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Additional file 1. SPIRIT checklist for Trials.

Additional file 3. Supplementary tables.

Additional file 2. Community Leader Information and Consent Form.

International audience; Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription activator-like effectors (TALEs) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed effector binding elements (EBEs). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance on Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC, which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance on African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis identified a rice locus named ATAC composed of the INCREASED LEAF INCLINATION 2 (ILI2) gene and a putative lncRNA that are shown to be bidirectionally upregulated in a TalC-dependent fashion. Gain-of-function approaches with designer TALEs inducing ATAC sequences did not complement the virulence of a Xoo strain defective for SWEET gene activation. While editing the TalC EBE at the ATAC loci compromised TalC-mediated induction, multiplex edited lines with mutations at the OsSWEET14 and ATAC loci remained essentially susceptible to African Xoo strains. Overall, this work indicates that ATAC is a probable TalC off-target locus but nonetheless documents the first example of divergent transcription activation by a native TALE during infection.

International audience; The creation of global research partnerships is critical to produce shared knowledge for the implementation of the UN 2030 Agenda for Sustainable Development. Sustainability science promotes the coproduction of inter-and transdisciplinary knowledge, with the expectation that studies will be carried out through groups and truly collaborative networks. As a consequence, sustainability research, in particular that published in high impact journals, should lead the way in terms of ethical partnership in scientific collaboration. Here, we examined this issue through a quantitative analysis of the articles published in Nature Sustainability (300 papers by 2135 authors) and Nature (2994 papers by 46,817 authors) from January 2018 to February 2021. Focusing on these journals allowed us to test whether research published under the banner of sustainability science favoured a more equitable involvement of authors from countries belonging to different income categories, by using the journal Nature as a control. While the findings provide evidence of still insufficient involvement of Low-and-Low-Middle-Income-Countries (LLMICs) in Nature Sustainability publications, they also point to promising improvements in the involvement of such authors. Proportionally, there were 4.6 times more authors from LLMICs in Nature Sustainability than in Nature articles, and 68.8-100% of local Global South studies were conducted with host country scientists (reflecting the discouragement of parachute research practices), with local scientists participating in key research steps. We therefore provide evidence of the promising, yet still insufficient, involvement of low-income countries in top sustainability science publications and discuss ongoing initiatives to improve this.

International audience; Rice blast, caused by the filamentous ascomycete Pyricularia oryzae, is one of the most devastating diseases of rice. Four genetic clusters were previously identified, and three have a large geographic distribution. Asia is the center of diversity and the origin of most migrations to other continents, and sexual reproduction persisted only in the South China-Laos-North Thailand region, which was identified as the putative center of origin of all P. oryzae populations on rice. Despite the importance of rice blast disease, little is known about the diversity and the population structure of the pathogen in Africa (including Madagascar). The present study was intended to describe the structure of African populations of P. oryzae and identify the relationship between African and worldwide genetic clusters. A set of 2,057 strains (937 African and 1,120 Madagascan strains) were genotyped with 12 simple sequence repeat markers to assess the diversity and the population structure of P. oryzae. Four genetic clusters were identified in Africa and Madagascar. All four clusters previously identified are present in Africa. Populations from West Africa, East Africa, and Madagascar are highly differentiated. The geographic structure is consistent with limited dispersion and with some migration events between neighboring countries. The two mating types are present in Africa with a dominance of Mat1.2, but no female-fertile strain was detected, supporting the absence of sexual reproduction on this continent. This study showed an unsuspected high level of genetic diversity of P. oryzae in Africa and suggested several independent introductions.

Additional file 1: Table S1. Kaplan Meier efficacy estimates and hazard ratios between AL and ASAQ, therapeutic efficacy monitoring, Mali, 2015–2016. Table S2. msp1, msp2, and glurp genotyping data (allele sizes are reported in base pairs (bp)).

Rice bran supplementation provides nutrients, prebiotics and phytochemicals that enhance gut immunity, reduce enteric pathogens and diarrhea, and warrants attention for improvement of environmental enteric dysfunction (EED) in children. EED is a subclinical condition associated with stunting due to impaired nutrient absorption. This study investigated the effects of rice bran supplementation on weight for age and length for age z-scores (WAZ, LAZ), EED stool biomarkers, as well as microbiota and metabolome signatures in weaning infants from 6 to 12 months old that reside in Nicaragua and Mali. Healthy infants were randomized to a control (no intervention) or a rice bran group that received daily supplementation with increasing doses at each month (1-5 g/day). Stool microbiota were characterized using 16S rDNA amplicon sequencing. Stool metabolomes were analyzed using ultra-high-performance liquid-chromatography tandem mass-spectrometry. Statistical comparisons were completed at 6, 8, and 12 months of age. Daily consumption of rice bran was safe and feasible to support changes in LAZ from 6-8 and 8-12 months of age in Nicaragua and Mali infants when compared to control. WAZ was significantly improved only for Mali infants at 8 and 12 months. Mali and Nicaraguan infants showed major differences in the overall gut microbiota and metabolome composition and structure at baseline, and thus each country cohort demonstrated distinct microbial and metabolite profile responses to rice bran supplementation when compared to control. Rice bran is a practical dietary intervention strategy that merits development in rice-growing regions that have a high prevalence of growth stunting due to malnutrition and diarrheal diseases. Rice is grown as a staple food, and the bran is used as animal feed or wasted in many low- and middle-income countries where EED and stunting is prevalent. Grand Challenges Explorations in Global Health award from the Bill and Melinda Gates Foundation [OPP1043255]; Fulbright Faculty Development scholarship award The authors thank the study participants, community health workers, and local clinical staff for their assistance in the conduct of the clinical trials. This study was supported by the Grand Challenges Explorations in Global Health award from the Bill and Melinda Gates Foundation (OPP1043255) and the Fulbright Faculty Development scholarship award.

Understanding the diversity of pathogen populations in a regional scale is crucial in order to develop strategies for sustainable control of plant diseases. Our work deals with the study of the plant pathogenic bacterium Xanthomonas axonopodis pv. manihotis (Xam), which is the causal agent of cassava bacterial blight (CBB). CBB occurs in the tropics including in West-Africa where it has recently been reported in Burkina Faso and Ivory Coast, sometimes imposing severe yield losses to cassava producers. The status of CBB in Mali still remains unstudied. To fill this gap, preliminary surveys were conducted in Dec. 2015 in two cassava production regions. Nearly 80 leaf samples were processed, leading to the isolation of about 50 Xam candidate isolates. Of these, 40 strains of Xanthomonas axonopodis pv. manihotis were validated through molecular diagnostic tests and pathogenicity assays. This study represents the first demonstration for the presence of CBB in Mali and enabled to initiate the establishment of a first collection of national Xam strains. Secondly, a MLVA strategy (Multiple-Locus Variable number tandem repeat Analysis) was developed based on the analysis of 14 microsatellites (VNTR) in order to assess the genetic diversity of the 40 strains isolated from our two regions under study, Bamako and Segou, which are 250km distant. Our results demonstrate a greater diversity in populations of the Bamako region relative to that of Segou, with reference to the values of diversity indices. Also, comparison of all strains of Mali with a collection of 215 strains from border regions in Burkina Faso suggested that the Malian strains are less diversified. Further surveys covering most areas of cassava production in Mali are in progress to better understand Xam invasion routes in this country.

A novel avian-origin H7N9 influenza strain emerged in China in April 2013. Since its re-emergence in October–November 2013, the number of reported cases has accelerated; more than 220 laboratory-confirmed cases and 112 deaths (case fatality rate of 20–30%) have been reported. The resurgence of H7N9 has re-emphasized the importance of making faster and more effective influenza vaccines than those that are currently available. Recombinant H7 hemagglutinin (H7-HA) vaccines have been produced, addressing the first problem. Unfortunately, these recombinant subunit vaccine products appear to have failed to address the second problem, influenza vaccine efficacy. Reported unadjuvanted H7N9 vaccine seroconversion rates were between 6% and 16%, nearly 10-fold lower than rates for unadjuvanted vaccine seroconversion to standard H1N1 monovalent (recombinant) vaccine (89% to pandemic H1N1). Could this state of affairs have been predicted? As it turns out, yes, and it was.1 In that previous analysis of available H7-HA sequences, we found fewer T-cell epitopes per protein than expected, and predicted that H7-HA-based vaccines would be much less antigenic than recent seasonal vaccines. Novel approaches to developing a more immunogenic HA were offered for consideration at the time, and now, as the low immunogenicity of H7N9 vaccines appears to indicate, they appear to be even more relevant. More effective H7N9 influenza vaccines can be produced, provided that the role of T-cell epitopes is carefully considered, and accumulated knowledge about the importance of cross-conserved epitopes between viral subtypes is applied to the design of those vaccines.

Cassava is the most important vegetatively propagated food staple crop in Africa. Even if its vegetative propagation through stem cuttings has many advantages, it also represents its Achilles heel. Pathogens are passed from one generation to the next and can easily accumulate, threatening cassava production. Two viral diseases are currently considered to be the greatest global threat to cassava production in Africa. Faced with the gravity of this situation, 43 scientists from African national and regional institutions and international agricultural research centres met in Saint-Pierre, La Réunion Island from 10 to 13 June 2014, to contribute to the surveillance and control of cassava diseases and pests that threaten the food security and livelihoods of millions Africans. The main action was to consolidate and develop a global alliance against cassava diseases in Africa and a strategic action plan with several international initiatives for the coming years. Firstly, the establishment of a Pan-African Cassava Surveillance Network (PACSUN) with an interactive website and an International Cassava Transit Site (ICTS) in La Réunion. Secondly, the development of diagnostic technologies to better identifying viruses, bacteria and vectors, and a comprehensive educational and training plan to support all these activities. (Texte intégral)

International audience; no abstract