Identification of Host-Specific Bacteroidales 16S rDNA Sequences from Human Sewage and Ruminant Feces

The need to identify the source of fecal contamination of water has led to the development of various fecal source identification methods, a field known as microbial source tracking (MST). One promising method of MST focuses on fecal members of the order Bacteroidales, some of which exhibit a high degree of host-specificity. In order to identify host-specific Bacteroidales genetic markers, a ∼1060 bp section of Bacteroidales 16S rDNA was amplified from human sewage (n = 6), and bovine (n = 6) and ovine fecal (n = 5) samples and used for the generation of three clone libraries. Phylogenetic analysis of sequences from the three clone libraries revealed that the Bacteroidales species found in both human sewage and bovine and ovine feces were a highly diverse group of organisms, many of which were not represented by previously characterised 16S rDNA. Ovine and bovine feces appear to host similar populations of Bacteroidales species and these species were more diverse and less closely related to cultivated species than the Bacteroidales population found in human sewage. Species of Bacteroidales from the ruminant and human feces formed isolated clusters containing putatively host-specific sequences. These sequences were subsequently exploited for the design of host-specific primers which were used in MST studies

Favelas: neue Wege in der Slumsanierung

In 1988 the Brazilian constitution declared the right to a sustainable city for everyone, but huge informal settlements (favelas), from which most Brazilian cities increasingly suffer, do appear as a threat to this objective. Therefore local and national governments over the last decades adopted new strategies for fighting the ongoing fragmentation and segregation of today’s cities by actively upgrading squatter settlements in order to integrate them and their inhabitants in the city and bring full citizenship to a previously excluded part of the population. As public space both in its physical and in its virtual form of a platform for democratic relationships is a very rare good in the context of informal settlements, it is believed to be a key point in the upgrading process. This work analyses case studies of local and national approaches to making the city a more inclusive place for the urban poor. The accessibility and quality of public space has been used as an indicator to the degree of inclusion into the formal city. Results have shown that good legal bases for full citizenship and economic inclusion have been laid, whilst integration in sense of physical opening up to the city often depends on the specific geographical situation. Drug traffic activities nourished by poverty, social vulnerability and physical environment, though, do have the power to make civil and physical inclusion and full citizenship a precarious achievement

„Sie sind zwar unsere Verwandten, aber die erbärmlichsten Menschen“: Friedrich der Große und die Markgrafen von Brandenburg-Schwedt

Das Verhältnis Friedrichs zu den Schwedter Markgrafen entwickelte sich parallel zu den Schwankungen, denen das Ansehen dieser Fürsten während des 18. Jahrhunderts ausgesetzt war. Markgraf Philipp Wilhelm (1669-1711) und seine Frau Johanna Charlotte von Anhalt-Dessau (1682-1750) waren enge Vertraute der ersten beiden preußischen Könige und nahmen unangefochten den ersten Platz in der höfischen Rangfolge ein. Die charakterlichen Unzulänglichkeiten der folgenden Generation führten jedoch zu einem rapiden Ansehensverlust der „Ersten Prinzen von Geblüt“. Die militärischen Karrieren der Markgrafen Friedrich Wilhelm (1700-1771) und Friedrich Heinrich (1709-1788) verliefen ebenso katastrophal wie ihre Ehen mit Sophie von Preußen (1719-1765) und Leopoldine Marie von Anhalt-Dessau (1716-1782). Vor allem Markgraf Friedrich Wilhelm wurde für Friedrich II. zu einem dauerhaften Ärgernis. Militärisches Eingreifen und eine faktische Entmündigung waren die Folge. Friedrichs Verhältnis zu seiner Schwester Sophie war hingegen lebenslang von gegenseitiger Zuneigung und Vertrautheit geprägt

Favelas: neue Wege in der Slumsanierung

In 1988 the Brazilian constitution declared the right to a sustainable city for everyone, but huge informal settlements (favelas), from which most Brazilian cities increasingly suffer, do appear as a threat to this objective. Therefore local and national governments over the last decades adopted new strategies for fighting the ongoing fragmentation and segregation of today’s cities by actively upgrading squatter settlements in order to integrate them and their inhabitants in the city and bring full citizenship to a previously excluded part of the population. As public space both in its physical and in its virtual form of a platform for democratic relationships is a very rare good in the context of informal settlements, it is believed to be a key point in the upgrading process. This work analyses case studies of local and national approaches to making the city a more inclusive place for the urban poor. The accessibility and quality of public space has been used as an indicator to the degree of inclusion into the formal city. Results have shown that good legal bases for full citizenship and economic inclusion have been laid, whilst integration in sense of physical opening up to the city often depends on the specific geographical situation. Drug traffic activities nourished by poverty, social vulnerability and physical environment, though, do have the power to make civil and physical inclusion and full citizenship a precarious achievement

Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts

A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/ Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts

Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions.

On December 17, 2018, the North American branch of the International Life Sciences Institute (ILSI North America) convened a workshop "Can We Begin to Define a Healthy Gut Microbiome Through Quantifiable Characteristics?" with >40 invited academic, government, and industry experts in Washington, DC. The workshop objectives were to 1) develop a collective expert assessment of the state of the evidence on the human gut microbiome and associated human health benefits, 2) see if there was sufficient evidence to establish measurable gut microbiome characteristics that could serve as indicators of "health," 3) identify short- and long-term research needs to fully characterize healthy gut microbiome-host relationships, and 4) publish the findings. Conclusions were as follows: 1) mechanistic links of specific changes in gut microbiome structure with function or markers of human health are not yet established; 2) it is not established if dysbiosis is a cause, consequence, or both of changes in human gut epithelial function and disease; 3) microbiome communities are highly individualized, show a high degree of interindividual variation to perturbation, and tend to be stable over years; 4) the complexity of microbiome-host interactions requires a comprehensive, multidisciplinary research agenda to elucidate relationships between gut microbiome and host health; 5) biomarkers and/or surrogate indicators of host function and pathogenic processes based on the microbiome need to be determined and validated, along with normal ranges, using approaches similar to those used to establish biomarkers and/or surrogate indicators based on host metabolic phenotypes; 6) future studies measuring responses to an exposure or intervention need to combine validated microbiome-related biomarkers and/or surrogate indicators with multiomics characterization of the microbiome; and 7) because static genetic sampling misses important short- and long-term microbiome-related dynamic changes to host health, future studies must be powered to account for inter- and intraindividual variation and should use repeated measures within individuals

Un_Gleich. Anmerkungen, die schließlich die Bedeutsamkeit einer Orientierung an postkommunitärer Solidarität für die politische Bildung in der (Post-)Pandemie betonen

Die mutmaßlich zu einem Ende gekommene SARS-CoV-2-Pandemie verweist auf zumindest zwei grundlegende gesellschaftliche Zusammenhänge, Gleichheit wie Ungleichheit (vgl. Mecheril/Karakaşoğlu 2020). Als infektiöse organische Struktur ohne eigenen Stoffwechsel, die ihr Erbgut in eine Zelle einschleust, mittels derer anschließend unzählbare Replikate hergestellt werden, behandelt das Virus die Menschen zunächst gleich. Hierin zeigt sich eine anthropologische Schlüsseldimension: Der Mensch ist vulnerabel. Vulnerabilität ist »grosso modo eine Eigenschaft und Fähigkeit des Menschen, die ihn seit der kulturellen Tradierung als Mensch antreibt und die die Grundlage der Herausbildung des homo sapiens ist, der versucht, seine Verletzlichkeit und damit verbundene Erinnerung an die eigene Verletzbarkeit und Endlichkeit praktisch wie theoretisch zu bewältigen« (Burghardt et al. 2017:35). (DIPF/Orig.

Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin

The definitive version is available at ww3.interscience.wiley.com. En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2009/publication-6801.pdfInternational audienceThe distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average approximately 3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured sedimentary Crenarchaeota. However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales, Marine Benthic Group D and other lineages probably involved in the methane cycle (Methanosarcinales, ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota, DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities