetration of the sigmoid colon to the posterior uterine wall secondary to diverticulitis.</p